*/bootstrap.js
*bootstrap-theme.css
build/package-test-dockerfiles/centos7/localrepo.repo
+build/package-test-dockerfiles/rocky8/localrepo.repo
build/package-test-dockerfiles/ubuntu1604/etc-apt-preferences.d-arvados
*by-sa-3.0.html
*by-sa-3.0.txt
sdk/cwl/tests/chipseq/data/Genomes/*
CITATION.cff
SECURITY.md
-*/testdata/fakestat/*
+lib/crunchstat/testdata/*
lib/controller/localdb/testdata/*.pub
# SPDX-License-Identifier: AGPL-3.0
case "$TARGET" in
- centos*)
+ centos*|rocky*)
fpm_depends+=(git bison make automake gcc gcc-c++ graphviz shared-mime-info)
;;
ubuntu1804)
-Scripts in this directory:
+Prerequisites
+=============
+
+In order to build packages, you will need:
+
+* Docker installed
+* permission to run Docker commands
+* the `WORKSPACE` environment variable set to the absolute path of an
+ Arvados Git work tree
+
+Quickstart
+==========
+
+Build and test all the packages for debian10 on your architecture by
+running:
+
+ ./run-build-test-packages-one-target.sh
+
+This will build package build and test Docker images for debian10, build all
+packages in a build container, then test all packages in a test container.
+
+Use a different distro by adding the `--target TARGET` option.
+
+Limit the build to a single architecture by adding the `--arch ARCH`
+option. Supported architectures are amd64 and arm64. Note cross-compilation
+from amd64 to arm64 is currently only supported on Debian 11+.
+
+Limit the build to a single package by adding the `--only-build
+PACKAGE_NAME` option. This is helpful when a build is mostly in good shape
+and you're tracking down last bugs in one or two packages.
+
+Get more verbose output by adding the `--debug` option.
+
+By default the script avoids rebuilding or retesting packages that it
+detects have already been done in past runs. You can force the script to
+rebuild or retest package(s) with the `--force-build` and `--force-test`
+options, respectively.
+
+Run the script with `--help` for more information about other options.
+
+Scripts in this directory
+=========================
run-tests.sh Run unit and integration test suite.
run-library.sh A library of functions shared by the
various scripts in this
directory.
+
+Adding a new target
+===================
+
+In order to build packages on a new distribution, you MUST:
+
+* Add a rule for `TARGET/generated` to `package-build-dockerfiles/Makefile`.
+* Add the new `TARGET/generated` rule to the `all` target in
+ `package-build-dockerfiles/Makefile`.
+* Write `package-build-dockerfiles/TARGET/Dockerfile`.
+* Add a rule for `TARGET/generated` to `package-test-dockerfiles/Makefile`.
+* Add the new `TARGET/generated` rule to the `all` target in
+ `package-test-dockerfiles/Makefile`.
+* Write `package-test-dockerfiles/TARGET/Dockerfile`.
+* Create `package-testing/test-packages-TARGET.sh`, ideally by making it a
+ symlink to `FORMAT-common-test-packages.sh`.
+
+Of course, any part of our package build or test infrastructure may need to
+be updated to accommodate the process for new distributions. If you're
+having trouble building lots of packages, consider grepping these build
+scripts for the identifier of the closest working target, and see if you may
+need to add branches or similar hooks for your target. If you're having
+trouble building specific packages, consider doing the same for those
+packages' `fpm-info.sh` files.
# SPDX-License-Identifier: AGPL-3.0
SHELL := '/bin/bash'
-all: centos7/generated debian10/generated debian11/generated ubuntu1804/generated ubuntu2004/generated
+all: centos7/generated debian10/generated debian11/generated rocky8/generated ubuntu1804/generated ubuntu2004/generated
centos7/generated: common-generated-all
test -d centos7/generated || mkdir centos7/generated
test -d debian11/generated || mkdir debian11/generated
cp -f -rlt debian11/generated common-generated/*
+rocky8/generated: common-generated-all
+ test -d rocky8/generated || mkdir rocky8/generated
+ cp -f -rlt rocky8/generated common-generated/*
+
ubuntu1804/generated: common-generated-all
test -d ubuntu1804/generated || mkdir ubuntu1804/generated
cp -f -rlt ubuntu1804/generated common-generated/*
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+ARG HOSTTYPE
+ARG BRANCH
+ARG GOVERSION
+
+FROM rockylinux:8.6-minimal as build_x86_64
+# Install go
+ONBUILD ARG GOVERSION
+ONBUILD ADD generated/go${GOVERSION}.linux-amd64.tar.gz /usr/local/
+ONBUILD RUN ln -s /usr/local/go/bin/go /usr/local/bin/
+# Install nodejs and npm
+ONBUILD ADD generated/node-v10.23.1-linux-x64.tar.xz /usr/local/
+ONBUILD RUN ln -s /usr/local/node-v10.23.1-linux-x64/bin/* /usr/local/bin/
+
+FROM rockylinux:8.6-minimal as build_aarch64
+# Install go
+ONBUILD ARG GOVERSION
+ONBUILD ADD generated/go${GOVERSION}.linux-arm64.tar.gz /usr/local/
+ONBUILD RUN ln -s /usr/local/go/bin/go /usr/local/bin/
+# Install nodejs and npm
+ONBUILD ADD generated/node-v10.23.1-linux-arm64.tar.xz /usr/local/
+ONBUILD RUN ln -s /usr/local/node-v10.23.1-linux-arm64/bin/* /usr/local/bin/
+
+FROM build_${HOSTTYPE}
+
+MAINTAINER Arvados Package Maintainers <packaging@arvados.org>
+
+# Install dependencies.
+RUN microdnf --assumeyes --enablerepo=devel install \
+ automake \
+ bison \
+ bzip2 \
+ fuse-devel \
+ gcc \
+ gcc-c++ \
+ git \
+ libattr-devel \
+ libcurl-devel \
+ libffi-devel \
+ libtool \
+ libyaml-devel \
+ make \
+ nss-devel \
+ openssl-devel \
+ pam-devel \
+ patch \
+ postgresql-devel \
+ procps-ng \
+ python3 \
+ python3-devel \
+ python3-pip \
+ python3-virtualenv \
+ readline-devel \
+ rpm-build \
+ ruby \
+ sqlite-devel \
+ tar \
+ unzip \
+ wget \
+ which \
+ xz-libs \
+ zlib-devel
+
+# Install RVM
+ADD generated/mpapis.asc /tmp/
+ADD generated/pkuczynski.asc /tmp/
+RUN gpg --import --no-tty /tmp/mpapis.asc && \
+ gpg --import --no-tty /tmp/pkuczynski.asc && \
+ curl -L https://get.rvm.io | bash -s stable && \
+ /usr/local/rvm/bin/rvm install 2.7 -j $(grep -c processor /proc/cpuinfo) && \
+ /usr/local/rvm/bin/rvm alias create default ruby-2.7 && \
+ echo "gem: --no-document" >> ~/.gemrc && \
+ /usr/local/rvm/bin/rvm-exec default gem install bundler --version 2.3.26 && \
+ /usr/local/rvm/bin/rvm-exec default gem install fpm --version 1.10.2
+
+RUN /usr/local/rvm/bin/rvm-exec default bundle config --global jobs $(let a=$(grep -c processor /proc/cpuinfo )-1; echo $a)
+# Cf. https://build.betterup.com/one-weird-trick-that-will-speed-up-your-bundle-install/
+ENV MAKE "make --jobs $(grep -c processor /proc/cpuinfo)"
+
+# Preseed the go module cache and the ruby gems, using the currently checked
+# out branch of the source tree. This avoids potential compatibility issues
+# between the version of Ruby and certain gems.
+RUN git clone --depth 1 git://git.arvados.org/arvados.git /tmp/arvados && \
+ cd /tmp/arvados && \
+ if [[ -n "${BRANCH}" ]]; then git checkout ${BRANCH}; fi && \
+ cd /tmp/arvados/services/api && \
+ /usr/local/rvm/bin/rvm-exec default bundle install && \
+ cd /tmp/arvados/apps/workbench && \
+ /usr/local/rvm/bin/rvm-exec default bundle install && \
+ cd /tmp/arvados && \
+ go mod download
+
+ENV WORKSPACE /arvados
+CMD ["/usr/local/rvm/bin/rvm-exec", "default", "bash", "/jenkins/run-build-packages.sh", "--target", "rocky8"]
#
# SPDX-License-Identifier: AGPL-3.0
-all: centos7/generated debian10/generated debian11/generated ubuntu1804/generated ubuntu2004/generated
+all: centos7/generated debian10/generated debian11/generated rocky8/generated ubuntu1804/generated ubuntu2004/generated
centos7/generated: common-generated-all
test -d centos7/generated || mkdir centos7/generated
test -d debian11/generated || mkdir debian11/generated
cp -f -rlt debian11/generated common-generated/*
+rocky8/generated: common-generated-all
+ test -d rocky8/generated || mkdir rocky8/generated
+ cp -f -rlt rocky8/generated common-generated/*
+
ubuntu1804/generated: common-generated-all
test -d ubuntu1804/generated || mkdir ubuntu1804/generated
cp -f -rlt ubuntu1804/generated common-generated/*
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+FROM rockylinux:8.6-minimal
+MAINTAINER Arvados Package Maintainers <packaging@arvados.org>
+
+# Install dependencies.
+RUN microdnf --assumeyes --enablerepo=devel install \
+ autoconf \
+ automake \
+ bison \
+ bzip2 \
+ cpio \
+ diffutils \
+ findutils \
+ gcc-c++ \
+ glibc-devel \
+ glibc-headers \
+ gzip \
+ libffi-devel \
+ libtool \
+ make \
+ openssl-devel \
+ patch \
+ procps-ng \
+ python3 \
+ readline-devel \
+ ruby \
+ shadow-utils \
+ sqlite-devel \
+ tar \
+ wget \
+ which \
+ zlib-devel
+
+# Install RVM
+ADD generated/mpapis.asc /tmp/
+ADD generated/pkuczynski.asc /tmp/
+RUN touch /var/lib/rpm/* && \
+ gpg --import --no-tty /tmp/mpapis.asc && \
+ gpg --import --no-tty /tmp/pkuczynski.asc && \
+ curl -L https://get.rvm.io | bash -s stable && \
+ /usr/local/rvm/bin/rvm install 2.7 -j $(grep -c processor /proc/cpuinfo) && \
+ /usr/local/rvm/bin/rvm alias create default ruby-2.7 && \
+ /usr/local/rvm/bin/rvm-exec default gem install bundler --version 2.3.26
+
+COPY localrepo.repo /etc/yum.repos.d/localrepo.repo
--- /dev/null
+[localrepo]
+name=Arvados Test
+baseurl=file:///arvados/packages/rocky8
+gpgcheck=0
+enabled=1
yum install --assumeyes httpd
yum reinstall --assumeyes "$PACKAGE_NAME"
;;
+ rocky*)
+ microdnf --assumeyes install httpd
+ microdnf --assumeyes reinstall "$PACKAGE_NAME"
+ ;;
*)
echo -e "$0: Unknown target '$TARGET'.\n" >&2
exit 1
STDERR_IF_DEBUG=/dev/stderr
fi
-target=$(basename "$0" | grep -Eo '\bcentos[[:digit:]]+\b')
+target="$(basename "$0" .sh)"
+target="${target##*-}"
-yum -q clean all
+case "$target" in
+ centos*) yum -q clean all ;;
+ rocky*) microdnf --assumeyes clean all ;;
+esac
touch /var/lib/rpm/*
export ARV_PACKAGES_DIR="/arvados/packages/$target"
rpm -qa | sort > "$ARV_PACKAGES_DIR/$1.before"
-yum install --assumeyes -e 0 $1
+case "$target" in
+ centos*) yum install --assumeyes -e 0 $1 ;;
+ rocky*) microdnf --assumeyes install $1 ;;
+esac
rpm -qa | sort > "$ARV_PACKAGES_DIR/$1.after"
--- /dev/null
+rpm-common-test-packages.sh
\ No newline at end of file
if [[ -n "$test_packages" ]]; then
if [[ -n "$(find $WORKSPACE/packages/$TARGET -name '*.rpm')" ]] ; then
- set +e
- /usr/bin/which createrepo >/dev/null
- if [[ "$?" != "0" ]]; then
+ CREATEREPO="$(command -v createrepo createrepo_c | tail -n1)"
+ if [[ -z "$CREATEREPO" ]]; then
echo >&2
- echo >&2 "Error: please install createrepo. E.g. sudo apt-get install createrepo"
+ echo >&2 "Error: please install createrepo. E.g. sudo apt install createrepo-c"
echo >&2
exit 1
fi
- set -e
- createrepo $WORKSPACE/packages/$TARGET
+ "$CREATEREPO" $WORKSPACE/packages/$TARGET
fi
if [[ -n "$(find $WORKSPACE/packages/$TARGET -name '*.deb')" ]] ; then
crunch-dispatch-local
crunch-dispatch-slurm
crunch-run
- crunchstat
keepproxy
keepstore
keep-balance
declare -a PYTHON3_BACKPORTS
PYTHON3_EXECUTABLE=python3
-PYTHON3_VERSION=$($PYTHON3_EXECUTABLE -c 'import sys; print("{v.major}.{v.minor}".format(v=sys.version_info))')
-
-## These defaults are suitable for any Debian-based distribution.
-# You can customize them as needed in distro sections below.
-PYTHON3_PACKAGE=python$PYTHON3_VERSION
PYTHON3_PKG_PREFIX=python3
PYTHON3_PREFIX=/usr
-PYTHON3_INSTALL_LIB=lib/python$PYTHON3_VERSION/dist-packages
-## End Debian Python defaults.
-
case "$TARGET" in
- debian*)
- FORMAT=deb
+ centos7)
+ FORMAT=rpm
+ # In CentOS 7, libcurl is linked against libnss. pycurl needs to know
+ # that in order to link to it correctly. This environment variable tells
+ # it that.
+ # libcurl is linked against openssl in RH8+ so this should not be
+ # necessary in later versions.
+ export PYCURL_SSL_LIBRARY=nss
;;
ubuntu1804)
FORMAT=deb
PYTHON3_EXECUTABLE=python3.8
- PYTHON3_VERSION=$($PYTHON3_EXECUTABLE -c 'import sys; print("{v.major}.{v.minor}".format(v=sys.version_info))')
- PYTHON3_PACKAGE=python$PYTHON3_VERSION
- PYTHON3_INSTALL_LIB=lib/python$PYTHON3_VERSION/dist-packages
- ;;
- ubuntu*)
- FORMAT=deb
;;
- centos*)
+ centos*|rocky*)
FORMAT=rpm
- PYTHON3_PACKAGE=$(rpm -qf "$(which python"$PYTHON3_VERSION")" --queryformat '%{NAME}\n')
- PYTHON3_PKG_PREFIX=$PYTHON3_PACKAGE
- PYTHON3_PREFIX=/usr
- PYTHON3_INSTALL_LIB=lib/python$PYTHON3_VERSION/site-packages
- export PYCURL_SSL_LIBRARY=nss
+ ;;
+ debian*|ubuntu*)
+ FORMAT=deb
;;
*)
echo -e "$0: Unknown target '$TARGET'.\n" >&2
exit 1
;;
esac
-
+: "${PYTHON3_VERSION:=$("$PYTHON3_EXECUTABLE" -c 'import sys; print("{v.major}.{v.minor}".format(v=sys.version_info))')}"
+case "$FORMAT" in
+ deb)
+ : "${PYTHON3_INSTALL_LIB:=lib/python$PYTHON3_VERSION/dist-packages}"
+ : "${PYTHON3_PACKAGE:=python$PYTHON3_VERSION}"
+ ;;
+ rpm)
+ : "${PYTHON3_INSTALL_LIB:=lib/python$PYTHON3_VERSION/site-packages}"
+ : "${PYTHON3_PACKAGE:=$(rpm -qf "$(command -v "python$PYTHON3_VERSION")" --queryformat '%{NAME}\n')}"
+ ;;
+esac
if [[ -z "$WORKSPACE" ]]; then
echo >&2 "$helpmessage"
"Dispatch Crunch containers to a SLURM cluster"
package_go_binary cmd/arvados-server crunch-run "$FORMAT" "$ARCH" \
"Supervise a single Crunch container"
-package_go_binary services/crunchstat crunchstat "$FORMAT" "$ARCH" \
- "Gather cpu/memory/network statistics of running Crunch jobs"
package_go_binary cmd/arvados-server arvados-health "$FORMAT" "$ARCH" \
"Check health of all Arvados cluster services"
package_go_binary cmd/arvados-server keep-balance "$FORMAT" "$ARCH" \
return 1
fi
- cross_compilation=1
- if [[ "$TARGET" == "centos7" ]]; then
- if [[ "$native_arch" == "amd64" ]] && [[ -n "$target_arch" ]] && [[ "$native_arch" != "$target_arch" ]]; then
- echo "Error: no cross compilation support for Go on $native_arch for $TARGET, can not build $prog for $target_arch"
- return 1
- fi
- cross_compilation=0
- fi
-
- if [[ "$package_format" == "deb" ]] &&
- [[ "$TARGET" == "debian10" ]] || [[ "$TARGET" == "ubuntu1804" ]] || [[ "$TARGET" == "ubuntu2004" ]]; then
- # Due to bug https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=983477 the libfuse-dev package for arm64 does
- # not install properly side by side with the amd64 version before Debian 11.
- if [[ "$native_arch" == "amd64" ]] && [[ -n "$target_arch" ]] && [[ "$native_arch" != "$target_arch" ]]; then
- echo "Error: no cross compilation support for Go on $native_arch for $TARGET, can not build $prog for $target_arch"
- return 1
- fi
- cross_compilation=0
- fi
+ case "$package_format-$TARGET" in
+ # Older Debian/Ubuntu do not support cross compilation because the
+ # libfuse package does not support multiarch. See
+ # <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=983477>.
+ # Red Hat-based distributions do not support native cross compilation at
+ # all (they use a qemu-based solution we haven't implemented yet).
+ deb-debian10|deb-ubuntu1804|deb-ubuntu2004|rpm-*)
+ cross_compilation=0
+ if [[ "$native_arch" == "amd64" ]] && [[ -n "$target_arch" ]] && [[ "$native_arch" != "$target_arch" ]]; then
+ echo "Error: no cross compilation support for Go on $native_arch for $TARGET, can not build $prog for $target_arch"
+ return 1
+ fi
+ ;;
+ *)
+ cross_compilation=1
+ ;;
+ esac
if [[ -n "$target_arch" ]]; then
archs=($target_arch)
LICENSE_STRING=`grep license $WORKSPACE/$PKG_DIR/setup.py|cut -f2 -d=|sed -e "s/[',\\"]//g"`
COMMAND_ARR+=('--license' "$LICENSE_STRING")
- if [[ "$package_format" == "rpm" ]]; then
- # Make sure to conflict with the old rh-python36 packages we used to publish
- COMMAND_ARR+=('--conflicts' "rh-python36-python-$PKG")
- fi
-
if [[ "$DEBUG" != "0" ]]; then
COMMAND_ARR+=('--verbose' '--log' 'info')
fi
fi
COMMAND_ARR+=('--depends' "$PYTHON3_PACKAGE")
-
- # avoid warning
- COMMAND_ARR+=('--deb-no-default-config-files')
+ case "$package_format" in
+ deb)
+ COMMAND_ARR+=(
+ # Avoid warning
+ --deb-no-default-config-files
+ ) ;;
+ rpm)
+ COMMAND_ARR+=(
+ # Conflict with older packages we used to publish
+ --conflicts "rh-python36-python-$PKG"
+ # Do not generate /usr/lib/.build-id links on RH8+
+ # (otherwise our packages conflict with platform-python)
+ --rpm-rpmbuild-define "_build_id_links none"
+ ) ;;
+ esac
# Append --depends X and other arguments specified by fpm-info.sh in
# the package source dir. These are added last so they can override
lib/service
services/api
services/githttpd
-services/crunchstat
services/dockercleaner
services/fuse
services/fuse:py3
fpm_depends+=(fuse)
case "$TARGET" in
- centos*)
+ centos*|rocky*)
fpm_depends+=(fuse-libs)
;;
esac
"git.arvados.org/arvados.git/lib/config"
"git.arvados.org/arvados.git/lib/controller"
"git.arvados.org/arvados.git/lib/crunchrun"
+ "git.arvados.org/arvados.git/lib/crunchstat"
"git.arvados.org/arvados.git/lib/dispatchcloud"
"git.arvados.org/arvados.git/lib/install"
"git.arvados.org/arvados.git/lib/lsf"
"config-dump": config.DumpCommand,
"controller": controller.Command,
"crunch-run": crunchrun.Command,
+ "crunchstat": crunchstat.Command,
"dispatch-cloud": dispatchcloud.Command,
"dispatch-lsf": lsf.DispatchCommand,
"dispatch-slurm": dispatchslurm.Command,
specs:
RedCloth (4.3.2)
coderay (1.1.3)
- colorize (0.8.1)
+ colorize (1.0.5)
commonjs (0.2.7)
kramdown (1.17.0)
less (2.6.0)
commonjs (~> 0.2.7)
- liquid (4.0.3)
+ liquid (4.0.4)
makerakeworkwell (1.0.4)
rake (>= 0.9.2, < 15)
- rake (13.0.1)
- zenweb (3.10.4)
+ rake (13.0.6)
+ zenweb (3.10.6)
coderay (~> 1.0)
kramdown (~> 1.4)
less (~> 2.0)
end
file "sdk/python/arvados/index.html" do |t|
- if ENV['NO_SDK'] || File.exists?("no-sdk")
+ if ENV['NO_SDK'] || File.exist?("no-sdk")
next
end
`which pdoc`
end
file "sdk/R/arvados/index.html" do |t|
- if ENV['NO_SDK'] || File.exists?("no-sdk")
+ if ENV['NO_SDK'] || File.exist?("no-sdk")
next
end
`which R`
end
file "sdk/java-v2/javadoc/index.html" do |t|
- if ENV['NO_SDK'] || File.exists?("no-sdk")
+ if ENV['NO_SDK'] || File.exist?("no-sdk")
next
end
`which java`
- user/index.html.textile.liquid
- user/getting_started/community.html.textile.liquid
- Walkthough:
- - user/tutorials/wgs-tutorial.html.textile.liquid
- - Using Workbench:
- user/getting_started/workbench.html.textile.liquid
- - user/tutorials/tutorial-workflow-workbench.html.textile.liquid
- - user/topics/workbench-migration.html.textile.liquid
+ - user/tutorials/wgs-tutorial.html.textile.liquid
- Working at the Command Line:
- user/getting_started/setup-cli.html.textile.liquid
- user/reference/api-tokens.html.textile.liquid
- user/getting_started/check-environment.html.textile.liquid
- - Access an Arvados virtual machine:
- - user/getting_started/vm-login-with-webshell.html.textile.liquid
- - user/getting_started/ssh-access-unix.html.textile.liquid
- - user/getting_started/ssh-access-windows.html.textile.liquid
- Working with data sets:
+ - user/tutorials/tutorial-projects.html.textile.liquid
- user/tutorials/tutorial-keep.html.textile.liquid
- user/tutorials/tutorial-keep-get.html.textile.liquid
+ - user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
+ - user/topics/arv-copy.html.textile.liquid
- user/tutorials/tutorial-keep-mount-gnu-linux.html.textile.liquid
- user/tutorials/tutorial-keep-mount-os-x.html.textile.liquid
- user/tutorials/tutorial-keep-mount-windows.html.textile.liquid
- - user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
- - user/topics/arv-copy.html.textile.liquid
- user/topics/collection-versioning.html.textile.liquid
- user/topics/storage-classes.html.textile.liquid
- Data Analysis with Workflows:
- - user/cwl/arvados-vscode-training.html.md.liquid
- - user/cwl/rnaseq-cwl-training.html.textile.liquid
+ - user/tutorials/tutorial-workflow-workbench.html.textile.liquid
- user/cwl/cwl-runner.html.textile.liquid
- user/cwl/cwl-run-options.html.textile.liquid
- - user/tutorials/writing-cwl-workflow.html.textile.liquid
+ - user/cwl/crunchstat-summary.html.textile.liquid
+ - user/debugging/container-shell-access.html.textile.liquid
+ - user/cwl/costanalyzer.html.textile.liquid
+ - user/cwl/federated-workflows.html.textile.liquid
+ - Common Workflow Language:
+ - user/cwl/rnaseq-cwl-training.html.textile.liquid
+ - user/cwl/arvados-vscode-training.html.md.liquid
- user/topics/arv-docker.html.textile.liquid
- user/cwl/cwl-style.html.textile.liquid
+ - user/tutorials/writing-cwl-workflow.html.textile.liquid
- user/cwl/cwl-extensions.html.textile.liquid
- - user/cwl/federated-workflows.html.textile.liquid
- user/cwl/cwl-versions.html.textile.liquid
- - user/cwl/crunchstat-summary.html.textile.liquid
- - user/cwl/costanalyzer.html.textile.liquid
- - user/debugging/container-shell-access.html.textile.liquid
- - Working with git repositories:
- - user/tutorials/add-new-repository.html.textile.liquid
- - user/tutorials/git-arvados-guide.html.textile.liquid
+ - Access an Arvados virtual machine:
+ - user/getting_started/vm-login-with-webshell.html.textile.liquid
+ - user/getting_started/ssh-access-unix.html.textile.liquid
+ - user/getting_started/ssh-access-windows.html.textile.liquid
- Reference:
+ - user/topics/workbench-migration.html.textile.liquid
- user/topics/link-accounts.html.textile.liquid
- user/reference/cookbook.html.textile.liquid
- Arvados License:
</code></pre>
</notextile>
-h4. CentOS
+h4. Alma/CentOS/Red Hat/Rocky
<notextile>
<pre><code>cp {{ca_cert_name}} /etc/pki/ca-trust/source/anchors/
After making changes, reboot the system to make these changes effective.
-h3. Red Hat and CentOS
+h3. Alma/CentOS/Red Hat/Rocky
<notextile>
<pre><code>~$ <span class="userinput">sudo grubby --update-kernel=ALL --args='cgroup_enable=memory swapaccount=1 systemd.unified_cgroup_hierarchy=0'</span>
{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+
packages_to_install should be a list
fallback on arvados_component if not defined
{% endcomment %}
h2(#install-packages). Install {{packages_to_install | join: " and " }}
-h3. Red Hat and Centos
+h3. Alma/CentOS/Red Hat/Rocky
<notextile>
-<pre><code># <span class="userinput">yum install {{packages_to_install | join: " "}}</span>
+<pre><code># <span class="userinput">dnf install {{packages_to_install | join: " "}}</span>
</code></pre>
</notextile>
Future versions of Arvados may require a newer version of Ruby than is packaged with your OS. Using OS packages simplifies initial install, but may complicate upgrades that rely on a newer Ruby. If this is a concern, we recommend using "RVM":#rvm.
{% include 'notebox_end' %}
-h3. Centos 7
+h3. Alma/CentOS/Red Hat/Rocky
-The Ruby version shipped with Centos 7 is too old. Use "RVM":#rvm to install a newer version of Ruby (we recommend installing version 2.7 or newer).
+The Ruby version shipped with version 7 of these distributions is too old. Use "RVM":#rvm to install a newer version of Ruby (we recommend installing version 2.7 or newer).
+
+Ruby 2.7 is available in a module with version 8 of these distributions. You can install it by running:
+
+<notextile>
+<pre><code># <span class="userinput">dnf module enable ruby:2.7</span>
+# <span class="userinput">dnf install --enablerepo=devel ruby ruby-devel</span></code></pre>
+</notextile>
h3. Debian and Ubuntu
h3. Install gpg and curl
-h4. Centos 7
+h4. Alma/CentOS/Red Hat/Rocky
<pre>
-yum install gpg curl which
+dnf install gpg curl which
</pre>
h4. Debian and Ubuntu
libssl-dev libxslt1.1 zlib1g-dev
</span></code></pre></notextile>
-Install prerequisites for CentOS 7:
+Install prerequisites for Alma/CentOS/Red Hat/Rocky:
<notextile>
-<pre><code><span class="userinput">sudo yum install \
+<pre><code><span class="userinput">sudo dnf install \
libyaml-devel glibc-headers autoconf gcc-c++ glibc-devel \
patch readline-devel zlib-devel libffi-devel openssl-devel \
make automake libtool bison sqlite-devel tar
h1(#workbench). Adding your key to Arvados Workbench
-h3. From the Workbench dashboard
+In the Workbench top navigation menu, click on the dropdown menu icon <i class="fa fa-lg fa-user"></i> to access the Account Management menu. Then, click on the menu item *Ssh keys* to go to the *SSH keys* page. Click on the <span class="btn btn-primary">+ ADD NEW SSH KEY</span> button in the upper-right on that page. You will see a popup as shown in this screenshot:
-In the Workbench top navigation menu, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> to access the user settings menu and click on the menu item *SSH keys* to go to the *SSH keys* page. Click on the <span class="btn btn-primary">*+* Add new SSH key</span> button in this page. This will open a popup as shown in this screenshot:
+!{width: 100%;}{{ site.baseurl }}/images/ssh-adding-public-key.png!
-!{{ site.baseurl }}/images/ssh-adding-public-key.png!
-Paste your public key into the text area labeled *Public Key*, and click on the <span class="btn btn-primary">Submit</span> button. You are now ready to "log into an Arvados VM":#login.
+Paste your _public_ key into the text area labeled *Public Key*, and click on the <span class="btn btn-sm btn-primary">ADD NEW SSH KEY</span> button in lower-right. You are now ready to "log into an Arvados VM":#login.
h1(#login). Using SSH to log into an Arvados VM
-To see a list of virtual machines that you have access to, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, then click on the menu item *Virtual machines* to go to the Virtual machines page.
+To see a list of virtual machines that you have access to, click on the dropdown menu icon <i class="fa fa-lg fa-user"></i> in the upper right corner of the top navigation menu to access the Account Management menu. Then, click on the menu item *Virtual Machines*.
-This page lists the virtual machines you can access. The *Host name* column lists the name of each available VM. The *Login name* column lists your login name on that VM. The *Command line* column provides a sample @ssh@ command line.
+You will then see a page that lists the virtual machines you can access. The *Host name* column lists the name of each available VM. The *Login name* column lists your login name on that VM. The *Command line* column provides a sample @ssh@ command.
+
+!{width: 100%;}{{ site.baseurl }}/images/vm-access-with-webshell.png!
At the bottom of the page there may be additional instructions for connecting your specific Arvados instance. If so, follow your site-specific instructions. If there are no site-specific instructions, you can probably connect directly with @ssh@.
-The following are generic instructions. In the examples the login will be *_you_* and the hostname will be *_shell.ClusterID.example.com_* and . Replace these with your login name and hostname as appropriate.
+The following are generic instructions. In these examples, the login name will be *_you_* and the host domain will be *_ClusterID.example.com_*. Replace these with your login name and hostname as appropriate.
table(table table-bordered table-condensed).
|_. *Supported Linux Distributions*|
+|AlmaLinux 8|
+|CentOS 8|
|CentOS 7|
+|Red Hat Enterprise Linux 8|
+|Rocky Linux 8|
|Debian 11 ("bullseye")|
|Debian 10 ("buster")|
|Ubuntu 20.04 ("focal")|
{% endcomment %}
{% include 'notebox_begin' %}
-This tutorial assumes that you have access to the "Arvados command line tools":{{ site.baseurl }}/user/getting_started/setup-cli.html and have set the "API token":{{site.baseurl}}/user/reference/api-tokens.html and confirmed a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html .
+This tutorial assumes that you have access to "Arvados command line tools":{{ site.baseurl }}/user/getting_started/setup-cli.html, configured your "API token":{{site.baseurl}}/user/reference/api-tokens.html, and confirmed a "working environment":{{site.baseurl}}/user/getting_started/check-environment.html.
{% include 'notebox_end' %}
</pre>
</notextile>
-The choice of subsystem ("memory" in this example) must correspond to one of the resource types enabled in Slurm's @cgroup.conf@. Limits for other resource types will also be respected. The specified subsystem is singled out only to let Crunch determine the name of the cgroup provided by Slurm. When doing this, you should also set "ReserveExtraRAM":#ReserveExtraRAM .
+When using cgroups v1, the choice of subsystem ("memory" in this example) must correspond to one of the resource types enabled in Slurm's @cgroup.conf@. The specified subsystem is singled out only to let Crunch determine the name of the cgroup provided by Slurm. Limits for other resource types will also be respected.
+
+When doing this, you should also set "ReserveExtraRAM":#ReserveExtraRAM .
{% include 'notebox_begin' %}
h2(#dependencies). Install dependencies
-h3. Centos 7
+h3. Alma/CentOS/Red Hat/Rocky
<notextile>
-<pre><code># <span class="userinput">yum install git perl-Data-Dumper openssh-server</span>
+<pre><code># <span class="userinput">dnf install git perl-Data-Dumper openssh-server</span>
</code></pre>
</notextile>
The arvados-git-httpd package provides HTTP access, using Arvados authentication tokens instead of passwords. It must be installed on the system where your git repositories are stored.
-h3. Centos 7
+h3. Alma/CentOS/Red Hat/Rocky
<notextile>
-<pre><code># <span class="userinput">yum install arvados-git-httpd</span>
+<pre><code># <span class="userinput">dnf install arvados-git-httpd</span>
</code></pre>
</notextile>
* "AWS":#aws
* "CentOS 7":#centos7
+* "Alma/CentOS/Red Hat/Rocky 8":#rh8
* "Debian or Ubuntu":#debian
h3(#aws). AWS
# Configure the database to launch at boot and start now
<notextile><pre># <span class="userinput">systemctl enable --now rh-postgresql12-postgresql</span></pre></notextile>
+h3(#rh8). Alma/CentOS/Red Hat/Rocky 8
+
+{% comment %}
+The default version on RH8 is PostgreSQL 10. You can install up to PostgreSQL 13.
+{% endcomment %}
+
+# Install PostgreSQL
+ <notextile><pre># <span class="userinput">dnf install postgresql-server postgresql-contrib</span></pre></notextile>
+# Initialize the database
+ <notextile><pre># <span class="userinput">postgresql-setup initdb</span></pre></notextile>
+# Configure the database to accept password connections from localhost
+ <notextile><pre><code># <span class="userinput">sed -ri -e 's/^(host +all +all +(127\.0\.0\.1\/32|::1\/128) +)ident$/\1md5/' /var/lib/pgsql/data/pg_hba.conf</span></code></pre></notextile>
+# Configure the database to accept password connections from the local network (replace @10.9.8.0/24@ with your private network mask)
+ <notextile><pre><code># <span class="userinput">echo 'host all all 10.9.8.0/24 md5' | tee -a /var/lib/pgsql/data/pg_hba.conf</span></code></pre></notextile>
+# Configure the database to launch at boot and start now
+ <notextile><pre># <span class="userinput">systemctl enable --now postgresql</span></pre></notextile>
+
h3(#debian). Debian or Ubuntu
Debian 10 (Buster) and Ubuntu 16.04 (Xenial) and later versions include a sufficiently recent version of Postgres.
h2(#config-shellinabox). Configure shellinabox
-h3. Red Hat and Centos
+h3. Alma/CentOS/Red Hat/Rocky
Edit @/etc/sysconfig/shellinaboxd@:
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-h3. Centos 7
+h3. CentOS 7
<notextile>
<pre><code># <span class="userinput">yum install epel-release</span></code>
<code># <span class="userinput">yum install nginx</span></code></pre>
</notextile>
+h3. Alma/CentOS/Red Hat/Rocky 8
+
+<notextile>
+<pre><code># <span class="userinput">dnf install nginx</span></code></pre>
+</notextile>
+
h3. Debian and Ubuntu
<notextile>
On any host where you install Arvados software, you'll need to add the Arvados package repository. They're available for several popular distributions.
-* "Centos 7":#centos7
+* "AlmaLinux, CentOS, RHEL, and Rocky Linux":#redhat
* "Debian and Ubuntu":#debian
-h3(#centos7). CentOS
+<notextile>
+<a id="centos7" style="display: none;"></a>
+</notextile>
+
+h3(#redhat). AlmaLinux, CentOS, RHEL, and Rocky Linux
+
+Packages are available for the following Red Hat-based distributions:
+
+* AlmaLinux 8
+* CentOS 7
+* CentOS 8
+* RHEL 8
+* Rocky Linux 8
-Packages are available for CentOS 7. To install them with yum, save this configuration block in @/etc/yum.repos.d/arvados.repo@:
+To install them with dnf or yum, save this configuration block in @/etc/yum.repos.d/arvados.repo@:
<notextile>
<pre><code>[arvados]
</code></pre>
</notextile>
-* On CentOS:
+* On Alma/CentOS/Red Hat/Rocky:
<notextile>
<pre><code>cp arvados-root-cert.pem /etc/pki/ca-trust/source/anchors/
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-The Arvados FUSE driver is a Python utility that allows you to see the Keep service as a normal filesystem, so that data can be accessed using standard tools. This driver requires the Python SDK installed in order to access Arvados services.
+The Arvados CWL Runner is a Python tool that allows you to register and submit workflows to Arvados. You can oversee a running workflow on your local system, or let that run inside an Arvados container. This tool requires the Python SDK installed in order to access Arvados services.
h2. Installation
-If you are logged in to a managed Arvados VM, the @arv-mount@ utility should already be installed.
+If you are logged in to a managed Arvados VM, the @arvados-cwl-runner@ utility should already be installed.
-To use the FUSE driver elsewhere, you can install from a distribution package, or PyPI.
+To use the CWL Runner elsewhere, you can install it from a distribution package or PyPI.
h2. Option 1: Install from distribution packages
-First, "add the appropriate package repository for your distribution":{{ site.baseurl }}/install/packages.html
+First, "add the appropriate package repository for your distribution":{{ site.baseurl }}/install/packages.html.
{% assign arvados_component = 'python3-arvados-cwl-runner' %}
Note:
-The SDK uses @pycurl@ which depends on the @libcurl@ C library. To build the module you may have to first install additional packages. On Debian 10 this is:
+The CWL Runner uses @pycurl@ which depends on the @libcurl@ C library. To build the module you may have to first install additional packages. On Debian-based distributions you can install them by running:
-<pre>
-$ apt-get install git build-essential python3-dev libcurl4-openssl-dev libssl1.0-dev python3-llfuse
-</pre>
+<notextile>
+<pre><code># <span class="userinput">apt install git build-essential python3-dev libcurl4-openssl-dev libssl-dev</span>
+</code></pre>
+</notextile>
-h3. Check Docker access
+h2. Check Docker access
In order to pull and upload Docker images, @arvados-cwl-runner@ requires access to Docker. You do not need Docker if the Docker images you intend to use are already available in Arvados.
If this returns an error, contact the sysadmin of your cluster for assistance.
-h3. Usage
+h2. Usage
-Please refer to the "Accessing Keep from GNU/Linux":{{site.baseurl}}/user/tutorials/tutorial-keep-mount-gnu-linux.html tutorial for more information.
+Please refer to the "Starting a Workflow at the Command Line":{{site.baseurl}}/user/cwl/cwl-runner.html tutorial for more information.
Note:
-The SDK uses @pycurl@ which depends on the @libcurl@ C library. To build the module you may have to first install additional packages. On Debian 10 this is:
+The FUSE driver uses @pycurl@ which depends on the @libcurl@ C library. To build the module you may have to first install additional packages. On Debian-based distributions you can install them by running:
+
+<notextile>
+<pre><code># <span class="userinput">apt install git build-essential python3-dev libcurl4-openssl-dev libssl-dev</span>
+</code></pre>
+</notextile>
<pre>
$ apt-get install git build-essential python3-dev libcurl4-openssl-dev libssl-dev python3-llfuse
This installation method is recommended to use the SDK in your own Python programs. If installed into a @virtualenv@, it can coexist with the system-wide installation method from a distribution package.
-The SDK uses @pycurl@ which depends on the @libcurl@ C library. To build the module you may have to first install additional packages. On Debian 10 you can do this by running:
+Note the Python SDK uses @pycurl@ which depends on the @libcurl@ C library. To build the module you may have to first install additional packages. On Debian-based distributions you can install them by running:
-<pre>
-$ apt-get install git build-essential python3-dev libcurl4-openssl-dev libssl-dev
-</pre>
+<notextile>
+<pre><code># <span class="userinput">apt install git build-essential python3-dev libcurl4-openssl-dev libssl-dev</span>
+</code></pre>
+</notextile>
Run @python3 -m pip install arvados-python-client@ in an appropriate installation environment, such as a @virtualenv@.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
+{% include 'tutorial_expectations' %}
+
{% include 'notebox_begin' %}
This is only applicable when Arvados runs in a cloud environment and @arvados-dispatch-cloud@ is used to dispatch @crunch@ jobs. The per node-hour price for each defined InstanceType most be supplied in "config.yml":{{site.baseurl}}/admin/config.html.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-The @crunchstat-summary@ tool can be used to analyze workflow and container performance. It can be installed from packages (@apt install python3-crunchstat-summary@ or @yum install rh-python36-python-crunchstat-summary@). @crunchstat-summary@ analyzes the crunchstat lines from the logs of a container or workflow and generates a report in text or html format.
+{% include 'tutorial_expectations' %}
+
+The @crunchstat-summary@ tool can be used to analyze workflow and container performance. It can be installed from packages (@apt install python3-crunchstat-summary@ or @yum install rh-python36-python-crunchstat-summary@), or in a Python virtualenv (@pip install crunchstat_summary@). @crunchstat-summary@ analyzes the crunchstat lines from the logs of a container or workflow and generates a report in text or html format.
h2(#syntax). Syntax
h2(#registering). Registering a workflow to use in Workbench
-Use @--create-workflow@ to register a CWL workflow with Arvados. Use @--project-uuid@ to upload the workflow to a specific project, along with its dependencies. You can share the workflow with other Arvados users by sharing that project. You can run the workflow by clicking the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button on the Workbench Dashboard, and on the command line by UUID.
+Use @--create-workflow@ to register a CWL workflow with Arvados. Use @--project-uuid@ to upload the workflow to a specific project, along with its dependencies. You can share the workflow with other Arvados users by sharing that project. You can run the workflow by clicking the <span class="btn btn-sm btn-primary">+ NEW</span> → <i class="fa fa-fw fa-gear"></i> *Run a process* menu items on the Workbench, and on the command line by UUID.
<notextile>
<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --project-uuid zzzzz-j7d0g-p32bi47ogkjke11 --create-workflow bwa-mem.cwl</span>
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
+{% include 'tutorial_expectations' %}
+
{% include 'notebox_begin' %}
To use this feature, your Arvados installation must be configured to allow container shell access. See "the install guide":{{site.baseurl}}/install/container-shell-access.html for more information.
Many operations in Arvados can be performed using either the web Workbench or through command line tools. Some operations can only be done using the command line.
-To use the command line tools, you can either log into an Arvados-managed VM instance where those tools are pre-installed, or install the Arvados tools on your own system.
+To use the command line tools, you can either log into an Arvados virtual machine where those tools are pre-installed, or install the Arvados tools on your own system.
-To log into an Arvados-managed VM, see instructions for "Webshell":{{site.baseurl}}/user/getting_started/vm-login-with-webshell.html or "Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html .
+h2. Option 1: Using an Arvados virtual machine
-To install the Arvados tools on your own system, you should install the "Command line SDK":{{site.baseurl}}/sdk/cli/install.html (requires Ruby) and "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html (requires Python). You may also want to install "arvados-cwl-runner":{{site.baseurl}}/sdk/python/arvados-cwl-runner.html to submit workflows and "arvados-fuse":{{site.baseurl}}/sdk/python/arvados-fuse.html to mount keep as a filesystem.
+This is the command line interface we recommend for most day-to-day work, because the tools are all preinstalled and preconfigured for you. You can log in to any virtual machine where you have permission by using:
-Once you are logged in or have command line tools installed, see "getting an API token":{{site.baseurl}}/user/reference/api-tokens.html and "check your environment":{{site.baseurl}}/user/getting_started/check-environment.html .
+* "the Webshell client":{{site.baseurl}}/user/getting_started/vm-login-with-webshell.html accessible through Arvados Workbench
+* "Unix SSH clients":{{site.baseurl}}/user/getting_started/ssh-access-unix.html
+* "Windows SSH clients":{{site.baseurl}}/user/getting_started/ssh-access-windows.html
+
+h2. Option 2: Installing Arvados tools on your own system
+
+This option gives you more flexibility in your work, but takes more time to set up.
+
+h3. Configure Arvados package repositories for your system
+
+Doing this isn't strictly required for most tools, but will streamline the installation process. Follow the "Arvados package repository instructions":{{site.baseurl}}/install/packages.html.
+
+h3. Install individual tool packages
+
+Here are the client packages you can install on your system. You can skip any you don't want or need except for the Python SDK (most other tools require it).
+
+* "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html: This provides an Arvados API client in Python, as well as low-level command line tools.
+* "Command-line SDK":{{site.baseurl}}/sdk/cli/install.html: This provides the high-level @arv@ command and user interface to the Arvados API.
+* "FUSE Driver":{{site.baseurl}}/sdk/python/arvados-fuse.html: This provides the @arv-mount@ command and FUSE driver that lets you access Keep using standard Linux filesystem tools.
+* "CWL Runner":{{site.baseurl}}/sdk/python/arvados-cwl-runner.html: This provides the @arvados-cwl-runner@ command to register and run workflows in Crunch.
+* "crunchstat-summary":{{site.baseurl}}/user/cwl/crunchstat-summary.html: This tool provides performance reports for Crunch containers.
+* "arvados-client":{{site.baseurl}}/user/debugging/container-shell-access.html: This tool provides subcommands for inspecting Crunch containers, both interactively while they're running and after they've finished.
+
+h2. After Installation: Check your environment
+
+Once you are logged in or have command line tools installed, move on to "getting an API token":{{site.baseurl}}/user/reference/api-tokens.html and "checking your environment":{{site.baseurl}}/user/getting_started/check-environment.html.
* @-t@ specifies the key type (must be "rsa")
* @-C@ specifies a comment (to remember which account the key is associated with)
-We strongly recommend that you protect your key with a passphrase. This means that when the key is used, you will be required to enter the passphrase. However, unlike logging into remote system using a password, the passphrase is never sent over the network, it is only used to decrypt your private key.
+We strongly recommend that you protect your key with a passphrase. This means that when the key is used, you will be required to enter the passphrase. However, unlike logging into remote system using a password, the passphrase is never sent over the network; it is only used to decrypt your private key locally.
-Display the contents of @~/.ssh/id_rsa.pub@ (this is your public key) using @cat@ and then copy it onto the clipboard:
+Display the contents of @~/.ssh/id_rsa.pub@ (this is your public key) using @cat@, and then copy it onto the clipboard. The content of the public key may look similar to the following example:
<notextile>
<pre><code>$ <span class="userinput">cat ~/.ssh/id_rsa.pub</span>
</code></pre>
</notextile>
+* The above is a specimen that cannot be used as a valid public key.
+
Now you can set up @ssh-agent@ (next) or proceed with "adding your key to the Arvados Workbench.":#workbench
h3. Set up ssh-agent (optional)
notextile. <pre><code>$ <span class="userinput">ssh-add -l</span></code></pre>
-If you get the error "Could not open a connection to your authentication agent" you will need to run @ssh-agent@ with the following command:
+If you get the error "_Could not open a connection to your authentication agent_", you will need to run @ssh-agent@ with the following command:
-notextile. <pre><code>$ <span class="userinput">eval $(ssh-agent -s)</span></code></pre>
+notextile. <pre><code>$ <span class="userinput">eval "$(ssh-agent -s)"</span></code></pre>
-@ssh-agent -s@ prints out values for environment variables SSH_AUTH_SOCK and SSH_AGENT_PID and then runs in the background. Using "eval" on the output as shown here causes those variables to be set in the current shell environment so that subsequent calls to SSH can discover how to access the agent process.
+@ssh-agent -s@ runs an agent process in the background to hold your SSH credentials, and it prints out the values of environment variables @SSH_AUTH_SOCK@ and @SSH_AGENT_PID@. By applying the shell builtin @eval@ to this output, as we show here using the shell command-substitution syntax, we set those variables in the current shell environment. In this way, subsequent invocations of @ssh@ in this shell session will be able to access the agent process for the credentials without asking you each time.
-After running @ssh-agent@, or if @ssh-add -l@ prints "The agent has no identities", add your key using the following command. The passphrase to decrypt the key is the same used to protect the key when it was created with @ssh-keygen@:
+After running @ssh-agent@, or if @ssh-add -l@ prints "_The agent has no identities_", add your private key to the SSH agent using the following command. The passphrase to decrypt the key is the same one used to protect the key when it was created with @ssh-keygen@:
<notextile>
<pre><code>$ <span class="userinput">ssh-add</span>
</code></pre>
</notextile>
-When everything is set up, @ssh-add -l@ should yield output that looks something like this:
+When everything is set up, @ssh-add -l@ should yield output that looks like this:
<notextile>
<pre><code>$ <span class="userinput">ssh-add -l</span>
h3. Connecting directly
-If the VM is available on the public Internet (or you are on the same private network as the VM) you can connect directly with @ssh@. You can probably copy-and-paste the text from *Command line* column directly into a terminal.
+If the VM is available on the public Internet (or you are on the same private network as the VM), you can connect directly with @ssh@. You can copy-and-paste the text from the *Command line* column (see the screenshot above) directly into a shell session.
-Use the following example command to connect as _you_ to the _shell.ClusterID.example.com_ VM instance. Replace *<code>you@shell.ClusterID.example.com</code>* at the end of the following command with your *login* and *hostname* from Workbench.
+Use the following example command to connect, as the user "_you_" to the VM instance at the hostname "_shell.ClusterID.example.com_". Replace *<code>you@shell.ClusterID.example.com</code>* at the end of the following command with your actual *login* and *hostname* from Workbench.
notextile. <pre><code>$ <span class="userinput">ssh <b>you@shell.ClusterID.example.com</b></span></code></pre>
h3. Connecting through switchyard
-Some Arvados installations use "switchyard" to isolate shell VMs from the public Internet.
+Some Arvados installations use "switchyard" to isolate shell VMs from the public Internet. In such cases, you cannot log in directly to virtual machines over the public Internet. Instead, you log into a "switchyard" server and then tell the switchyard which virtual machine you want to connect to.
Use the following example command to connect to the _shell_ VM instance as _you_. Replace *<code>you@shell</code>* at the end of the following command with your *login* and *hostname* from Workbench:
notextile. <pre><code>$ <span class="userinput">ssh -o "ProxyCommand ssh -p2222 turnout@switchyard.ClusterID.example.com -x -a <b>shell</b>" -x <b>you@shell</b></span></code></pre>
-This command does several things at once. You usually cannot log in directly to virtual machines over the public Internet. Instead, you log into a "switchyard" server and then tell the switchyard which virtual machine you want to connect to.
+This command does several things at once.
* @-o "ProxyCommand ..."@ configures SSH to run the specified command to create a proxy and route your connection through it.
* @-p2222@ specifies that the switchyard is running on non-standard port 2222.
* <code>turnout@switchyard.{{ site.arvados_api_host }}</code> specifies the user (@turnout@) and hostname (@switchyard.{{ site.arvados_api_host }}@) of the switchyard server that will proxy our connection to the VM.
* @-x@ tells SSH not to forward your X session to the switchyard.
* @-a@ tells SSH not to forward your ssh-agent credentials to the switchyard.
-* *@shell@* is the name of the VM that we want to connect to. This is sent to the switchyard server as if it were an SSH command, and the switchyard server connects to the VM on our behalf.
-* After the ProxyCommand section, we repeat @-x@ to disable X session forwarding to the virtual machine.
+* *@shell@* is the host name of the VM that we want to connect to. In summary, the string inside the quotation marks is sent to the switchyard server, as if it were an SSH command, and the switchyard server connects to the VM on our behalf.
+* After the @ProxyCommand@ section, we repeat @-x@ to disable X session forwarding to the virtual machine.
* Finally, *<code>you@shell</code>* specifies your login name and repeats the hostname of the VM. The username can be found in the *logins* column in the VMs Workbench page, discussed in the previous section.
You should now be able to log into the Arvados VM and "check your environment.":check-environment.html
Some Arvados clusters may not have webshell set up. If you do not see a "Log in" button or "web shell" column, you will have to follow the "Unix":ssh-access-unix.html or "Windows":ssh-access-windows.html @ssh@ instructions.
{% include 'notebox_end' %}
-In the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Virtual machines* to see the list of virtual machines you can access. If you do not have access to any virtual machines, please click on <span class="btn btn-sm btn-primary">Send request for shell access</span> (if present) or contact your system administrator. For the Arvados Playground, this is "info@curii.com":mailto:info@curii.com .
+In the Arvados Workbench, click on the dropdown menu icon <i class="fa fa-lg fa-user"></i> in the upper right corner of the top navigation menu to access the _Account Management_ menu, and click on the menu item *Virtual machines* to see the list of virtual machines you can access. If you do not have access to any virtual machines, please click on <span class="btn btn-sm btn-primary">SEND REQUEST FOR SHELL ACCESS</span> (if present) or contact your system administrator. For the Arvados Playground, this is "info@curii.com":mailto:info@curii.com .
-Each row in the Virtual Machines panel lists the hostname of the VM, along with a <code>Log in as *you*</code> button under the column "Web shell". Clicking on this button will open up a webshell terminal for you in a new browser tab and log you in.
+Each row in the Virtual Machines panel lists the hostname of the VM, along with a <span class="btn btn-sm btn-default" style="background-color: #e0e0e0">Log in as [your name]</span> button under the column "*Web shell*". Clicking on this button will open up a webshell terminal for you in a new browser tab and log you in.
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/vm-access-with-webshell.png!
+!{width: 100%;}{{ site.baseurl }}/images/vm-access-with-webshell.png!
You are now ready to work in your Arvados VM.
{% endcomment %}
{% include 'notebox_begin' %}
-This guide covers the classic Arvados Workbench web application, sometimes referred to as "Workbench 1". There is also a new Workbench web application under development called "Workbench 2". This guide will be updated to cover "Workbench 2" in the future. See "Workbench 2 migration":{{site.baseurl}}/user/topics/workbench-migration.html for more information.
+This guide covers modern Arvados Workbench web application, which may be referred to as "Workbench 2" to distinguish it from the previous Arvados Workbench web application ("Workbench 1"). Documentation for the classic Workbench can be found in "older versions of the user guide":https://doc.arvados.org/v2.6/user/getting_started/workbench.html . See also "Workbench 2 migration":{{site.baseurl}}/user/topics/workbench-migration.html for more information.
{% include 'notebox_end' %}
You can access the Arvados Workbench used in this guide using this link:
You will be asked to log in. Arvados uses only your name and email address for identification, and will never access any personal information. If you are accessing Arvados for the first time, the Workbench may indicate your account status is *New / inactive*. If this is the case, contact the administrator of the Arvados instance to request activation of your account.
-Once your account is active, logging in to the Workbench will present you with the Dashboard. This gives a summary of your projects and recent activity in the Arvados instance. You are now ready to "upload data":{{ site.baseurl }}/user/tutorials/tutorial-keep.html or "run your first workflow.":{{ site.baseurl }}/user/tutorials/tutorial-workflow-workbench.html
+Once your account is active, logging in to the Workbench will present you with an overview of your Home Projects. You are now ready to "upload data":{{ site.baseurl }}/user/tutorials/tutorial-keep.html or "run your first workflow.":{{ site.baseurl }}/user/tutorials/tutorial-workflow-workbench.html
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/workbench-dashboard.png!
+!{width: 100%;}{{ site.baseurl }}/images/workbench-first-page.png!
Open a shell on the system where you want to use the Arvados client. This may be your local workstation, or an Arvados virtual machine accessed with "Webshell":{{site.baseurl}}/user/getting_started/vm-login-with-webshell.html or SSH (instructions for "Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html#login or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html#login).
-In the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Current token*, which lists your current token and instructions to set up your environment.
+In the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> in the upper right corner of the top navigation menu to access the _Account Management_ menu. Then, in the pop-up menu, click on the menu item *Get API token*. This will open a dialog box that lists your current token and the instructions for setting up your environment.
h2. Setting environment variables
-The *Current token* page, accessed using the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu, includes a command you may copy and paste directly into the shell. It will look something as the following.
+In the dialog box opened after clicking on the *Get API token* menu item, there is a sequence of commands you may copy and paste directly into the shell. It will look something as the following.
bc. HISTIGNORE=$HISTIGNORE:'export ARVADOS_API_TOKEN=*'
export ARVADOS_API_TOKEN=2jv9346o396exampledonotuseexampledonotuseexes7j1ld
</code></pre>
</notextile>
+* The output-redirection operator @>@ in the first command will cause the target file @~/.config/arvados/settings.conf@ to be created anew, wiping out the content of any existing file at that path.
+* The @>>@ operator in the second command appends to the target file.
+
h2. .bashrc
-Alternately, you may add the declarations of @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ to the @~/.bashrc@ file on the system on which you intend to use the Arvados client. If you have already put the variables into the environment following the instructions above, you can use these commands to append the environment variables to your @~/.bashrc@:
+Alternately, you may add the definitions of @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ to the @~/.bashrc@ file on the system where you intend to use the Arvados client. If you have already put the variables into the environment following the instructions above, you can use the commands below to append to your @~/.bashrc@, which tells Bash to export them as environment variables in newly-started interactive shell sessions:
<notextile>
<pre><code>$ <span class="userinput">echo "export ARVADOS_API_HOST=$ARVADOS_API_HOST" >> ~/.bashrc</span>
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-Arvados is in the process of migrating from the classic web application, referred to as "Workbench 1", to a completely new web application, referred to as "Workbench 2".
+Beginning in version 2.7, Arvados now defaults to a new web application, referred to as "Workbench 2". This is a major step in the migration from the classic web application, referred to as "Workbench 1". Workbench 1 should be considered deprecated and suppport for the Workbench 1 application will be dropped in a future Arvados release.
!{width: 90%}{{ site.baseurl }}/images/wb2-example.png!
-Workbench 2 is the new Workbench web application that will, over time, replace Workbench 1. Workbench 2 is being built based on user feedback, and it is approaching feature parity with Workbench 1. Workbench 2 has a modern look and feel and offers several advanced features and performance enhancements. Arvados clusters typically have both Workbench applications installed and have a dropdown menu option in the user menu to switch between versions.
+Workbench 2 is the new Workbench web application that replaces Workbench 1. Workbench 2 is being built based on user feedback, and has feature parity with Workbench 1. Workbench 2 has a modern look and feel and offers many advanced features and performance enhancements over the previous Workbench application.
+
+To facilitate migration, Arvados may have both Workbench applications installed and have a dropdown menu option in the user menu to switch between versions.
!{{ site.baseurl }}/images/switch-to-wb2.png!
-Workbench 2 is stable and recommended for general use, but still lacks some features available in the classic Workbench 1 application. When necessary, you can easily switch back:
+Workbench 2 is stable and recommended for general use. However, if you find that you need something in Workbench 1, you can easily switch back:
!{{ site.baseurl }}/images/switch-to-wb1.png!
h2. Add "tutorial" repository
-On the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Repositories*.
+On the Arvados Workbench, click on the dropdown menu icon <i class="fa fa-lg fa-user"></i> (Account Management) in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Repositories*.
-In the *Repositories* page, you will see the *Add new repository* button.
+In the *Repositories* page, you will see the <span class="btn btn-sm btn-primary">+ NEW REPOSITORY</span> button.
-!{display: block;margin-left: 25px;margin-right: auto;}{{ site.baseurl }}/images/repositories-panel.png!
+!{width: 100%;}{{ site.baseurl }}/images/repositories-panel.png!
-Click the *Add new Repository* button to open the popup to add a new arvados repository. You will see a text box where you can enter the name of the repository. Enter *tutorial* in this text box and click on *Create*.
+Click the <span class="btn btn-sm btn-primary">+ NEW REPOSITORY</span> button to open the popup to add a new Arvados repository. You will see a text box where you can enter the name of the repository. Enter *tutorial* in this text box and click on *Create*.
{% include 'notebox_begin' %}
The name you enter here must begin with a letter and can only contain alphanumeric characters.
{% include 'notebox_end' %}
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/add-new-repository.png!
+!{width: 100%;}{{ site.baseurl }}/images/add-new-repository.png!
This will create a new repository with the name @$USER/tutorial@. It can be accessed using the URL <notextile><code>https://git.{{ site.arvados_api_host }}/$USER/tutorial.git</code></notextile> or <notextile><code>git@git.{{ site.arvados_api_host }}:$USER/tutorial.git</code></notextile>
~$ <span class="userinput">git config --global user.email $USER@example.com</span></code></pre>
</notextile>
-On the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Repositories*. In the *Repositories* page, you should see the @$USER/tutorial@ repository listed in the *name* column. Next to *name* is the column *URL*. Copy the *URL* value associated with your repository. This should look like <notextile><code>https://git.{{ site.arvados_api_host }}/$USER/tutorial.git</code></notextile>. Alternatively, you can use <notextile><code>git@git.{{ site.arvados_api_host }}:$USER/tutorial.git</code></notextile>
+On the Arvados Workbench, click on the dropdown menu icon <i class="fa fa-lg fa-user"></i> in the upper right corner of the top navigation menu to access the Account Management menu, and click on the menu item *Repositories*. In the *Repositories* page, you should see the @$USER/tutorial@ repository listed in the *name* column. Next to *name* is the column *URL*. Copy the *URL* value associated with your repository. This should look like <notextile><code>https://git.{{ site.arvados_api_host }}/$USER/tutorial.git</code></notextile>. Alternatively, you can use <notextile><code>git@git.{{ site.arvados_api_host }}:$USER/tutorial.git</code></notextile>
Next, on the Arvados virtual machine, clone your Git repository:
h3. Untrashing a collection using workbench
-To untrash a collection using workbench, go to trash page on workbench by clicking on the "Trash" icon in the top navigation in workbench and use the recycle icon or selection dropdown option.
+To untrash a collection using Workbench, go to the *Trash* page from the right-side panel, locate the trashed collection, and click on the "clock" or _Restore_ button at the end of the row. The *Restore* button is also available from the right-click context menu.
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/trash-button-topnav.png!
+!{width: 80%}{{ site.baseurl }}/images/trash-buttons.png!
h3. Untrashing a collection using arv command line tool
Arvados Data collections can be downloaded using either the arv commands or using Workbench.
# "*Download using Workbench*":#download-using-workbench
-# "*Sharing collections*":#download-shared-collection
+# "*Creating a special download URL for a collection*":#download-shared-collection
# "*Download using command line tools*":#download-using-arv
h2(#download-using-workbench). Download using Workbench
You can also download Arvados data collections using the Workbench.
-Visit the Workbench *Dashboard*. Click on *Projects*<span class="caret"></span> dropdown menu in the top navigation menu, select your *Home* project. You will see the *Data collections* tab, which lists the collections in this project.
+When you visit a project in Workbench (for instance, the <i class="fa fa-fw fa-folder"></i> *Home Projects* or any projects under it), the collections will show up on the project details page, with "_Data collection_" in the *Type* column.
-You can access the contents of a collection by clicking on the *<i class="fa fa-fw fa-archive"></i> Show* button next to the collection. This will take you to the collection's page. Using this page you can see the collection's contents, and download individual files.
+Clicking on a collection will bring you to its details page. There, the lower panel acts like a file manager where you can navigate to or search for files, select them for actions, and download them.
-You can now download the collection files by clicking on the <span class="btn btn-sm btn-info"><i class="fa fa-download"></i></span> button(s).
+To download a file, simply click on the file, or bring up the context menu using right-click or the triple-dot button on its row, and then select the menu item *Download*.
-h2(#download-shared-collection). Sharing collections
+h2(#download-shared-collection). Creating a special download URL for a collection
-h3. Sharing with other Arvados users
+To share a collection with users that do not have an account on your Arvados cluster, locate the collection and then go to the *Sharing settings* dialog box as described above. There, select the *SHARING URLS* tab.
-Collections can be shared with other users on the Arvados cluster by sharing the parent project. Navigate to the parent project using the "breadcrumbs" bar, then click on the *Sharing* tab. From the sharing tab, you can choose which users or groups to share with, and their level of access.
+You can then generate a new sharing URL using the <span class="btn btn-sm btn-primary">CREATE SHARING URL</span> button, with the option to set an expiration time for the URL. You can then copy the URL to the clipboard for sharing with others. To revoke (that is, delete) a sharing URL, click on the cross icon beside it.
-h3. Creating a special download URL
+<figure>!{width: 80%}{{ site.baseurl }}/images/sharing-collection-url.png!<figcaption>_The_ *SHARING URLS* _tab in the_ *Sharing settings* _dialog box, showing the created URL with an expiration time_</figcaption></figure>
-To share a collection with users that do not have an account on your Arvados cluster, visit the collection page using Workbench as described in the above section. Once on this page, click on the <span class="btn btn-sm btn-primary" >Create sharing link</span> button.
+Any user with the sharing URL can download this collection by simply accessing this URL using browser. It will present a downloadable version of the collection as shown below.
-This will create a sharing link for the collection as shown below. You can copy the sharing link in this page and share it with other users.
-
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/shared-collection.png!
+!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/download-shared-collection.png!
-A user with this url can download this collection by simply accessing this url using browser. It will present a downloadable version of the collection as shown below.
+When a collection is being shared by URL, in the *WITH USERS/GROUS* tab of *Sharing settings*, the following message will appear if *General access* is Private: _Although there aren't specific permissions set, this is publicly accessible via Sharing URL(s)._
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/download-shared-collection.png!
+* *Note:* Sharing by URL is specific to collections. Projects or individual files cannot be shared in this way.
h2(#download-using-arv). Download using command line tools
Arvados Data collections can be uploaded using either Workbench or the @arv-put@ command line tool.
# "*Upload using Workbench*":#upload-using-workbench
-# "*Creating projects*":#creating-projects
# "*Upload using command line tool*":#upload-using-command
h2(#upload-using-workbench). Upload using Workbench
-To upload using Workbench, visit the Workbench *Dashboard*. Click on *Projects*<span class="caret"></span> dropdown menu in the top navigation menu and select your *Home* project or any other project of your choosing. You will see the *Data collections* tab for this project, which lists the collections in this project.
+To upload using Workbench, first identify the project to upload the files into. This is done by browsing your projects in the navigation menu on the left, or to search for the project using the search field on the top.
-To upload files into a new collection, click on *Add data*<span class="caret"></span> dropdown menu and select *Upload files from my computer*.
+Having navigated to the project, click on the <span class="btn btn-sm btn-primary">+ NEW</span> button in the top-left corner. In the pop-up menu, select the item *New collection*.
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/upload-using-workbench.png!
+<figure> !{width: 80%;}{{ site.baseurl }}/images/add-new-collection-wb2.png! <figcaption> _Creating a new collection in the project "WGS Processing Tutorial"_ </figcaption></figure>
-<br/>This will create a new empty collection in your chosen project and will take you to the *Upload* tab for that collection.
+In the dialog box that follows, you will be prompted to create a new collection in your chosen project. Here, the *Collection Name* field is required. After entering the name for this new collection (and optionally other fields), you have the choice to create it with new file updates -- by drag-and-drop into the *Files* area or with the traditional file-upload dialog opened by your browser.
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/upload-tab-in-new-collection.png!
+<figure>!{width: 100%;}{{ site.baseurl }}/images/new-collection-modal-wb2.png!<figcaption>_Providing the new collection with a name (required). Optionally, you can upload files in this step._</figcaption></figure>
-Click on the *Browse...* button and select the files you would like to upload. Selected files will be added to a list of files to be uploaded. After you are done selecting files to upload, click on the *<i class="fa fa-fw fa-play"></i> Start* button to start upload. This will start uploading files to Arvados and Workbench will show you the progress bar. When upload is completed, you will see an indication to that effect.
+You can then click on the <span class="btn btn-sm btn-primary">CREATE A COLLECTION</span> button and proceed to the newly-created collection's page. If you don't upload any data when creating the collection, the new collection will be empty, and you can upload files into it later.
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/files-uploaded.png!
+<figure>!{width: 100%;}{{ site.baseurl }}/images/newly-created-collection-empty-wb2.png!<figcaption>_The newly-created collection without any files yet._</figcaption></figure>
-*Note:* If you leave the collection page during the upload, the upload process will be aborted and you will need to upload the files again.
+In the <span class="btn btn-sm btn-primary">FILES</span> panel, there is a button labeled <span class="btn btn-sm btn-primary">UPLOAD DATA</span>. Click on it, and you will be prompted to upload files by drag-and-drop or the file-selection dialog opened by your browser.
-*Note:* You can also use the Upload tab to add additional files to an existing collection.
+The files you choose to upload will then be displayed, and you can review them before clicking on the <span class="btn btn-sm btn-primary">UPLOAD DATA</span> button to initiate the actual file transfer.
-notextile. <div class="spaced-out">
+<figure>!{width: 100%;}{{ site.baseurl }}/images/upload-data-prompt-with-files-wb2.png!<figcaption>_Selecting the files to upload_</figcaption></figure>
-h2(#creating-projects). Creating projects
+Once the file upload completes, you will be notified by a message, and the files will appear under the <span class="btn btn-sm btn-primary">FILES</span> panel shortly.
-Files are organized into Collections, and Collections are organized by Projects.
+<figure>!{width: 100%;}{{ site.baseurl }}/images/upload-data-progress-wb2.png!<figcaption>_Upload status being displayed, with the files to appear shortly_</figcaption></figure>
-Click on *Projects*<span class="caret"></span> <span class="rarr">→</span> <i class="fa fa-fw fa-plus"></i>*Add a new project* to add a top level project.
+*Note:* If you leave the collection page during the upload, the upload process will be aborted and you will need to upload the files again.
-To create a subproject, navigate to the parent project, and click on <i class="fa fa-fw fa-plus"></i>*Add a subproject*.
+*Note:* You can also use the <span class="btn btn-sm btn-primary">UPLOAD DATA</span> button to add additional files to an existing collection.
+
+notextile. <div class="spaced-out">
-See "Sharing collections":tutorial-keep-get.html#download-shared-collection for information about sharing projects and collections with other users.
h2(#upload-using-command). Upload using command line tool
h3. Locate your collection in Workbench
-Visit the Workbench *Dashboard*. Click on *Projects*<span class="caret"></span> dropdown menu in the top navigation menu, select your *Home* project. Your newly uploaded collection should appear near the top of the *Data collections* tab. The collection name printed by @arv-put@ will appear under the *name* column.
+Visit the Workbench and go to your <i class="fa fa-fw fa-folder"></i> *Home Projects*. Your newly uploaded collection should appear in the main panel. The collection name printed by @arv-put@ will appear under the *Name* column, and its *Type* will be "_Data collection_".
-To move the collection to a different project, check the box at the left of the collection row. Pull down the *Selection...*<span class="caret"></span> menu near the top of the page tab, and select *Move selected...* button. This will open a dialog box where you can select a destination project for the collection. Click a project, then finally the <span class="btn btn-sm btn-primary">Move</span> button.
+Click on the collection's name will lead you to its Workbench page, where you can see the collection's contents and download individual files.
-!{display: block;margin-left: 25px;margin-right: auto;}{{ site.baseurl }}/images/workbench-move-selected.png!
+To move the collection to a different project, locate the collection and right-click on it. This will bring up a context menu with *Move to*. Click on this item, and you will see a dialog box where you can select the target project to move this collection to, by search or navigation. This context menu is also available from the triple-dot button in the project/collection listing or the collection details page.
-Click on the *<i class="fa fa-fw fa-archive"></i> Show* button next to the collection's listing on a project page to go to the Workbench page for your collection. On this page, you can see the collection's contents, download individual files, and set sharing options.
+<figure>!{width: 80%;}{{ site.baseurl }}/images/workbench-move-wb2.png!<figcaption> _Context menu with the_ *Move to* _item_ </figcaption></figure>
notextile. </div>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Organizating data"
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+h2. Projects and Collections
+
+In Arvados, files are organized into "collections", and collections are organized by "project".
+
+Only collections can contain files. A collection is a distinct database record identified by a universal unique id (UUID). Arvados maintains a history of changes to the collection. Every collection version has an immutable identifier called a "portable data hash" which is computed from the file content of the collection. This can be used to refer to the immutable file content independently of the collection UUID. If two collections have the same portable data hash, they have the same file content.
+
+Projects contain collections, workflows and workflow runs, and other projects (subprojects). Both collections and projects can have user-provided metadata.
+
+Projects are the main unit of organization and sharing. See "Sharing collections":#sharing-projects for information about sharing projects and collections with other users.
+
+h2(#creating-projects). Creating a project
+
+When you have navigated to any existing project, clicking on <span class="btn btn-sm btn-primary">+ NEW</span> <span class="rarr">→</span> <i class="fa fa-fw fa-folder"></i> *New project* will prompt you to create a new subproject under the current project.
+
+If you're at the top-level <i class="fa fa-fw fa-folder"></i> *Home Projects*, a new top-level project will be created.
+
+Alternatively, you can right-click on the link to an existing project to bring up a context menu, and select *New project*.
+
+h2(#sharing-projects). Sharing projects
+
+Projects can be shared with other users on the Arvados cluster. First, locate the collection or project using any available means (for instance, by manually navigating in the Workbench, or using the Search bar). Then right-click on its link in a listing, or click on the triple-dot button in the details page. You will find the menu item *Share*, which opens the dialog box *Sharing settings*.
+
+To share with other Arvados users, select the *WITH USERS/GROUPS* tab in the *Sharing settings* dialog box. Under *Add people and groups*, in the input field you can search for the user or group names. Select one you will be sharing with, choose the *Authorization* level (Read/Write/Manage) in the drop-down menu, and click on the plus sign (+) on the right. This can be repeated for other users or groups, each with their own *Authorization* level. The selected ones will appear under *People with access*. You can revisit the *Sharing settings* dialog box to modify the users or their access levels at a later time.
+
+The *General access* drop-down menu controls the default sharing setting, with the following choices:
+
+* *Private*: This is the initial state when no users or groups have been selected for sharing. At any time, by setting *General access* to private, the current sharing setting will be cleared, and any users or groups formerly with access will lose that access.
+* *Public*: This means the list of *People with access* will include _Anonymous users_, even if they are not users of the current cluster. You can further set their access level in the *Authorization* level.
+* *All users*: This means sharing with other users who are logged in on the current cluster.
+* *Shared*: When you choose to share with specific people or groups, *General access* will be set to *Shared*. From this state, you can further specify the default sharing settings for *Public* and *All users*.
notextile. <div class="spaced-out">
-# Start from the *Workbench Dashboard*. You can access the Dashboard by clicking on *<i class="fa fa-lg fa-fw fa-dashboard"></i> Dashboard* in the upper left corner of any Workbench page.
-# Click on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button. This will open a dialog box titled *Choose a pipeline or workflow to run*.
-# In the search box, type in *bwa-mem.cwl*.
-# Select *<i class="fa fa-fw fa-gear"></i> bwa-mem.cwl* and click the <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span> button. This will create a new process in your *Home* project and will open it. You can now supply the inputs for the process. Please note that all required inputs are populated with default values and you can change them if you prefer.
-# For example, let's see how to set read pair *read_p1* and *read_p2* for this workflow. Click the <span class="btn btn-sm btn-primary">Choose</span> button beneath the *read_p1* header. This will open a dialog box titled *Choose a file*.
-# In the file dialog, click on *Home <span class="caret"></span>* menu and then select *All Projects*.
-# Enter *HWI-ST1027* into the search box. You will see one or more collections. Click on *<i class="fa fa-fw fa-archive"></i> HWI-ST1027_129_D0THKACXX for CWL tutorial*
-# The right hand panel will list two files. Click on the first one ending in "_1" and click the <span class="btn btn-sm btn-primary" >OK</span> button.
-# Repeat the steps 5-8 to set the *read_p2* except selecting the second file ending in "_2"
-# Scroll to the bottom of the "Inputs" panel and click on the <span class="btn btn-sm btn-primary" >Run <i class="fa fa-fw fa-play"></i></span> button. The page updates to show you that the process has been submitted to run on the Arvados cluster.
-# Once the process starts running, you can track the progress by watching log messages from the component(s). This page refreshes automatically. You will see a <span class="label label-success">complete</span> label when the process completes successfully.
-# Click on the *Output* link to see the results of the process. This will load a new page listing the output files from this process. You'll see the output SAM file from the alignment tool under the *Files* tab.
-# Click on the <span class="btn btn-sm btn-info"><i class="fa fa-download"></i></span> download button to the right of the SAM file to download your results.
+# Click on the <span class="btn btn-sm btn-primary">+ NEW</span> button in the top-left.
+# In the pop-up menu, select *<i class="fa fa-fw fa-gear"></i> Run a workflow*. This will open the _Run Process_ panel in the Workbench.
+# In the search field under *Choose a workflow*, type in _bwa-mem.cwl_.
+# Select *bwa-mem.cwl* in the search results, and click the <span class="btn btn-sm btn-primary" >NEXT</span> button. This will create a new process in one of your Home Projects and will open it. To specify the project for the workflow run, click on the input line below "*Project where the workflow will run*", and in the pop-up dialog box, choose a project under your Home Projects.
+# You can now supply the inputs for the process. Please note that all required inputs are populated with default values and you can change them if you prefer.
+# For example, let's see how to set read pair *read_p1* and *read_p2* for this workflow. Click on the input line under the *read_p1* header. This will open a dialog box titled *Choose a file*.
+# Enter the search terms _user guide resources_ into the *Search for a Project* field on the left. You will see one or more collections in the search results appearing below and, among them, the one with the exact title *<i class="fa fa-fw fa-folder"></i> User guide resources*. Your goal is to locate the file _HWI-ST1027_129_D0THKACXX.1_1.fastq_.
+# You may either locate the file manually, by clicking on the triangles â–¶ to the left of each item to expand them (projects and the collections under it) until you find the file, or by filtering the search results using the *Filter Collections list in Projects* field, for example, with a term like "_HWI-ST1027_".
+# Either way, you will find the file <i class="fa fa-fw fa-file"></i> *HWI-ST1027_129_D0THKACXX.1_1.fastq* in the search results. Click on it, and then the <span class="btn btn-sm btn-primary">OK</span> button in the bottom-right.
+# Repeat the steps 7--9 to set the value for *read_p2*, except selecting the file ending in "_2"
+# Scroll to the bottom of the "Inputs" panel and click on the <span class="btn btn-sm btn-primary" >RUN WORKFLOW</span> button. The page updates to show you that the process has been queued to run on the Arvados cluster.
+# Once the process starts running, you can track the progress by watching the log messages from the component(s) (scroll down to the *Logs* panel). This page refreshes automatically, and you can also click on the <span class="btn btn-sm btn-primary">REFRESH</span> button on the top of the page. You will see a <span class="label label-success">Completed</span> label when the process completes successfully.
+# The output of the workflow can be found by following the link "Output from bwa-mem.cwl" under the heading *Output collection* in the main or <span class="btn btn-sm btn-primary">DETAILS</span> panel, or in the <span class="btn btn-sm btn-primary">OUTPUTS</span> panel further down. Click on the *Output from bwa-mem.cwl* link to see the detailed results from the workflow run. This will lead you to a page that lists the metadata of the outputs, and you'll see the output SAM file there, in the <span class="btn btn-sm btn-primary">FILES</span> panel.
+# To download your results, simply click on the SAM file name.
notextile. </div>
github.com/bradleypeabody/godap v0.0.0-20170216002349-c249933bc092
github.com/coreos/go-oidc/v3 v3.5.0
github.com/coreos/go-systemd v0.0.0-20190321100706-95778dfbb74e
- github.com/creack/pty v1.1.7
- github.com/docker/docker v17.12.0-ce-rc1.0.20210128214336-420b1d36250f+incompatible
+ github.com/creack/pty v1.1.18
+ github.com/docker/docker v24.0.2+incompatible
github.com/dustin/go-humanize v1.0.0
github.com/fsnotify/fsnotify v1.4.9
github.com/ghodss/yaml v1.0.0
github.com/sirupsen/logrus v1.8.1
golang.org/x/crypto v0.5.0
golang.org/x/net v0.9.0
- golang.org/x/oauth2 v0.4.0
+ golang.org/x/oauth2 v0.7.0
golang.org/x/sys v0.7.0
- google.golang.org/api v0.30.0
+ google.golang.org/api v0.114.0
gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c
gopkg.in/square/go-jose.v2 v2.5.1
gopkg.in/src-d/go-billy.v4 v4.0.1
)
require (
- cloud.google.com/go v0.65.0 // indirect
+ cloud.google.com/go/compute v1.19.1 // indirect
+ cloud.google.com/go/compute/metadata v0.2.3 // indirect
github.com/Azure/go-ansiterm v0.0.0-20230124172434-306776ec8161 // indirect
github.com/Azure/go-autorest v14.2.0+incompatible // indirect
github.com/Azure/go-autorest/autorest/adal v0.9.17 // indirect
github.com/beorn7/perks v1.0.1 // indirect
github.com/bgentry/speakeasy v0.1.0 // indirect
github.com/cespare/xxhash/v2 v2.2.0 // indirect
- github.com/containerd/containerd v1.5.18 // indirect
github.com/davecgh/go-spew v1.1.1 // indirect
github.com/dimchansky/utfbom v1.1.1 // indirect
github.com/dnaeon/go-vcr v1.2.0 // indirect
github.com/go-jose/go-jose/v3 v3.0.0 // indirect
github.com/golang-jwt/jwt/v4 v4.1.0 // indirect
github.com/golang/groupcache v0.0.0-20200121045136-8c9f03a8e57e // indirect
- github.com/golang/protobuf v1.5.2 // indirect
- github.com/googleapis/gax-go/v2 v2.0.5 // indirect
+ github.com/golang/protobuf v1.5.3 // indirect
+ github.com/google/uuid v1.3.0 // indirect
+ github.com/googleapis/enterprise-certificate-proxy v0.2.3 // indirect
+ github.com/googleapis/gax-go/v2 v2.7.1 // indirect
github.com/hashicorp/go-cleanhttp v0.5.2 // indirect
github.com/jbenet/go-context v0.0.0-20150711004518-d14ea06fba99 // indirect
github.com/jmespath/go-jmespath v0.4.0 // indirect
github.com/kr/text v0.1.0 // indirect
github.com/matttproud/golang_protobuf_extensions v1.0.4 // indirect
github.com/mitchellh/go-homedir v1.1.0 // indirect
+ github.com/moby/term v0.5.0 // indirect
github.com/morikuni/aec v1.0.0 // indirect
github.com/opencontainers/go-digest v1.0.0 // indirect
github.com/opencontainers/image-spec v1.0.2 // indirect
github.com/shabbyrobe/gocovmerge v0.0.0-20180507124511-f6ea450bfb63 // indirect
github.com/src-d/gcfg v1.3.0 // indirect
github.com/xanzy/ssh-agent v0.1.0 // indirect
- go.opencensus.io v0.22.4 // indirect
+ go.opencensus.io v0.24.0 // indirect
golang.org/x/text v0.9.0 // indirect
+ golang.org/x/time v0.0.0-20200630173020-3af7569d3a1e // indirect
golang.org/x/tools v0.6.0 // indirect
google.golang.org/appengine v1.6.7 // indirect
- google.golang.org/genproto v0.0.0-20201110150050-8816d57aaa9a // indirect
- google.golang.org/grpc v1.33.2 // indirect
- google.golang.org/protobuf v1.28.1 // indirect
+ google.golang.org/genproto v0.0.0-20230410155749-daa745c078e1 // indirect
+ google.golang.org/grpc v1.56.1 // indirect
+ google.golang.org/protobuf v1.30.0 // indirect
gopkg.in/asn1-ber.v1 v1.0.0-20181015200546-f715ec2f112d // indirect
gopkg.in/src-d/go-git-fixtures.v3 v3.5.0 // indirect
gopkg.in/warnings.v0 v0.1.2 // indirect
gopkg.in/yaml.v2 v2.4.0 // indirect
- gotest.tools v2.2.0+incompatible // indirect
+ gotest.tools/v3 v3.0.3 // indirect
)
replace github.com/AdRoll/goamz => github.com/arvados/goamz v0.0.0-20190905141525-1bba09f407ef
cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw=
-cloud.google.com/go v0.34.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw=
-cloud.google.com/go v0.38.0/go.mod h1:990N+gfupTy94rShfmMCWGDn0LpTmnzTp2qbd1dvSRU=
-cloud.google.com/go v0.44.1/go.mod h1:iSa0KzasP4Uvy3f1mN/7PiObzGgflwredwwASm/v6AU=
-cloud.google.com/go v0.44.2/go.mod h1:60680Gw3Yr4ikxnPRS/oxxkBccT6SA1yMk63TGekxKY=
-cloud.google.com/go v0.45.1/go.mod h1:RpBamKRgapWJb87xiFSdk4g1CME7QZg3uwTez+TSTjc=
-cloud.google.com/go v0.46.3/go.mod h1:a6bKKbmY7er1mI7TEI4lsAkts/mkhTSZK8w33B4RAg0=
-cloud.google.com/go v0.50.0/go.mod h1:r9sluTvynVuxRIOHXQEHMFffphuXHOMZMycpNR5e6To=
-cloud.google.com/go v0.52.0/go.mod h1:pXajvRH/6o3+F9jDHZWQ5PbGhn+o8w9qiu/CffaVdO4=
-cloud.google.com/go v0.53.0/go.mod h1:fp/UouUEsRkN6ryDKNW/Upv/JBKnv6WDthjR6+vze6M=
-cloud.google.com/go v0.54.0/go.mod h1:1rq2OEkV3YMf6n/9ZvGWI3GWw0VoqH/1x2nd8Is/bPc=
-cloud.google.com/go v0.56.0/go.mod h1:jr7tqZxxKOVYizybht9+26Z/gUq7tiRzu+ACVAMbKVk=
-cloud.google.com/go v0.57.0/go.mod h1:oXiQ6Rzq3RAkkY7N6t3TcE6jE+CIBBbA36lwQ1JyzZs=
-cloud.google.com/go v0.62.0/go.mod h1:jmCYTdRCQuc1PHIIJ/maLInMho30T/Y0M4hTdTShOYc=
-cloud.google.com/go v0.65.0 h1:Dg9iHVQfrhq82rUNu9ZxUDrJLaxFUe/HlCVaLyRruq8=
-cloud.google.com/go v0.65.0/go.mod h1:O5N8zS7uWy9vkA9vayVHs65eM1ubvY4h553ofrNHObY=
-cloud.google.com/go/bigquery v1.0.1/go.mod h1:i/xbL2UlR5RvWAURpBYZTtm/cXjCha9lbfbpx4poX+o=
-cloud.google.com/go/bigquery v1.3.0/go.mod h1:PjpwJnslEMmckchkHFfq+HTD2DmtT67aNFKH1/VBDHE=
-cloud.google.com/go/bigquery v1.4.0/go.mod h1:S8dzgnTigyfTmLBfrtrhyYhwRxG72rYxvftPBK2Dvzc=
-cloud.google.com/go/bigquery v1.5.0/go.mod h1:snEHRnqQbz117VIFhE8bmtwIDY80NLUZUMb4Nv6dBIg=
-cloud.google.com/go/bigquery v1.7.0/go.mod h1://okPTzCYNXSlb24MZs83e2Do+h+VXtc4gLoIoXIAPc=
-cloud.google.com/go/bigquery v1.8.0/go.mod h1:J5hqkt3O0uAFnINi6JXValWIb1v0goeZM77hZzJN/fQ=
+cloud.google.com/go v0.110.0 h1:Zc8gqp3+a9/Eyph2KDmcGaPtbKRIoqq4YTlL4NMD0Ys=
+cloud.google.com/go/compute v1.19.1 h1:am86mquDUgjGNWxiGn+5PGLbmgiWXlE/yNWpIpNvuXY=
+cloud.google.com/go/compute v1.19.1/go.mod h1:6ylj3a05WF8leseCdIf77NK0g1ey+nj5IKd5/kvShxE=
cloud.google.com/go/compute/metadata v0.2.0/go.mod h1:zFmK7XCadkQkj6TtorcaGlCW1hT1fIilQDwofLpJ20k=
-cloud.google.com/go/datastore v1.0.0/go.mod h1:LXYbyblFSglQ5pkeyhO+Qmw7ukd3C+pD7TKLgZqpHYE=
-cloud.google.com/go/datastore v1.1.0/go.mod h1:umbIZjpQpHh4hmRpGhH4tLFup+FVzqBi1b3c64qFpCk=
-cloud.google.com/go/pubsub v1.0.1/go.mod h1:R0Gpsv3s54REJCy4fxDixWD93lHJMoZTyQ2kNxGRt3I=
-cloud.google.com/go/pubsub v1.1.0/go.mod h1:EwwdRX2sKPjnvnqCa270oGRyludottCI76h+R3AArQw=
-cloud.google.com/go/pubsub v1.2.0/go.mod h1:jhfEVHT8odbXTkndysNHCcx0awwzvfOlguIAii9o8iA=
-cloud.google.com/go/pubsub v1.3.1/go.mod h1:i+ucay31+CNRpDW4Lu78I4xXG+O1r/MAHgjpRVR+TSU=
-cloud.google.com/go/storage v1.0.0/go.mod h1:IhtSnM/ZTZV8YYJWCY8RULGVqBDmpoyjwiyrjsg+URw=
-cloud.google.com/go/storage v1.5.0/go.mod h1:tpKbwo567HUNpVclU5sGELwQWBDZ8gh0ZeosJ0Rtdos=
-cloud.google.com/go/storage v1.6.0/go.mod h1:N7U0C8pVQ/+NIKOBQyamJIeKQKkZ+mxpohlUTyfDhBk=
-cloud.google.com/go/storage v1.8.0/go.mod h1:Wv1Oy7z6Yz3DshWRJFhqM/UCfaWIRTdp0RXyy7KQOVs=
-cloud.google.com/go/storage v1.10.0/go.mod h1:FLPqc6j+Ki4BU591ie1oL6qBQGu2Bl/tZ9ullr3+Kg0=
-dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU=
+cloud.google.com/go/compute/metadata v0.2.3 h1:mg4jlk7mCAj6xXp9UJ4fjI9VUI5rubuGBW5aJ7UnBMY=
+cloud.google.com/go/compute/metadata v0.2.3/go.mod h1:VAV5nSsACxMJvgaAuX6Pk2AawlZn8kiOGuCv6gTkwuA=
+cloud.google.com/go/longrunning v0.4.1 h1:v+yFJOfKC3yZdY6ZUI933pIYdhyhV8S3NpWrXWmg7jM=
github.com/Azure/azure-sdk-for-go v45.1.0+incompatible h1:kxtaPD8n2z5Za+9e3sKsYG2IX6PG2R6VXtgS7gAbh3A=
github.com/Azure/azure-sdk-for-go v45.1.0+incompatible/go.mod h1:9XXNKU+eRnpl9moKnB4QOLf1HestfXbmab5FXxiDBjc=
github.com/Azure/go-ansiterm v0.0.0-20230124172434-306776ec8161 h1:L/gRVlceqvL25UVaW/CKtUDjefjrs0SPonmDGUVOYP0=
github.com/Azure/go-autorest/tracing v0.6.0 h1:TYi4+3m5t6K48TGI9AUdb+IzbnSxvnvUMfuitfgcfuo=
github.com/Azure/go-autorest/tracing v0.6.0/go.mod h1:+vhtPC754Xsa23ID7GlGsrdKBpUA79WCAKPPZVC2DeU=
github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU=
-github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym/WlBOVXweHU+Q+/VP0lqqI8lqeDx9IjBqo=
github.com/Microsoft/go-winio v0.5.2 h1:a9IhgEQBCUEk6QCdml9CiJGhAws+YwffDHEMp1VMrpA=
github.com/Microsoft/go-winio v0.5.2/go.mod h1:WpS1mjBmmwHBEWmogvA2mj8546UReBk4v8QkMxJ6pZY=
github.com/alcortesm/tgz v0.0.0-20161220082320-9c5fe88206d7 h1:uSoVVbwJiQipAclBbw+8quDsfcvFjOpI5iCf4p/cqCs=
github.com/census-instrumentation/opencensus-proto v0.2.1/go.mod h1:f6KPmirojxKA12rnyqOA5BBL4O983OfeGPqjHWSTneU=
github.com/cespare/xxhash/v2 v2.2.0 h1:DC2CZ1Ep5Y4k3ZQ899DldepgrayRUGE6BBZ/cd9Cj44=
github.com/cespare/xxhash/v2 v2.2.0/go.mod h1:VGX0DQ3Q6kWi7AoAeZDth3/j3BFtOZR5XLFGgcrjCOs=
-github.com/chzyer/logex v1.1.10/go.mod h1:+Ywpsq7O8HXn0nuIou7OrIPyXbp3wmkHB+jjWRnGsAI=
-github.com/chzyer/readline v0.0.0-20180603132655-2972be24d48e/go.mod h1:nSuG5e5PlCu98SY8svDHJxuZscDgtXS6KTTbou5AhLI=
-github.com/chzyer/test v0.0.0-20180213035817-a1ea475d72b1/go.mod h1:Q3SI9o4m/ZMnBNeIyt5eFwwo7qiLfzFZmjNmxjkiQlU=
github.com/client9/misspell v0.3.4/go.mod h1:qj6jICC3Q7zFZvVWo7KLAzC3yx5G7kyvSDkc90ppPyw=
github.com/cncf/udpa/go v0.0.0-20191209042840-269d4d468f6f/go.mod h1:M8M6+tZqaGXZJjfX53e64911xZQV5JYwmTeXPW+k8Sc=
-github.com/containerd/containerd v1.5.18 h1:doHr6cNxfOLTotWmZs6aZF6LrfJFcjmYFcWlRmQgYPM=
-github.com/containerd/containerd v1.5.18/go.mod h1:7IN9MtIzTZH4WPEmD1gNH8bbTQXVX68yd3ZXxSHYCis=
github.com/coreos/go-oidc/v3 v3.5.0 h1:VxKtbccHZxs8juq7RdJntSqtXFtde9YpNpGn0yqgEHw=
github.com/coreos/go-oidc/v3 v3.5.0/go.mod h1:ecXRtV4romGPeO6ieExAsUK9cb/3fp9hXNz1tlv8PIM=
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# down.
MaxInstances: 64
- # Maximum fraction of CloudVMs.MaxInstances allowed to run
- # "supervisor" containers at any given time. A supervisor is a
- # container whose purpose is mainly to submit and manage other
- # containers, such as arvados-cwl-runner workflow runner.
+ # The minimum number of instances expected to be runnable
+ # without reaching a provider-imposed quota.
+ #
+ # This is used as the initial value for the dispatcher's
+ # dynamic instance limit, which increases (up to MaxInstances)
+ # as containers start up successfully and decreases in
+ # response to high API load and cloud quota errors.
+ #
+ # Setting this too high creates a risk that the dispatcher
+ # will cause deadlock by starting so many supervisor
+ # containers (based on SupervisorFraction and MaxInstances)
+ # that the cloud quota prevents them from running any child
+ # containers.
+ #
+ # Setting this too low causes the dispatcher to be
+ # unnecessarily slow to start up new instances after a
+ # restart.
+ InitialQuotaEstimate: 16
+
+ # Maximum fraction of available instance capacity allowed to
+ # run "supervisor" containers at any given time. A supervisor
+ # is a container whose purpose is mainly to submit and manage
+ # other containers, such as arvados-cwl-runner workflow
+ # runner.
#
# If there is a hard limit on the amount of concurrent
# containers that the cluster can run, it is important to
import (
"bytes"
"fmt"
- "io/ioutil"
+ "io/fs"
)
// Return the current process's cgroup for the given subsystem.
-func findCgroup(subsystem string) (string, error) {
+//
+// If the host has cgroups v2 and not v1 (i.e., unified mode), return
+// the current process's cgroup.
+func findCgroup(fsys fs.FS, subsystem string) (string, error) {
subsys := []byte(subsystem)
- cgroups, err := ioutil.ReadFile("/proc/self/cgroup")
+ cgroups, err := fs.ReadFile(fsys, "proc/self/cgroup")
if err != nil {
return "", err
}
if len(toks) < 3 {
continue
}
+ if len(toks[1]) == 0 && string(toks[0]) == "0" {
+ // cgroups v2: "0::$PATH"
+ //
+ // In "hybrid" mode, this entry is last, so we
+ // use it when the specified subsystem doesn't
+ // match a cgroups v1 entry.
+ //
+ // In "unified" mode, this is the only entry,
+ // so we use it regardless of which subsystem
+ // was specified.
+ return string(toks[2]), nil
+ }
for _, s := range bytes.Split(toks[1], []byte(",")) {
+ // cgroups v1: "7:cpu,cpuacct:/user.slice"
if bytes.Compare(s, subsys) == 0 {
return string(toks[2]), nil
}
package crunchrun
import (
+ "bytes"
+ "os"
+ "os/exec"
+ "strings"
+
. "gopkg.in/check.v1"
)
var _ = Suite(&CgroupSuite{})
func (s *CgroupSuite) TestFindCgroup(c *C) {
- for _, s := range []string{"devices", "cpu", "cpuset"} {
- g, err := findCgroup(s)
- if c.Check(err, IsNil) {
- c.Check(g, Not(Equals), "", Commentf("subsys %q", s))
+ var testfiles []string
+ buf, err := exec.Command("find", "../crunchstat/testdata", "-name", "cgroup", "-type", "f").Output()
+ c.Assert(err, IsNil)
+ for _, testfile := range bytes.Split(buf, []byte{'\n'}) {
+ if len(testfile) > 0 {
+ testfiles = append(testfiles, string(testfile))
+ }
+ }
+ testfiles = append(testfiles, "/proc/self/cgroup")
+
+ tmpdir := c.MkDir()
+ err = os.MkdirAll(tmpdir+"/proc/self", 0777)
+ c.Assert(err, IsNil)
+ fsys := os.DirFS(tmpdir)
+
+ for _, trial := range []struct {
+ match string // if non-empty, only check testfiles containing this string
+ subsys string
+ expect string // empty means "any" (we never actually expect empty string)
+ }{
+ {"debian11", "blkio", "/user.slice/user-1000.slice/session-5424.scope"},
+ {"debian12", "cpuacct", "/user.slice/user-1000.slice/session-4.scope"},
+ {"debian12", "bogus-does-not-matter", "/user.slice/user-1000.slice/session-4.scope"},
+ {"ubuntu1804", "blkio", "/user.slice"},
+ {"ubuntu1804", "cpuacct", "/user.slice"},
+ {"", "cpu", ""},
+ {"", "cpuset", ""},
+ {"", "devices", ""},
+ {"", "bogus-does-not-matter", ""},
+ } {
+ for _, testfile := range testfiles {
+ if !strings.Contains(testfile, trial.match) {
+ continue
+ }
+ c.Logf("trial %+v testfile %s", trial, testfile)
+
+ // Copy cgroup file into our fake proc/self/ dir
+ buf, err := os.ReadFile(testfile)
+ c.Assert(err, IsNil)
+ err = os.WriteFile(tmpdir+"/proc/self/cgroup", buf, 0777)
+ c.Assert(err, IsNil)
+
+ cgroup, err := findCgroup(fsys, trial.subsys)
+ if !c.Check(err, IsNil) {
+ continue
+ }
+ c.Logf("\tcgroup = %q", cgroup)
+ c.Check(cgroup, Not(Equals), "")
+ if trial.expect != "" {
+ c.Check(cgroup, Equals, trial.expect)
+ }
}
- c.Logf("cgroup(%q) == %q", s, g)
}
}
"flag"
"fmt"
"io"
+ "io/fs"
"io/ioutil"
"log"
"net"
hoststatLogger io.WriteCloser
hoststatReporter *crunchstat.Reporter
statInterval time.Duration
- cgroupRoot string
- // What we expect the container's cgroup parent to be.
- expectCgroupParent string
// What we tell docker to use as the container's cgroup
- // parent. Note: Ideally we would use the same field for both
- // expectCgroupParent and setCgroupParent, and just make it
- // default to "docker". However, when using docker < 1.10 with
- // systemd, specifying a non-empty cgroup parent (even the
- // default value "docker") hits a docker bug
- // (https://github.com/docker/docker/issues/17126). Using two
- // separate fields makes it possible to use the "expect cgroup
- // parent to be X" feature even on sites where the "specify
- // cgroup parent" feature breaks.
+ // parent.
setCgroupParent string
+ // Fake root dir where crunchstat.Reporter should read OS
+ // files, for testing.
+ crunchstatFakeFS fs.FS
cStateLock sync.Mutex
cCancelled bool // StopContainer() invoked
}
runner.hoststatLogger = NewThrottledLogger(w)
runner.hoststatReporter = &crunchstat.Reporter{
- Logger: log.New(runner.hoststatLogger, "", 0),
- CgroupRoot: runner.cgroupRoot,
+ Logger: log.New(runner.hoststatLogger, "", 0),
+ // Our own cgroup is the "host" cgroup, in the sense
+ // that it accounts for resource usage outside the
+ // container. It doesn't count _all_ resource usage on
+ // the system.
+ //
+ // TODO?: Use the furthest ancestor of our own cgroup
+ // that has stats available. (Currently crunchstat
+ // does not have that capability.)
+ Pid: os.Getpid,
PollPeriod: runner.statInterval,
}
runner.hoststatReporter.Start()
}
runner.statLogger = NewThrottledLogger(w)
runner.statReporter = &crunchstat.Reporter{
- CgroupParent: runner.expectCgroupParent,
- CgroupRoot: runner.cgroupRoot,
- CID: runner.executor.CgroupID(),
- Logger: log.New(runner.statLogger, "", 0),
+ Pid: runner.executor.Pid,
+ FS: runner.crunchstatFakeFS,
+ Logger: log.New(runner.statLogger, "", 0),
MemThresholds: map[string][]crunchstat.Threshold{
"rss": crunchstat.NewThresholdsFromPercentages(runner.Container.RuntimeConstraints.RAM, []int64{90, 95, 99}),
},
log := log.New(stderr, "", 0)
flags := flag.NewFlagSet(prog, flag.ContinueOnError)
statInterval := flags.Duration("crunchstat-interval", 10*time.Second, "sampling period for periodic resource usage reporting")
- cgroupRoot := flags.String("cgroup-root", "/sys/fs/cgroup", "path to sysfs cgroup tree")
- cgroupParent := flags.String("cgroup-parent", "docker", "name of container's parent cgroup (ignored if -cgroup-parent-subsystem is used)")
- cgroupParentSubsystem := flags.String("cgroup-parent-subsystem", "", "use current cgroup for given subsystem as parent cgroup for container")
+ flags.String("cgroup-root", "/sys/fs/cgroup", "path to sysfs cgroup tree (obsolete, ignored)")
+ flags.String("cgroup-parent", "docker", "name of container's parent cgroup (obsolete, ignored)")
+ cgroupParentSubsystem := flags.String("cgroup-parent-subsystem", "", "use current cgroup for given `subsystem` as parent cgroup for container (subsystem argument is only relevant for cgroups v1; in cgroups v2 / unified mode, any non-empty value means use current cgroup); if empty, use the docker daemon's default cgroup parent. See https://doc.arvados.org/install/crunch2-slurm/install-dispatch.html#CrunchRunCommand-cgroups")
caCertsPath := flags.String("ca-certs", "", "Path to TLS root certificates")
detach := flags.Bool("detach", false, "Detach from parent process and run in the background")
stdinConfig := flags.Bool("stdin-config", false, "Load config and environment variables from JSON message on stdin")
cr.parentTemp = parentTemp
cr.statInterval = *statInterval
- cr.cgroupRoot = *cgroupRoot
- cr.expectCgroupParent = *cgroupParent
cr.enableMemoryLimit = *enableMemoryLimit
cr.enableNetwork = *enableNetwork
cr.networkMode = *networkMode
if *cgroupParentSubsystem != "" {
- p, err := findCgroup(*cgroupParentSubsystem)
+ p, err := findCgroup(os.DirFS("/"), *cgroupParentSubsystem)
if err != nil {
log.Printf("fatal: cgroup parent subsystem: %s", err)
return 1
}
cr.setCgroupParent = p
- cr.expectCgroupParent = p
}
if conf.EC2SpotCheck {
"path"
"regexp"
"runtime/pprof"
- "strconv"
"strings"
"sync"
"sync/atomic"
keepmountTmp []string
testDispatcherKeepClient KeepTestClient
testContainerKeepClient KeepTestClient
+ debian12MemoryCurrent int64
+ debian12SwapCurrent int64
+}
+
+func (s *TestSuite) SetUpSuite(c *C) {
+ buf, err := os.ReadFile("../crunchstat/testdata/debian12/sys/fs/cgroup/user.slice/user-1000.slice/session-4.scope/memory.current")
+ c.Assert(err, IsNil)
+ _, err = fmt.Sscanf(string(buf), "%d", &s.debian12MemoryCurrent)
+ c.Assert(err, IsNil)
+
+ buf, err = os.ReadFile("../crunchstat/testdata/debian12/sys/fs/cgroup/user.slice/user-1000.slice/session-4.scope/memory.swap.current")
+ c.Assert(err, IsNil)
+ _, err = fmt.Sscanf(string(buf), "%d", &s.debian12SwapCurrent)
+ c.Assert(err, IsNil)
}
func (s *TestSuite) SetUpTest(c *C) {
go func() { e.exit <- e.runFunc() }()
return e.startErr
}
-func (e *stubExecutor) CgroupID() string { return "cgroupid" }
-func (e *stubExecutor) Stop() error { e.stopped = true; go func() { e.exit <- -1 }(); return e.stopErr }
-func (e *stubExecutor) Close() { e.closed = true }
+func (e *stubExecutor) Pid() int { return 1115883 } // matches pid in ../crunchstat/testdata/debian12/proc/
+func (e *stubExecutor) Stop() error { e.stopped = true; go func() { e.exit <- -1 }(); return e.stopErr }
+func (e *stubExecutor) Close() { e.closed = true }
func (e *stubExecutor) Wait(context.Context) (int, error) {
return <-e.exit, e.waitErr
}
}
func (s *TestSuite) TestCrunchstat(c *C) {
+ s.runner.crunchstatFakeFS = os.DirFS("../crunchstat/testdata/debian12")
s.fullRunHelper(c, `{
"command": ["sleep", "1"],
"container_image": "`+arvadostest.DockerImage112PDH+`",
c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
- // We didn't actually start a container, so crunchstat didn't
- // find accounting files and therefore didn't log any stats.
- // It should have logged a "can't find accounting files"
- // message after one poll interval, though, so we can confirm
- // it's alive:
c.Assert(s.api.Logs["crunchstat"], NotNil)
- c.Check(s.api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files have not appeared after 100ms.*`)
+ c.Check(s.api.Logs["crunchstat"].String(), Matches, `(?ms).*mem \d+ swap \d+ pgmajfault \d+ rss.*`)
- // The "files never appeared" log assures us that we called
- // (*crunchstat.Reporter)Stop(), and that we set it up with
- // the correct container ID "abcde":
- c.Check(s.api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files never appeared for cgroupid\n`)
+ // Check that we called (*crunchstat.Reporter)Stop().
+ c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*Maximum crunch-run memory rss usage was \d+ bytes\n.*`)
}
func (s *TestSuite) TestNodeInfoLog(c *C) {
c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*Using container runtime: stub.*`)
}
-func (s *TestSuite) testLogRSSThresholds(c *C, ram int, expected []int, notExpected int) {
- s.runner.cgroupRoot = "testdata/fakestat"
+func (s *TestSuite) testLogRSSThresholds(c *C, ram int64, expected []int, notExpected int) {
+ s.runner.crunchstatFakeFS = os.DirFS("../crunchstat/testdata/debian12")
s.fullRunHelper(c, `{
"command": ["true"],
"container_image": "`+arvadostest.DockerImage112PDH+`",
"mounts": {"/tmp": {"kind": "tmp"} },
"output_path": "/tmp",
"priority": 1,
- "runtime_constraints": {"ram": `+strconv.Itoa(ram)+`},
+ "runtime_constraints": {"ram": `+fmt.Sprintf("%d", ram)+`},
"state": "Locked"
}`, nil, func() int { return 0 })
+ c.Logf("=== crunchstat logs\n%s\n", s.api.Logs["crunchstat"].String())
logs := s.api.Logs["crunch-run"].String()
- pattern := logLineStart + `Container using over %d%% of memory \(rss 734003200/%d bytes\)`
+ pattern := logLineStart + `Container using over %d%% of memory \(rss %d/%d bytes\)`
var threshold int
for _, threshold = range expected {
- c.Check(logs, Matches, fmt.Sprintf(pattern, threshold, ram))
+ c.Check(logs, Matches, fmt.Sprintf(pattern, threshold, s.debian12MemoryCurrent, ram))
}
if notExpected > threshold {
- c.Check(logs, Not(Matches), fmt.Sprintf(pattern, notExpected, ram))
+ c.Check(logs, Not(Matches), fmt.Sprintf(pattern, notExpected, s.debian12MemoryCurrent, ram))
}
}
func (s *TestSuite) TestLogNoRSSThresholds(c *C) {
- s.testLogRSSThresholds(c, 7340032000, []int{}, 90)
+ s.testLogRSSThresholds(c, s.debian12MemoryCurrent*10, []int{}, 90)
}
func (s *TestSuite) TestLogSomeRSSThresholds(c *C) {
- onePercentRSS := 7340032
+ onePercentRSS := s.debian12MemoryCurrent / 100
s.testLogRSSThresholds(c, 102*onePercentRSS, []int{90, 95}, 99)
}
func (s *TestSuite) TestLogAllRSSThresholds(c *C) {
- s.testLogRSSThresholds(c, 734003299, []int{90, 95, 99}, 0)
+ s.testLogRSSThresholds(c, s.debian12MemoryCurrent, []int{90, 95, 99}, 0)
}
func (s *TestSuite) TestLogMaximaAfterRun(c *C) {
- s.runner.cgroupRoot = "testdata/fakestat"
+ s.runner.crunchstatFakeFS = os.DirFS("../crunchstat/testdata/debian12")
s.runner.parentTemp = c.MkDir()
s.fullRunHelper(c, `{
"command": ["true"],
"mounts": {"/tmp": {"kind": "tmp"} },
"output_path": "/tmp",
"priority": 1,
- "runtime_constraints": {"ram": 7340032000},
+ "runtime_constraints": {"ram": `+fmt.Sprintf("%d", s.debian12MemoryCurrent*10)+`},
"state": "Locked"
}`, nil, func() int { return 0 })
logs := s.api.Logs["crunch-run"].String()
for _, expected := range []string{
`Maximum disk usage was \d+%, \d+/\d+ bytes`,
- `Maximum container memory cache usage was 73400320 bytes`,
- `Maximum container memory swap usage was 320 bytes`,
- `Maximum container memory pgmajfault usage was 20 faults`,
- `Maximum container memory rss usage was 10%, 734003200/7340032000 bytes`,
+ fmt.Sprintf(`Maximum container memory swap usage was %d bytes`, s.debian12SwapCurrent),
+ `Maximum container memory pgmajfault usage was \d+ faults`,
+ fmt.Sprintf(`Maximum container memory rss usage was 10%%, %d/%d bytes`, s.debian12MemoryCurrent, s.debian12MemoryCurrent*10),
`Maximum crunch-run memory rss usage was \d+ bytes`,
} {
c.Check(logs, Matches, logLineStart+expected)
func (e *dockerExecutor) Create(spec containerSpec) error {
cfg, hostCfg := e.config(spec)
- created, err := e.dockerclient.ContainerCreate(context.TODO(), &cfg, &hostCfg, nil, e.containerUUID)
+ created, err := e.dockerclient.ContainerCreate(context.TODO(), &cfg, &hostCfg, nil, nil, e.containerUUID)
if err != nil {
return fmt.Errorf("While creating container: %v", err)
}
return e.startIO(spec.Stdin, spec.Stdout, spec.Stderr)
}
-func (e *dockerExecutor) CgroupID() string {
- return e.containerID
+func (e *dockerExecutor) Pid() int {
+ ctx, cancel := context.WithDeadline(context.Background(), time.Now().Add(10*time.Second))
+ defer cancel()
+ ctr, err := e.dockerclient.ContainerInspect(ctx, e.containerID)
+ if err != nil && ctr.State != nil {
+ return ctr.State.Pid
+ } else {
+ return 0
+ }
}
func (e *dockerExecutor) Start() error {
// Start the container
Start() error
- // CID the container will belong to
- CgroupID() string
+ // Process ID of a process in the container. Return 0 if
+ // container is finished or no process has started yet.
+ Pid() int
// Stop the container immediately
Stop() error
return nil
}
-func (e *singularityExecutor) CgroupID() string {
- return ""
+func (e *singularityExecutor) Pid() int {
+ // see https://dev.arvados.org/issues/17244#note-21
+ return 0
}
func (e *singularityExecutor) Stop() error {
--- /dev/null
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package crunchstat
+
+import (
+ "flag"
+ "fmt"
+ "io"
+ "log"
+ "os/exec"
+ "syscall"
+ "time"
+
+ "git.arvados.org/arvados.git/lib/cmd"
+)
+
+var Command = command{}
+
+type command struct{}
+
+func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
+ flags := flag.NewFlagSet(prog, flag.ExitOnError)
+ poll := flags.Duration("poll", 10*time.Second, "reporting interval")
+ debug := flags.Bool("debug", false, "show additional debug info")
+ dump := flags.String("dump", "", "save snapshot of OS files in given `directory` (for creating test cases)")
+ getVersion := flags.Bool("version", false, "print version information and exit")
+
+ if ok, code := cmd.ParseFlags(flags, prog, args, "program [args ...]", stderr); !ok {
+ return code
+ } else if *getVersion {
+ fmt.Printf("%s %s\n", prog, cmd.Version.String())
+ return 0
+ } else if flags.NArg() == 0 {
+ fmt.Fprintf(stderr, "missing required argument: program (try -help)\n")
+ return 2
+ }
+
+ reporter := &Reporter{
+ Logger: log.New(stderr, prog+": ", 0),
+ Debug: *debug,
+ PollPeriod: *poll,
+ }
+ reporter.Logger.Printf("%s %s", prog, cmd.Version.String())
+ reporter.Logger.Printf("running %v", flags.Args())
+ cmd := exec.Command(flags.Arg(0), flags.Args()[1:]...)
+
+ // Child process will use our stdin and stdout pipes (we close
+ // our copies below)
+ cmd.Stdin = stdin
+ cmd.Stdout = stdout
+ // Child process stderr and our stats will both go to stderr
+ cmd.Stderr = stderr
+
+ if err := cmd.Start(); err != nil {
+ reporter.Logger.Printf("error in cmd.Start: %v", err)
+ return 1
+ }
+ reporter.Pid = func() int {
+ return cmd.Process.Pid
+ }
+ reporter.Start()
+ defer reporter.Stop()
+ if stdin, ok := stdin.(io.Closer); ok {
+ stdin.Close()
+ }
+ if stdout, ok := stdout.(io.Closer); ok {
+ stdout.Close()
+ }
+
+ failed := false
+ if *dump != "" {
+ err := reporter.dumpSourceFiles(*dump)
+ if err != nil {
+ fmt.Fprintf(stderr, "error dumping source files: %s\n", err)
+ failed = true
+ }
+ }
+
+ err := cmd.Wait()
+
+ if err, ok := err.(*exec.ExitError); ok {
+ // The program has exited with an exit code != 0
+
+ // This works on both Unix and Windows. Although
+ // package syscall is generally platform dependent,
+ // WaitStatus is defined for both Unix and Windows and
+ // in both cases has an ExitStatus() method with the
+ // same signature.
+ if status, ok := err.Sys().(syscall.WaitStatus); ok {
+ return status.ExitStatus()
+ } else {
+ reporter.Logger.Printf("ExitError without WaitStatus: %v", err)
+ return 1
+ }
+ } else if err != nil {
+ reporter.Logger.Printf("error running command: %v", err)
+ return 1
+ }
+
+ if failed {
+ return 1
+ }
+ return 0
+}
"errors"
"fmt"
"io"
+ "io/fs"
"io/ioutil"
"os"
+ "path/filepath"
"regexp"
"sort"
"strconv"
// A Reporter gathers statistics for a cgroup and writes them to a
// log.Logger.
type Reporter struct {
- // CID of the container to monitor. If empty, read the CID
- // from CIDFile (first waiting until a non-empty file appears
- // at CIDFile). If CIDFile is also empty, report host
- // statistics.
- CID string
-
- // Path to a file we can read CID from.
- CIDFile string
-
- // Where cgroup accounting files live on this system, e.g.,
- // "/sys/fs/cgroup".
- CgroupRoot string
-
- // Parent cgroup, e.g., "docker".
- CgroupParent string
+ // Func that returns the pid of a process inside the desired
+ // cgroup. Reporter will call Pid periodically until it
+ // returns a positive number, then start reporting stats for
+ // the cgroup that process belongs to.
+ //
+ // Pid is used when cgroups v2 is available. For cgroups v1,
+ // see below.
+ Pid func() int
// Interval between samples. Must be positive.
PollPeriod time.Duration
- // Temporary directory, will be monitored for available, used & total space.
+ // Temporary directory, will be monitored for available, used
+ // & total space.
TempDir string
// Where to write statistics. Must not be nil.
// When the corresponding stat exceeds a threshold, that will be logged.
MemThresholds map[string][]Threshold
+ // Filesystem to read /proc entries and cgroup stats from.
+ // Non-nil for testing, nil for real root filesystem.
+ FS fs.FS
+
+ // Enable debug messages.
+ Debug bool
+
+ // available cgroup hierarchies
+ statFiles struct {
+ cpusetCpus string // v1,v2 (via /proc/$PID/cpuset)
+ cpuacctStat string // v1 (via /proc/$PID/cgroup => cpuacct)
+ cpuStat string // v2
+ ioServiceBytes string // v1 (via /proc/$PID/cgroup => blkio)
+ ioStat string // v2
+ memoryStat string // v1 and v2 (but v2 is missing some entries)
+ memoryCurrent string // v2
+ memorySwapCurrent string // v2
+ netDev string // /proc/$PID/net/dev
+ }
+
kernelPageSize int64
- reportedStatFile map[string]string
lastNetSample map[string]ioSample
lastDiskIOSample map[string]ioSample
lastCPUSample cpuSample
maxDiskSpaceSample diskSpaceSample
maxMemSample map[memoryKey]int64
+ // process returned by Pid(), whose cgroup stats we are
+ // reporting
+ pid int
+
+ // individual processes whose memory size we are reporting
reportPIDs map[string]int
reportPIDsMu sync.Mutex
done chan struct{} // closed when we should stop reporting
+ ready chan struct{} // have pid and stat files
flushed chan struct{} // closed when we have made our last report
}
// Callers should not modify public data fields after calling Start.
func (r *Reporter) Start() {
r.done = make(chan struct{})
+ r.ready = make(chan struct{})
r.flushed = make(chan struct{})
+ if r.FS == nil {
+ r.FS = os.DirFS("/")
+ }
go r.run()
}
<-r.flushed
}
+var v1keys = map[string]bool{
+ "blkio": true,
+ "cpuacct": true,
+ "cpuset": true,
+ "memory": true,
+}
+
+// Find cgroup hierarchies in /proc/mounts, e.g.,
+//
+// {
+// "blkio": "/sys/fs/cgroup/blkio",
+// "unified": "/sys/fs/cgroup/unified",
+// }
+func (r *Reporter) cgroupMounts() map[string]string {
+ procmounts, err := fs.ReadFile(r.FS, "proc/mounts")
+ if err != nil {
+ r.Logger.Printf("error reading /proc/mounts: %s", err)
+ return nil
+ }
+ mounts := map[string]string{}
+ for _, line := range bytes.Split(procmounts, []byte{'\n'}) {
+ fields := bytes.SplitN(line, []byte{' '}, 6)
+ if len(fields) != 6 {
+ continue
+ }
+ switch string(fields[2]) {
+ case "cgroup2":
+ // cgroup /sys/fs/cgroup/unified cgroup2 rw,nosuid,nodev,noexec,relatime 0 0
+ mounts["unified"] = string(fields[1])
+ case "cgroup":
+ // cgroup /sys/fs/cgroup/blkio cgroup rw,nosuid,nodev,noexec,relatime,blkio 0 0
+ options := bytes.Split(fields[3], []byte{','})
+ for _, option := range options {
+ option := string(option)
+ if v1keys[option] {
+ mounts[option] = string(fields[1])
+ break
+ }
+ }
+ }
+ }
+ return mounts
+}
+
+// generate map of cgroup controller => path for r.pid.
+//
+// the "unified" controller represents cgroups v2.
+func (r *Reporter) cgroupPaths(mounts map[string]string) map[string]string {
+ if len(mounts) == 0 {
+ return nil
+ }
+ procdir := fmt.Sprintf("proc/%d", r.pid)
+ buf, err := fs.ReadFile(r.FS, procdir+"/cgroup")
+ if err != nil {
+ r.Logger.Printf("error reading cgroup file: %s", err)
+ return nil
+ }
+ paths := map[string]string{}
+ for _, line := range bytes.Split(buf, []byte{'\n'}) {
+ // The entry for cgroup v2 is always in the format
+ // "0::$PATH" --
+ // https://docs.kernel.org/admin-guide/cgroup-v2.html
+ if bytes.HasPrefix(line, []byte("0::/")) && mounts["unified"] != "" {
+ paths["unified"] = mounts["unified"] + string(line[3:])
+ continue
+ }
+ // cgroups v1 entries look like
+ // "6:cpu,cpuacct:/user.slice"
+ fields := bytes.SplitN(line, []byte{':'}, 3)
+ if len(fields) != 3 {
+ continue
+ }
+ for _, key := range bytes.Split(fields[1], []byte{','}) {
+ key := string(key)
+ if mounts[key] != "" {
+ paths[key] = mounts[key] + string(fields[2])
+ }
+ }
+ }
+ // In unified mode, /proc/$PID/cgroup doesn't have a cpuset
+ // entry, but we still need it -- there's no cpuset.cpus file
+ // in the cgroup2 subtree indicated by the 0::$PATH entry. We
+ // have to get the right path from /proc/$PID/cpuset.
+ if _, found := paths["cpuset"]; !found && mounts["unified"] != "" {
+ buf, _ := fs.ReadFile(r.FS, procdir+"/cpuset")
+ cpusetPath := string(bytes.TrimRight(buf, "\n"))
+ paths["cpuset"] = mounts["unified"] + cpusetPath
+ }
+ return paths
+}
+
+func (r *Reporter) findStatFiles() {
+ mounts := r.cgroupMounts()
+ paths := r.cgroupPaths(mounts)
+ done := map[*string]bool{}
+ for _, try := range []struct {
+ statFile *string
+ pathkey string
+ file string
+ }{
+ {&r.statFiles.cpusetCpus, "cpuset", "cpuset.cpus.effective"},
+ {&r.statFiles.cpusetCpus, "cpuset", "cpuset.cpus"},
+ {&r.statFiles.cpuacctStat, "cpuacct", "cpuacct.stat"},
+ {&r.statFiles.cpuStat, "unified", "cpu.stat"},
+ // blkio.throttle.io_service_bytes must precede
+ // blkio.io_service_bytes -- on ubuntu1804, the latter
+ // is present but reports 0
+ {&r.statFiles.ioServiceBytes, "blkio", "blkio.throttle.io_service_bytes"},
+ {&r.statFiles.ioServiceBytes, "blkio", "blkio.io_service_bytes"},
+ {&r.statFiles.ioStat, "unified", "io.stat"},
+ {&r.statFiles.memoryStat, "unified", "memory.stat"},
+ {&r.statFiles.memoryStat, "memory", "memory.stat"},
+ {&r.statFiles.memoryCurrent, "unified", "memory.current"},
+ {&r.statFiles.memorySwapCurrent, "unified", "memory.swap.current"},
+ } {
+ startpath, ok := paths[try.pathkey]
+ if !ok || done[try.statFile] {
+ continue
+ }
+ // /proc/$PID/cgroup says cgroup path is
+ // /exa/mple/exa/mple, however, sometimes the file we
+ // need is not under that path, it's only available in
+ // a parent cgroup's dir. So we start at
+ // /sys/fs/cgroup/unified/exa/mple/exa/mple/ and walk
+ // up to /sys/fs/cgroup/unified/ until we find the
+ // desired file.
+ //
+ // This might mean our reported stats include more
+ // cgroups in the cgroup tree, but it's the best we
+ // can do.
+ for path := startpath; path != "" && path != "/" && (path == startpath || strings.HasPrefix(path, mounts[try.pathkey])); path, _ = filepath.Split(strings.TrimRight(path, "/")) {
+ target := strings.TrimLeft(filepath.Join(path, try.file), "/")
+ buf, err := fs.ReadFile(r.FS, target)
+ if err != nil || len(buf) == 0 || bytes.Equal(buf, []byte{'\n'}) {
+ if r.Debug {
+ if os.IsNotExist(err) {
+ // don't stutter
+ err = os.ErrNotExist
+ }
+ r.Logger.Printf("skip /%s: %s", target, err)
+ }
+ continue
+ }
+ *try.statFile = target
+ done[try.statFile] = true
+ r.Logger.Printf("notice: reading stats from /%s", target)
+ break
+ }
+ }
+
+ netdev := fmt.Sprintf("proc/%d/net/dev", r.pid)
+ if buf, err := fs.ReadFile(r.FS, netdev); err == nil && len(buf) > 0 {
+ r.statFiles.netDev = netdev
+ r.Logger.Printf("using /%s", netdev)
+ }
+}
+
func (r *Reporter) reportMemoryMax(logger logPrinter, source, statName string, value, limit int64) {
var units string
switch statName {
return content, err
}
-// Open the cgroup stats file in /sys/fs corresponding to the target
-// cgroup, and return an io.ReadCloser. If no stats file is available,
-// return nil.
-//
-// Log the file that was opened, if it isn't the same file opened on
-// the last openStatFile for this stat.
-//
-// Log "not available" if no file is found and either this stat has
-// been available in the past, or verbose==true.
-//
-// TODO: Instead of trying all options, choose a process in the
-// container, and read /proc/PID/cgroup to determine the appropriate
-// cgroup root for the given statgroup. (This will avoid falling back
-// to host-level stats during container setup and teardown.)
-func (r *Reporter) openStatFile(statgroup, stat string, verbose bool) (io.ReadCloser, error) {
- var paths []string
- if r.CID != "" {
- // Collect container's stats
- paths = []string{
- fmt.Sprintf("%s/%s/%s/%s/%s", r.CgroupRoot, statgroup, r.CgroupParent, r.CID, stat),
- fmt.Sprintf("%s/%s/%s/%s", r.CgroupRoot, r.CgroupParent, r.CID, stat),
- }
- } else {
- // Collect this host's stats
- paths = []string{
- fmt.Sprintf("%s/%s/%s", r.CgroupRoot, statgroup, stat),
- fmt.Sprintf("%s/%s", r.CgroupRoot, stat),
- }
- }
- var path string
- var file *os.File
- var err error
- for _, path = range paths {
- file, err = os.Open(path)
- if err == nil {
- break
- } else {
- path = ""
- }
- }
- if pathWas := r.reportedStatFile[stat]; pathWas != path {
- // Log whenever we start using a new/different cgroup
- // stat file for a given statistic. This typically
- // happens 1 to 3 times per statistic, depending on
- // whether we happen to collect stats [a] before any
- // processes have been created in the container and
- // [b] after all contained processes have exited.
- if path == "" && verbose {
- r.Logger.Printf("notice: stats not available: stat %s, statgroup %s, cid %s, parent %s, root %s\n", stat, statgroup, r.CID, r.CgroupParent, r.CgroupRoot)
- } else if pathWas != "" {
- r.Logger.Printf("notice: stats moved from %s to %s\n", r.reportedStatFile[stat], path)
- } else {
- r.Logger.Printf("notice: reading stats from %s\n", path)
- }
- r.reportedStatFile[stat] = path
- }
- return file, err
-}
-
-func (r *Reporter) getContainerNetStats() (io.Reader, error) {
- procsFile, err := r.openStatFile("cpuacct", "cgroup.procs", true)
- if err != nil {
- return nil, err
- }
- defer procsFile.Close()
- reader := bufio.NewScanner(procsFile)
- for reader.Scan() {
- taskPid := reader.Text()
- statsFilename := fmt.Sprintf("/proc/%s/net/dev", taskPid)
- stats, err := ioutil.ReadFile(statsFilename)
- if err != nil {
- r.Logger.Printf("notice: %v", err)
- continue
- }
- return strings.NewReader(string(stats)), nil
- }
- return nil, errors.New("Could not read stats for any proc in container")
-}
-
type ioSample struct {
sampleTime time.Time
txBytes int64
}
func (r *Reporter) doBlkIOStats() {
- c, err := r.openStatFile("blkio", "blkio.io_service_bytes", true)
- if err != nil {
- return
- }
- defer c.Close()
- b := bufio.NewScanner(c)
var sampleTime = time.Now()
newSamples := make(map[string]ioSample)
- for b.Scan() {
- var device, op string
- var val int64
- if _, err := fmt.Sscanf(string(b.Text()), "%s %s %d", &device, &op, &val); err != nil {
- continue
+
+ if r.statFiles.ioStat != "" {
+ statfile, err := fs.ReadFile(r.FS, r.statFiles.ioStat)
+ if err != nil {
+ return
}
- var thisSample ioSample
- var ok bool
- if thisSample, ok = newSamples[device]; !ok {
- thisSample = ioSample{sampleTime, -1, -1}
+ for _, line := range bytes.Split(statfile, []byte{'\n'}) {
+ // 254:16 rbytes=72163328 wbytes=117370880 rios=3811 wios=3906 dbytes=0 dios=0
+ words := bytes.Split(line, []byte{' '})
+ if len(words) < 2 {
+ continue
+ }
+ thisSample := ioSample{sampleTime, -1, -1}
+ for _, kv := range words[1:] {
+ if bytes.HasPrefix(kv, []byte("rbytes=")) {
+ fmt.Sscanf(string(kv[7:]), "%d", &thisSample.rxBytes)
+ } else if bytes.HasPrefix(kv, []byte("wbytes=")) {
+ fmt.Sscanf(string(kv[7:]), "%d", &thisSample.txBytes)
+ }
+ }
+ if thisSample.rxBytes >= 0 && thisSample.txBytes >= 0 {
+ newSamples[string(words[0])] = thisSample
+ }
+ }
+ } else if r.statFiles.ioServiceBytes != "" {
+ statfile, err := fs.ReadFile(r.FS, r.statFiles.ioServiceBytes)
+ if err != nil {
+ return
}
- switch op {
- case "Read":
- thisSample.rxBytes = val
- case "Write":
- thisSample.txBytes = val
+ for _, line := range bytes.Split(statfile, []byte{'\n'}) {
+ var device, op string
+ var val int64
+ if _, err := fmt.Sscanf(string(line), "%s %s %d", &device, &op, &val); err != nil {
+ continue
+ }
+ var thisSample ioSample
+ var ok bool
+ if thisSample, ok = newSamples[device]; !ok {
+ thisSample = ioSample{sampleTime, -1, -1}
+ }
+ switch op {
+ case "Read":
+ thisSample.rxBytes = val
+ case "Write":
+ thisSample.txBytes = val
+ }
+ newSamples[device] = thisSample
}
- newSamples[device] = thisSample
}
+
for dev, sample := range newSamples {
if sample.txBytes < 0 || sample.rxBytes < 0 {
continue
}
func (r *Reporter) getMemSample() {
- c, err := r.openStatFile("memory", "memory.stat", true)
+ thisSample := memSample{time.Now(), make(map[string]int64)}
+
+ // memory.stat contains "pgmajfault" in cgroups v1 and v2. It
+ // also contains "rss", "swap", and "cache" in cgroups v1.
+ c, err := r.FS.Open(r.statFiles.memoryStat)
if err != nil {
return
}
defer c.Close()
b := bufio.NewScanner(c)
- thisSample := memSample{time.Now(), make(map[string]int64)}
for b.Scan() {
var stat string
var val int64
continue
}
thisSample.memStat[stat] = val
+ }
+
+ // In cgroups v2, we need to read "memory.current" and
+ // "memory.swap.current" as well.
+ for stat, fnm := range map[string]string{
+ // memory.current includes cache. We don't get
+ // separate rss/cache values, so we call
+ // memory usage "rss" for compatibility, and
+ // omit "cache".
+ "rss": r.statFiles.memoryCurrent,
+ "swap": r.statFiles.memorySwapCurrent,
+ } {
+ if fnm == "" {
+ continue
+ }
+ buf, err := fs.ReadFile(r.FS, fnm)
+ if err != nil {
+ continue
+ }
+ var val int64
+ _, err = fmt.Sscanf(string(buf), "%d", &val)
+ if err != nil {
+ continue
+ }
+ thisSample.memStat[stat] = val
+ }
+ for stat, val := range thisSample.memStat {
maxKey := memoryKey{statName: stat}
if val > r.maxMemSample[maxKey] {
r.maxMemSample[maxKey] = val
// assign "don't try again" value in case we give up
// and return without assigning the real value
r.kernelPageSize = -1
- buf, err := os.ReadFile("/proc/self/smaps")
+ buf, err := fs.ReadFile(r.FS, "proc/self/smaps")
if err != nil {
r.Logger.Printf("error reading /proc/self/smaps: %s", err)
return
procmem := ""
for _, procname := range procnames {
pid := r.reportPIDs[procname]
- buf, err := os.ReadFile(fmt.Sprintf("/proc/%d/stat", pid))
+ buf, err := fs.ReadFile(r.FS, fmt.Sprintf("proc/%d/stat", pid))
if err != nil {
continue
}
}
func (r *Reporter) doNetworkStats() {
+ if r.statFiles.netDev == "" {
+ return
+ }
sampleTime := time.Now()
- stats, err := r.getContainerNetStats()
+ stats, err := r.FS.Open(r.statFiles.netDev)
if err != nil {
return
}
-
+ defer stats.Close()
scanner := bufio.NewScanner(stats)
for scanner.Scan() {
var ifName string
// Return the number of CPUs available in the container. Return 0 if
// we can't figure out the real number of CPUs.
func (r *Reporter) getCPUCount() int64 {
- cpusetFile, err := r.openStatFile("cpuset", "cpuset.cpus", true)
+ buf, err := fs.ReadFile(r.FS, r.statFiles.cpusetCpus)
if err != nil {
return 0
}
- defer cpusetFile.Close()
- b, err := r.readAllOrWarn(cpusetFile)
- if err != nil {
- return 0
- }
- sp := strings.Split(string(b), ",")
cpus := int64(0)
- for _, v := range sp {
+ for _, v := range bytes.Split(buf, []byte{','}) {
var min, max int64
- n, _ := fmt.Sscanf(v, "%d-%d", &min, &max)
+ n, _ := fmt.Sscanf(string(v), "%d-%d", &min, &max)
if n == 2 {
cpus += (max - min) + 1
} else {
}
func (r *Reporter) doCPUStats() {
- statFile, err := r.openStatFile("cpuacct", "cpuacct.stat", true)
- if err != nil {
- return
- }
- defer statFile.Close()
- b, err := r.readAllOrWarn(statFile)
- if err != nil {
- return
- }
+ var nextSample cpuSample
+ if r.statFiles.cpuStat != "" {
+ // v2
+ f, err := r.FS.Open(r.statFiles.cpuStat)
+ if err != nil {
+ return
+ }
+ defer f.Close()
+ nextSample = cpuSample{
+ hasData: true,
+ sampleTime: time.Now(),
+ cpus: r.getCPUCount(),
+ }
+ for {
+ var stat string
+ var val int64
+ n, err := fmt.Fscanf(f, "%s %d\n", &stat, &val)
+ if err != nil || n != 2 {
+ break
+ }
+ if stat == "user_usec" {
+ nextSample.user = float64(val) / 1000000
+ } else if stat == "system_usec" {
+ nextSample.sys = float64(val) / 1000000
+ }
+ }
+ } else if r.statFiles.cpuacctStat != "" {
+ // v1
+ b, err := fs.ReadFile(r.FS, r.statFiles.cpuacctStat)
+ if err != nil {
+ return
+ }
- var userTicks, sysTicks int64
- fmt.Sscanf(string(b), "user %d\nsystem %d", &userTicks, &sysTicks)
- userHz := float64(100)
- nextSample := cpuSample{
- hasData: true,
- sampleTime: time.Now(),
- user: float64(userTicks) / userHz,
- sys: float64(sysTicks) / userHz,
- cpus: r.getCPUCount(),
+ var userTicks, sysTicks int64
+ fmt.Sscanf(string(b), "user %d\nsystem %d", &userTicks, &sysTicks)
+ userHz := float64(100)
+ nextSample = cpuSample{
+ hasData: true,
+ sampleTime: time.Now(),
+ user: float64(userTicks) / userHz,
+ sys: float64(sysTicks) / userHz,
+ cpus: r.getCPUCount(),
+ }
}
delta := ""
defer close(r.flushed)
r.maxMemSample = make(map[memoryKey]int64)
- r.reportedStatFile = make(map[string]string)
- if !r.waitForCIDFile() || !r.waitForCgroup() {
+ if !r.waitForPid() {
return
}
+ r.findStatFiles()
+ close(r.ready)
r.lastNetSample = make(map[string]ioSample)
r.lastDiskIOSample = make(map[string]ioSample)
r.getMemSample()
r.doAllStats()
+ if r.PollPeriod < 1 {
+ r.PollPeriod = time.Second * 10
+ }
+
memTicker := time.NewTicker(time.Second)
mainTicker := time.NewTicker(r.PollPeriod)
for {
}
}
-// If CID is empty, wait for it to appear in CIDFile. Return true if
-// we get it before we learn (via r.done) that someone called Stop.
-func (r *Reporter) waitForCIDFile() bool {
- if r.CID != "" || r.CIDFile == "" {
- return true
- }
-
+// Wait for Pid() to return a real pid. Return true if this succeeds
+// before Stop is called.
+func (r *Reporter) waitForPid() bool {
ticker := time.NewTicker(100 * time.Millisecond)
defer ticker.Stop()
+ warningTimer := time.After(r.PollPeriod)
for {
- cid, err := ioutil.ReadFile(r.CIDFile)
- if err == nil && len(cid) > 0 {
- r.CID = string(cid)
- return true
+ r.pid = r.Pid()
+ if r.pid > 0 {
+ break
}
select {
case <-ticker.C:
+ case <-warningTimer:
+ r.Logger.Printf("warning: Pid() did not return a process ID after %v (config error?) -- still waiting...", r.PollPeriod)
case <-r.done:
- r.Logger.Printf("warning: CID never appeared in %+q: %v", r.CIDFile, err)
+ r.Logger.Printf("warning: Pid() never returned a process ID")
return false
}
}
+ return true
}
-// Wait for the cgroup stats files to appear in cgroup_root. Return
-// true if they appear before r.done indicates someone called Stop. If
-// they don't appear within one poll interval, log a warning and keep
-// waiting.
-func (r *Reporter) waitForCgroup() bool {
- ticker := time.NewTicker(100 * time.Millisecond)
- defer ticker.Stop()
- warningTimer := time.After(r.PollPeriod)
- for {
- c, err := r.openStatFile("cpuacct", "cgroup.procs", false)
- if err == nil {
- c.Close()
- return true
+func (r *Reporter) dumpSourceFiles(destdir string) error {
+ select {
+ case <-r.done:
+ return errors.New("reporter was never ready")
+ case <-r.ready:
+ }
+ todo := []string{
+ fmt.Sprintf("proc/%d/cgroup", r.pid),
+ fmt.Sprintf("proc/%d/cpuset", r.pid),
+ "proc/mounts",
+ "proc/self/smaps",
+ r.statFiles.cpusetCpus,
+ r.statFiles.cpuacctStat,
+ r.statFiles.cpuStat,
+ r.statFiles.ioServiceBytes,
+ r.statFiles.ioStat,
+ r.statFiles.memoryStat,
+ r.statFiles.memoryCurrent,
+ r.statFiles.memorySwapCurrent,
+ r.statFiles.netDev,
+ }
+ for _, path := range todo {
+ if path == "" {
+ continue
}
- select {
- case <-ticker.C:
- case <-warningTimer:
- r.Logger.Printf("warning: cgroup stats files have not appeared after %v (config error?) -- still waiting...", r.PollPeriod)
- case <-r.done:
- r.Logger.Printf("warning: cgroup stats files never appeared for %v", r.CID)
- return false
+ err := r.createParentsAndCopyFile(destdir, path)
+ if err != nil {
+ return err
+ }
+ }
+ r.reportPIDsMu.Lock()
+ r.reportPIDsMu.Unlock()
+ for _, pid := range r.reportPIDs {
+ path := fmt.Sprintf("proc/%d/stat", pid)
+ err := r.createParentsAndCopyFile(destdir, path)
+ if err != nil {
+ return err
+ }
+ }
+ if proc, err := os.FindProcess(r.pid); err != nil || proc.Signal(syscall.Signal(0)) != nil {
+ return fmt.Errorf("process %d no longer exists, snapshot is probably broken", r.pid)
+ }
+ return nil
+}
+
+func (r *Reporter) createParentsAndCopyFile(destdir, path string) error {
+ buf, err := fs.ReadFile(r.FS, path)
+ if os.IsNotExist(err) {
+ return nil
+ } else if err != nil {
+ return err
+ }
+ if parent, _ := filepath.Split(path); parent != "" {
+ err = os.MkdirAll(destdir+"/"+parent, 0777)
+ if err != nil {
+ return fmt.Errorf("mkdir %s: %s", destdir+"/"+parent, err)
}
}
+ destfile := destdir + "/" + path
+ r.Logger.Printf("copy %s to %s -- size %d", path, destfile, len(buf))
+ return os.WriteFile(destfile, buf, 0777)
}
import (
"bytes"
- "errors"
"fmt"
+ "io/fs"
"os"
- "path"
"regexp"
+ "runtime"
"strconv"
"testing"
"time"
)
const logMsgPrefix = `(?m)(.*\n)*.* msg="`
-const GiB = int64(1024 * 1024 * 1024)
-type fakeStat struct {
- cgroupRoot string
- statName string
- unit string
- value int64
+func Test(t *testing.T) {
+ TestingT(t)
}
-var fakeRSS = fakeStat{
- cgroupRoot: "testdata/fakestat",
- statName: "mem rss",
- unit: "bytes",
- // Note this is the value of total_rss, not rss, because that's what should
- // always be reported for thresholds and maxima.
- value: 750 * 1024 * 1024,
+var _ = Suite(&suite{})
+
+type testdatasource struct {
+ fspath string
+ pid int
}
-func Test(t *testing.T) {
- TestingT(t)
+func (s testdatasource) Pid() int {
+ return s.pid
+}
+func (s testdatasource) FS() fs.FS {
+ return os.DirFS(s.fspath)
}
-var _ = Suite(&suite{
- logger: logrus.New(),
-})
+// To generate a test case for a new OS target, build
+// cmd/arvados-server and run
+//
+// arvados-server crunchstat -dump ./testdata/example1234 sleep 2
+var testdata = map[string]testdatasource{
+ "debian11": {fspath: "testdata/debian11", pid: 4153022},
+ "debian12": {fspath: "testdata/debian12", pid: 1115883},
+ "ubuntu1804": {fspath: "testdata/ubuntu1804", pid: 2523},
+ "ubuntu2004": {fspath: "testdata/ubuntu2004", pid: 1360},
+ "ubuntu2204": {fspath: "testdata/ubuntu2204", pid: 1967},
+}
type suite struct {
- cgroupRoot string
- logbuf bytes.Buffer
- logger *logrus.Logger
+ logbuf bytes.Buffer
+ logger *logrus.Logger
+ debian12MemoryCurrent int64
}
func (s *suite) SetUpSuite(c *C) {
+ s.logger = logrus.New()
s.logger.Out = &s.logbuf
+
+ buf, err := os.ReadFile("testdata/debian12/sys/fs/cgroup/user.slice/user-1000.slice/session-4.scope/memory.current")
+ c.Assert(err, IsNil)
+ _, err = fmt.Sscanf(string(buf), "%d", &s.debian12MemoryCurrent)
+ c.Assert(err, IsNil)
}
func (s *suite) SetUpTest(c *C) {
- s.cgroupRoot = ""
s.logbuf.Reset()
}
-func (s *suite) tempCgroup(c *C, sourceDir string) error {
- tempDir := c.MkDir()
- dirents, err := os.ReadDir(sourceDir)
- if err != nil {
- return err
+// Report stats for the current (go test) process's cgroup, using the
+// test host's real procfs/sysfs.
+func (s *suite) TestReportCurrent(c *C) {
+ r := Reporter{
+ Pid: os.Getpid,
+ Logger: s.logger,
+ PollPeriod: time.Second,
+ }
+ r.Start()
+ defer r.Stop()
+ checkPatterns := []string{
+ `(?ms).*rss.*`,
+ `(?ms).*net:.*`,
+ `(?ms).*blkio:.*`,
+ `(?ms).* [\d.]+ user [\d.]+ sys ` + fmt.Sprintf("%d", runtime.NumCPU()) + ` cpus -- .*`,
}
- for _, dirent := range dirents {
- srcData, err := os.ReadFile(path.Join(sourceDir, dirent.Name()))
- if err != nil {
- return err
+ for deadline := time.Now().Add(4 * time.Second); !c.Failed(); time.Sleep(time.Millisecond) {
+ done := true
+ for _, pattern := range checkPatterns {
+ if m := regexp.MustCompile(pattern).FindSubmatch(s.logbuf.Bytes()); len(m) == 0 {
+ done = false
+ if time.Now().After(deadline) {
+ c.Errorf("timed out waiting for %s", pattern)
+ }
+ }
}
- destPath := path.Join(tempDir, dirent.Name())
- err = os.WriteFile(destPath, srcData, 0o600)
- if err != nil {
- return err
+ if done {
+ break
}
}
- s.cgroupRoot = tempDir
- return nil
-}
-
-func (s *suite) addPidToCgroup(pid int) error {
- if s.cgroupRoot == "" {
- return errors.New("cgroup has not been set up for this test")
- }
- procsPath := path.Join(s.cgroupRoot, "cgroup.procs")
- procsFile, err := os.OpenFile(procsPath, os.O_APPEND|os.O_CREATE|os.O_WRONLY, 0o600)
- if err != nil {
- return err
- }
- pidLine := strconv.Itoa(pid) + "\n"
- _, err = procsFile.Write([]byte(pidLine))
- if err != nil {
- procsFile.Close()
- return err
- }
- return procsFile.Close()
-}
-
-func (s *suite) TestReadAllOrWarnFail(c *C) {
- rep := Reporter{Logger: s.logger}
-
- // The special file /proc/self/mem can be opened for
- // reading, but reading from byte 0 returns an error.
- f, err := os.Open("/proc/self/mem")
- c.Assert(err, IsNil)
- defer f.Close()
- _, err = rep.readAllOrWarn(f)
- c.Check(err, NotNil)
- c.Check(s.logbuf.String(), Matches, ".* msg=\"warning: read /proc/self/mem: .*\n")
-}
-
-func (s *suite) TestReadAllOrWarnSuccess(c *C) {
- rep := Reporter{Logger: s.logger}
-
- f, err := os.Open("./crunchstat_test.go")
- c.Assert(err, IsNil)
- defer f.Close()
- data, err := rep.readAllOrWarn(f)
- c.Check(err, IsNil)
- c.Check(string(data), Matches, "(?ms).*\npackage crunchstat\n.*")
- c.Check(s.logbuf.String(), Equals, "")
+ c.Logf("%s", s.logbuf.String())
}
+// Report stats for a the current (go test) process.
func (s *suite) TestReportPIDs(c *C) {
r := Reporter{
+ Pid: func() int { return 1 },
Logger: s.logger,
- CgroupRoot: "/sys/fs/cgroup",
PollPeriod: time.Second,
}
r.Start()
+ defer r.Stop()
r.ReportPID("init", 1)
r.ReportPID("test_process", os.Getpid())
r.ReportPID("nonexistent", 12345) // should be silently ignored/omitted
c.Logf("%s", s.logbuf.String())
}
+func (s *suite) TestAllTestdata(c *C) {
+ for platform, datasource := range testdata {
+ s.logbuf.Reset()
+ c.Logf("=== %s", platform)
+ rep := Reporter{
+ Pid: datasource.Pid,
+ FS: datasource.FS(),
+ Logger: s.logger,
+ PollPeriod: time.Second,
+ ThresholdLogger: s.logger,
+ Debug: true,
+ }
+ rep.Start()
+ rep.Stop()
+ logs := s.logbuf.String()
+ c.Logf("%s", logs)
+ c.Check(logs, Matches, `(?ms).* \d\d+ rss\\n.*`)
+ c.Check(logs, Matches, `(?ms).*blkio:\d+:\d+ \d+ write \d+ read\\n.*`)
+ c.Check(logs, Matches, `(?ms).*net:\S+ \d+ tx \d+ rx\\n.*`)
+ c.Check(logs, Matches, `(?ms).* [\d.]+ user [\d.]+ sys [2-9]\d* cpus.*`)
+ }
+}
+
func (s *suite) testRSSThresholds(c *C, rssPercentages []int64, alertCount int) {
c.Assert(alertCount <= len(rssPercentages), Equals, true)
rep := Reporter{
- CgroupRoot: fakeRSS.cgroupRoot,
- Logger: s.logger,
+ Pid: testdata["debian12"].Pid,
+ FS: testdata["debian12"].FS(),
+ Logger: s.logger,
MemThresholds: map[string][]Threshold{
- "rss": NewThresholdsFromPercentages(GiB, rssPercentages),
+ "rss": NewThresholdsFromPercentages(s.debian12MemoryCurrent*3/2, rssPercentages),
},
PollPeriod: time.Second * 10,
ThresholdLogger: s.logger,
logCheck = Not(Matches)
}
pattern := fmt.Sprintf(`%sContainer using over %d%% of memory \(rss %d/%d bytes\)"`,
- logMsgPrefix, expectPercentage, fakeRSS.value, GiB)
+ logMsgPrefix, expectPercentage, s.debian12MemoryCurrent, s.debian12MemoryCurrent*3/2)
c.Check(logs, logCheck, pattern)
}
}
}
func (s *suite) TestMultipleRSSThresholdsSomePassed(c *C) {
- s.testRSSThresholds(c, []int64{60, 70, 80, 90}, 2)
+ s.testRSSThresholds(c, []int64{45, 60, 75, 90}, 2)
}
func (s *suite) TestMultipleRSSThresholdsAllPassed(c *C) {
}
func (s *suite) TestLogMaxima(c *C) {
- err := s.tempCgroup(c, fakeRSS.cgroupRoot)
- c.Assert(err, IsNil)
rep := Reporter{
- CgroupRoot: s.cgroupRoot,
+ Pid: testdata["debian12"].Pid,
+ FS: testdata["debian12"].FS(),
Logger: s.logger,
PollPeriod: time.Second * 10,
- TempDir: s.cgroupRoot,
+ TempDir: "/",
}
rep.Start()
rep.Stop()
- rep.LogMaxima(s.logger, map[string]int64{"rss": GiB})
+ rep.LogMaxima(s.logger, map[string]int64{"rss": s.debian12MemoryCurrent * 3 / 2})
logs := s.logbuf.String()
c.Logf("%s", logs)
expectRSS := fmt.Sprintf(`Maximum container memory rss usage was %d%%, %d/%d bytes`,
- 100*fakeRSS.value/GiB, fakeRSS.value, GiB)
+ 66, s.debian12MemoryCurrent, s.debian12MemoryCurrent*3/2)
for _, expected := range []string{
`Maximum disk usage was \d+%, \d+/\d+ bytes`,
- `Maximum container memory cache usage was 73400320 bytes`,
- `Maximum container memory swap usage was 320 bytes`,
- `Maximum container memory pgmajfault usage was 20 faults`,
+ `Maximum container memory swap usage was \d\d+ bytes`,
+ `Maximum container memory pgmajfault usage was \d\d+ faults`,
expectRSS,
} {
pattern := logMsgPrefix + expected + `"`
}
func (s *suite) TestLogProcessMemMax(c *C) {
- err := s.tempCgroup(c, fakeRSS.cgroupRoot)
- c.Assert(err, IsNil)
- pid := os.Getpid()
- err = s.addPidToCgroup(pid)
- c.Assert(err, IsNil)
-
rep := Reporter{
- CgroupRoot: s.cgroupRoot,
+ Pid: os.Getpid,
Logger: s.logger,
PollPeriod: time.Second * 10,
- TempDir: s.cgroupRoot,
}
- rep.ReportPID("test-run", pid)
+ rep.ReportPID("test-run", os.Getpid())
rep.Start()
rep.Stop()
rep.LogProcessMemMax(s.logger)
--- /dev/null
+0::/user.slice/user-1000.slice/session-5424.scope
--- /dev/null
+/user.slice
--- /dev/null
+Inter-| Receive | Transmit
+ face |bytes packets errs drop fifo frame compressed multicast|bytes packets errs drop fifo colls carrier compressed
+ lo: 161155690314 90375905 0 0 0 0 0 0 161155690314 90375905 0 0 0 0 0 0
+ ens3: 163923112 1884265 0 0 0 0 0 0 43218121 239766 0 0 0 0 0 0
+ ens9: 24574250159 83081845 0 0 0 0 0 0 49312502353 91591944 0 0 0 0 0 0
+docker0: 6958795 109630 0 0 0 0 0 0 671569248 187319 0 0 0 0 0 0
+tailscale0: 82192857 118550 0 0 0 0 0 0 6898232 100243 0 0 0 0 0 0
--- /dev/null
+sysfs /sys sysfs rw,nosuid,nodev,noexec,relatime 0 0
+proc /proc proc rw,nosuid,nodev,noexec,relatime 0 0
+udev /dev devtmpfs rw,nosuid,relatime,size=4055540k,nr_inodes=1013885,mode=755 0 0
+devpts /dev/pts devpts rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000 0 0
+tmpfs /run tmpfs rw,nosuid,nodev,noexec,relatime,size=814692k,mode=755 0 0
+/dev/vdb1 / ext4 rw,relatime,errors=remount-ro 0 0
+securityfs /sys/kernel/security securityfs rw,nosuid,nodev,noexec,relatime 0 0
+tmpfs /dev/shm tmpfs rw,nosuid,nodev 0 0
+tmpfs /run/lock tmpfs rw,nosuid,nodev,noexec,relatime,size=5120k 0 0
+cgroup2 /sys/fs/cgroup cgroup2 rw,nosuid,nodev,noexec,relatime,nsdelegate,memory_recursiveprot 0 0
+pstore /sys/fs/pstore pstore rw,nosuid,nodev,noexec,relatime 0 0
+none /sys/fs/bpf bpf rw,nosuid,nodev,noexec,relatime,mode=700 0 0
+systemd-1 /proc/sys/fs/binfmt_misc autofs rw,relatime,fd=30,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=9589 0 0
+hugetlbfs /dev/hugepages hugetlbfs rw,relatime,pagesize=2M 0 0
+mqueue /dev/mqueue mqueue rw,nosuid,nodev,noexec,relatime 0 0
+debugfs /sys/kernel/debug debugfs rw,nosuid,nodev,noexec,relatime 0 0
+tracefs /sys/kernel/tracing tracefs rw,nosuid,nodev,noexec,relatime 0 0
+configfs /sys/kernel/config configfs rw,nosuid,nodev,noexec,relatime 0 0
+fusectl /sys/fs/fuse/connections fusectl rw,nosuid,nodev,noexec,relatime 0 0
+none /tmp tmpfs rw,relatime 0 0
+tmpfs /run/user/1000 tmpfs rw,nosuid,nodev,relatime,size=814688k,nr_inodes=203672,mode=700,uid=1000,gid=1000 0 0
+binfmt_misc /proc/sys/fs/binfmt_misc binfmt_misc rw,nosuid,nodev,noexec,relatime 0 0
+arvados-client /home/tom/keep fuse.arvados-client rw,nosuid,nodev,relatime,user_id=1000,group_id=1000 0 0
--- /dev/null
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+7f754b0ca000-7f754b0d5000 r--p 0002c000 fd:00 10938 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
+Size: 44 kB
+KernelPageSize: 4 kB
+MMUPageSize: 4 kB
+Rss: 44 kB
+Pss: 1 kB
+Shared_Clean: 44 kB
+Shared_Dirty: 0 kB
+Private_Clean: 0 kB
+Private_Dirty: 0 kB
+Referenced: 44 kB
+Anonymous: 0 kB
+LazyFree: 0 kB
+AnonHugePages: 0 kB
+ShmemPmdMapped: 0 kB
+FilePmdMapped: 0 kB
+Shared_Hugetlb: 0 kB
+Private_Hugetlb: 0 kB
+Swap: 0 kB
+SwapPss: 0 kB
+Locked: 0 kB
+THPeligible: 0
+VmFlags: rd mr mw me sd
+7f754b0d6000-7f754b0d8000 r--p 00037000 fd:00 10938 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
+Size: 8 kB
+KernelPageSize: 4 kB
+MMUPageSize: 4 kB
+Rss: 8 kB
+Pss: 8 kB
+Shared_Clean: 0 kB
+Shared_Dirty: 0 kB
+Private_Clean: 0 kB
+Private_Dirty: 8 kB
+Referenced: 8 kB
+Anonymous: 8 kB
+LazyFree: 0 kB
+AnonHugePages: 0 kB
+ShmemPmdMapped: 0 kB
+FilePmdMapped: 0 kB
+Shared_Hugetlb: 0 kB
+Private_Hugetlb: 0 kB
+Swap: 0 kB
+SwapPss: 0 kB
+Locked: 0 kB
+THPeligible: 0
+VmFlags: rd mr mw me ac sd
+7f754b0d8000-7f754b0da000 rw-p 00039000 fd:00 10938 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
+Size: 8 kB
+KernelPageSize: 4 kB
+MMUPageSize: 4 kB
+Rss: 8 kB
+Pss: 8 kB
+Shared_Clean: 0 kB
+Shared_Dirty: 0 kB
+Private_Clean: 0 kB
+Private_Dirty: 8 kB
+Referenced: 8 kB
+Anonymous: 8 kB
+LazyFree: 0 kB
+AnonHugePages: 0 kB
+ShmemPmdMapped: 0 kB
+FilePmdMapped: 0 kB
+Shared_Hugetlb: 0 kB
+Private_Hugetlb: 0 kB
+Swap: 0 kB
+SwapPss: 0 kB
+Locked: 0 kB
+THPeligible: 0
+VmFlags: rd wr mr mw me ac sd
+7ffed2e14000-7ffed2e35000 rw-p 00000000 00:00 0 [stack]
+Size: 132 kB
+KernelPageSize: 4 kB
+MMUPageSize: 4 kB
+Rss: 16 kB
+Pss: 16 kB
+Shared_Clean: 0 kB
+Shared_Dirty: 0 kB
+Private_Clean: 0 kB
+Private_Dirty: 16 kB
+Referenced: 16 kB
+Anonymous: 16 kB
+LazyFree: 0 kB
+AnonHugePages: 0 kB
+ShmemPmdMapped: 0 kB
+FilePmdMapped: 0 kB
+Shared_Hugetlb: 0 kB
+Private_Hugetlb: 0 kB
+Swap: 0 kB
+SwapPss: 0 kB
+Locked: 0 kB
+THPeligible: 0
+VmFlags: rd wr mr mw me gd ac
+7ffed2fc4000-7ffed2fc8000 r--p 00000000 00:00 0 [vvar]
+Size: 16 kB
+KernelPageSize: 4 kB
+MMUPageSize: 4 kB
+Rss: 0 kB
+Pss: 0 kB
+Shared_Clean: 0 kB
+Shared_Dirty: 0 kB
+Private_Clean: 0 kB
+Private_Dirty: 0 kB
+Referenced: 0 kB
+Anonymous: 0 kB
+LazyFree: 0 kB
+AnonHugePages: 0 kB
+ShmemPmdMapped: 0 kB
+FilePmdMapped: 0 kB
+Shared_Hugetlb: 0 kB
+Private_Hugetlb: 0 kB
+Swap: 0 kB
+SwapPss: 0 kB
+Locked: 0 kB
+THPeligible: 0
+VmFlags: rd mr pf io de dd sd
+7ffed2fc8000-7ffed2fca000 r-xp 00000000 00:00 0 [vdso]
+Size: 8 kB
+KernelPageSize: 4 kB
+MMUPageSize: 4 kB
+Rss: 4 kB
+Pss: 0 kB
+Shared_Clean: 4 kB
+Shared_Dirty: 0 kB
+Private_Clean: 0 kB
+Private_Dirty: 0 kB
+Referenced: 4 kB
+Anonymous: 0 kB
+LazyFree: 0 kB
+AnonHugePages: 0 kB
+ShmemPmdMapped: 0 kB
+FilePmdMapped: 0 kB
+Shared_Hugetlb: 0 kB
+Private_Hugetlb: 0 kB
+Swap: 0 kB
+SwapPss: 0 kB
+Locked: 0 kB
+THPeligible: 0
+VmFlags: rd ex mr mw me de sd
+ffffffffff600000-ffffffffff601000 --xp 00000000 00:00 0 [vsyscall]
+Size: 4 kB
+KernelPageSize: 4 kB
+MMUPageSize: 4 kB
+Rss: 0 kB
+Pss: 0 kB
+Shared_Clean: 0 kB
+Shared_Dirty: 0 kB
+Private_Clean: 0 kB
+Private_Dirty: 0 kB
+Referenced: 0 kB
+Anonymous: 0 kB
+LazyFree: 0 kB
+AnonHugePages: 0 kB
+ShmemPmdMapped: 0 kB
+FilePmdMapped: 0 kB
+Shared_Hugetlb: 0 kB
+Private_Hugetlb: 0 kB
+Swap: 0 kB
+SwapPss: 0 kB
+Locked: 0 kB
+THPeligible: 0
+VmFlags: ex
--- /dev/null
+252:0 rbytes=3551232 wbytes=147263488 rios=141 wios=208 dbytes=0 dios=0
+253:0 rbytes=3551232 wbytes=147263488 rios=141 wios=109 dbytes=0 dios=0
--- /dev/null
+usage_usec 1750563
+user_usec 703305
+system_usec 1047257
--- /dev/null
+anon 13606912
+file 52432896
+kernel_stack 180224
+pagetables 438272
+percpu 0
+sock 0
+shmem 4096
+file_mapped 25767936
+file_dirty 86016
+file_writeback 0
+swapcached 0
+anon_thp 0
+file_thp 0
+shmem_thp 0
+inactive_anon 13574144
+active_anon 20480
+inactive_file 26722304
+active_file 25669632
+unevictable 0
+slab_reclaimable 1646344
+slab_unreclaimable 328072
+slab 1974416
+workingset_refault_anon 0
+workingset_refault_file 0
+workingset_activate_anon 0
+workingset_activate_file 0
+workingset_restore_anon 0
+workingset_restore_file 0
+workingset_nodereclaim 0
+pgfault 33355
+pgmajfault 27
+pgrefill 0
+pgscan 0
+pgsteal 0
+pgactivate 6253
+pgdeactivate 0
+pglazyfree 0
+pglazyfreed 0
+thp_fault_alloc 0
+thp_collapse_alloc 0
if pollInterval <= 0 {
pollInterval = defaultPollInterval
}
- sched := scheduler.New(disp.Context, disp.ArvClient, disp.queue, disp.pool, disp.Registry, staleLockTimeout, pollInterval, disp.Cluster.Containers.CloudVMs.MaxInstances, disp.Cluster.Containers.CloudVMs.SupervisorFraction)
+ sched := scheduler.New(disp.Context, disp.ArvClient, disp.queue, disp.pool, disp.Registry, staleLockTimeout, pollInterval,
+ disp.Cluster.Containers.CloudVMs.InitialQuotaEstimate,
+ disp.Cluster.Containers.CloudVMs.MaxInstances,
+ disp.Cluster.Containers.CloudVMs.SupervisorFraction)
sched.Start()
defer sched.Stop()
DispatchPrivateKey: string(dispatchprivraw),
StaleLockTimeout: arvados.Duration(5 * time.Millisecond),
RuntimeEngine: "stub",
+ MaxDispatchAttempts: 10,
CloudVMs: arvados.CloudVMsConfig{
Driver: "test",
SyncInterval: arvados.Duration(10 * time.Millisecond),
TimeoutProbe: arvados.Duration(15 * time.Millisecond),
TimeoutShutdown: arvados.Duration(5 * time.Millisecond),
MaxCloudOpsPerSecond: 500,
+ InitialQuotaEstimate: 8,
PollInterval: arvados.Duration(5 * time.Millisecond),
ProbeInterval: arvados.Duration(5 * time.Millisecond),
MaxProbesPerSecond: 1000,
select {
case <-done:
// loop will end because len(waiting)==0
- case <-time.After(3 * time.Second):
+ case <-time.After(5 * time.Second):
if len(waiting) >= waswaiting {
- c.Fatalf("timed out; no progress in 3s while waiting for %d containers: %q", len(waiting), waiting)
+ c.Fatalf("timed out; no progress in 5 s while waiting for %d containers: %q", len(waiting), waiting)
}
}
}
if sch.maxInstances > 0 && sch.maxConcurrency > sch.maxInstances {
sch.maxConcurrency = sch.maxInstances
}
+ if sch.pool.AtQuota() && len(running) > 0 && (sch.maxConcurrency == 0 || sch.maxConcurrency > len(running)) {
+ // Consider current workload to be the maximum
+ // allowed, for the sake of reporting metrics and
+ // calculating max supervisors.
+ //
+ // Now that sch.maxConcurrency is set, we will only
+ // raise it past len(running) by 10%. This helps
+ // avoid running an inappropriate number of
+ // supervisors when we reach the cloud-imposed quota
+ // (which may be based on # CPUs etc) long before the
+ // configured MaxInstances.
+ sch.maxConcurrency = len(running)
+ }
sch.mMaxContainerConcurrency.Set(float64(sch.maxConcurrency))
maxSupervisors := int(float64(sch.maxConcurrency) * sch.supervisorFraction)
running: map[string]time.Time{},
canCreate: 0,
}
- New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0).runQueue()
+ New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0, 0).runQueue()
c.Check(pool.creates, check.DeepEquals, []arvados.InstanceType{test.InstanceType(1), test.InstanceType(1), test.InstanceType(1)})
c.Check(pool.starts, check.DeepEquals, []string{test.ContainerUUID(4)})
c.Check(pool.running, check.HasLen, 1)
starts: []string{},
canCreate: 0,
}
- sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0)
+ sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0, 0)
sch.sync()
sch.runQueue()
sch.sync()
starts: []string{},
canCreate: 0,
}
- sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0)
+ sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0, 0)
sch.last503time = time.Now()
sch.maxConcurrency = 3
sch.sync()
starts: []string{},
canCreate: 0,
}
- sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 8, 0.5)
+ sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 8, 0.5)
sch.sync()
sch.runQueue()
sch.sync()
starts: []string{},
canCreate: 0,
}
- sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 8, 0.5)
+ sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 8, 0.5)
sch.sync()
sch.runQueue()
sch.sync()
starts: []string{},
canCreate: 0,
}
- sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0)
+ sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0, 0)
for i := 0; i < 30; i++ {
sch.runQueue()
sch.sync()
},
}
queue.Update()
- New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0).runQueue()
+ New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0, 0).runQueue()
c.Check(pool.creates, check.DeepEquals, []arvados.InstanceType{test.InstanceType(2), test.InstanceType(1)})
c.Check(pool.starts, check.DeepEquals, []string{uuids[6], uuids[5], uuids[3], uuids[2]})
running := map[string]bool{}
},
}
queue.Update()
- sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0)
+ sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0, 0)
c.Check(pool.running, check.HasLen, 1)
sch.sync()
for deadline := time.Now().Add(time.Second); len(pool.Running()) > 0 && time.Now().Before(deadline); time.Sleep(time.Millisecond) {
pool := stubPool{
unalloc: map[arvados.InstanceType]int{test.InstanceType(1): 1},
}
- sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0)
+ sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0, 0)
sch.runQueue()
sch.updateMetrics()
// 'over quota' metric will be 1 because no workers are available and canCreate defaults
// to zero.
pool = stubPool{}
- sch = New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0)
+ sch = New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0, 0)
sch.runQueue()
sch.updateMetrics()
unalloc: map[arvados.InstanceType]int{test.InstanceType(1): 1},
running: map[string]time.Time{},
}
- sch = New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0)
+ sch = New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0, 0)
sch.runQueue()
sch.updateMetrics()
running: map[string]time.Time{},
canCreate: 0,
}
- New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 10, 0.2).runQueue()
+ New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 10, 0.2).runQueue()
c.Check(pool.creates, check.DeepEquals, []arvados.InstanceType(nil))
c.Check(pool.starts, check.DeepEquals, []string{test.ContainerUUID(4), test.ContainerUUID(3), test.ContainerUUID(1)})
}
//
// Any given queue and pool should not be used by more than one
// scheduler at a time.
-func New(ctx context.Context, client *arvados.Client, queue ContainerQueue, pool WorkerPool, reg *prometheus.Registry, staleLockTimeout, queueUpdateInterval time.Duration, maxInstances int, supervisorFraction float64) *Scheduler {
+func New(ctx context.Context, client *arvados.Client, queue ContainerQueue, pool WorkerPool, reg *prometheus.Registry, staleLockTimeout, queueUpdateInterval time.Duration, minQuota, maxInstances int, supervisorFraction float64) *Scheduler {
sch := &Scheduler{
logger: ctxlog.FromContext(ctx),
client: client,
stop: make(chan struct{}),
stopped: make(chan struct{}),
uuidOp: map[string]string{},
- maxConcurrency: maxInstances, // initial value -- will be dynamically adjusted
supervisorFraction: supervisorFraction,
maxInstances: maxInstances,
}
+ if minQuota > 0 {
+ sch.maxConcurrency = minQuota
+ } else {
+ sch.maxConcurrency = maxInstances
+ }
sch.registerMetrics(reg)
return sch
}
Help: "Dynamically assigned limit on number of containers scheduled concurrency, set after receiving 503 errors from API.",
})
reg.MustRegister(sch.mMaxContainerConcurrency)
+ reg.MustRegister(prometheus.NewGaugeFunc(prometheus.GaugeOpts{
+ Namespace: "arvados",
+ Subsystem: "dispatchcloud",
+ Name: "at_quota",
+ Help: "Flag indicating the cloud driver is reporting an at-quota condition.",
+ }, func() float64 {
+ if sch.pool.AtQuota() {
+ return 1
+ } else {
+ return 0
+ }
+ }))
}
func (sch *Scheduler) updateMetrics() {
ents, _ := queue.Entries()
c.Check(ents, check.HasLen, 1)
- sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0)
+ sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0, 0)
sch.sync()
ents, _ = queue.Entries()
ents, _ := queue.Entries()
c.Check(ents, check.HasLen, 1)
- sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0)
+ sch := New(ctx, arvados.NewClientFromEnv(), &queue, &pool, nil, time.Millisecond, time.Millisecond, 0, 0, 0)
// Sync shouldn't cancel the container because it might be
// running on the VM with state=="unknown".
# SPDX-License-Identifier: Apache-2.0
fpm_depends+=(ca-certificates)
+case "$TARGET" in
+ rocky*) fpm_depends+=(pam) ;;
+esac
fpm_args+=(--conflicts=libpam-arvados)
max_res_pars = ("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax")
sum_res_pars = ("outdirMin", "outdirMax")
+_basetype_re = re.compile(r'''(?:
+Directory
+|File
+|array
+|boolean
+|double
+|enum
+|float
+|int
+|long
+|null
+|record
+|string
+)(?:\[\])?\??''', re.VERBOSE)
+
def make_wrapper_workflow(arvRunner, main, packed, project_uuid, name, git_info, tool):
col = arvados.collection.Collection(api_client=arvRunner.api,
keep_client=arvRunner.keep_client)
return os.path.join(r, p3)
def is_basetype(tp):
- basetypes = ("null", "boolean", "int", "long", "float", "double", "string", "File", "Directory", "record", "array", "enum")
- for b in basetypes:
- if re.match(b+"(\[\])?\??", tp):
- return True
- return False
-
+ return _basetype_re.match(tp) is not None
def update_refs(d, baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix):
if isinstance(d, MutableSequence):
MaxProbesPerSecond int
MaxConcurrentInstanceCreateOps int
MaxInstances int
+ InitialQuotaEstimate int
SupervisorFraction float64
PollInterval Duration
ProbeInterval Duration
Installing under your user account
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-This method lets you install the package without root access.
-However, other users on the same system won't be able to use it.
+This method lets you install the package without root access. However,
+other users on the same system will need to reconfigure their shell in order
+to be able to use it. Run the following to install the package in an
+environment at ``~/arvclients``::
-1. Run ``pip install --user arvados-python-client``.
+ python3 -m venv ~/arvclients
+ ~/arvclients/bin/pip install arvados-python-client
-2. In your shell configuration, make sure you add ``$HOME/.local/bin``
- to your PATH environment variable. For example, you could add the
- command ``PATH=$PATH:$HOME/.local/bin`` to your ``.bashrc`` file.
+Command line tools will be installed under ``~/arvclients/bin``. You can
+test one by running::
-3. Reload your shell configuration. For example, bash users could run
- ``source ~/.bashrc``.
+ ~/arvclients/bin/arv-get --version
+
+You can run these tools by specifying the full path every time, or you can
+add the directory to your shell's search path by running::
+
+ export PATH="$PATH:$HOME/arvclients/bin"
+
+You can make this search path change permanent by adding this command to
+your shell's configuration, for example ``~/.bashrc`` if you're using bash.
+You can test the change by running::
+
+ arv-get --version
Installing on Debian systems
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
import re
def escape(path):
- path = re.sub('\\\\', lambda m: '\\134', path)
- path = re.sub('[:\000-\040]', lambda m: "\\%03o" % ord(m.group(0)), path)
- return path
+ return re.sub(r'[\\:\000-\040]', lambda m: "\\%03o" % ord(m.group(0)), path)
def normalize_stream(stream_name, stream):
"""Take manifest stream and return a list of tokens in normalized format.
yield data
def decompressed_name(self):
- return re.sub('\.(bz2|gz)$', '', self.name)
+ return re.sub(r'\.(bz2|gz)$', '', self.name)
@_FileLikeObjectBase._before_close
def seek(self, pos, whence=os.SEEK_SET):
_segment_re = re.compile(r'(\d+):(\d+):(\S+)')
def _unescape_manifest_path(self, path):
- return re.sub('\\\\([0-3][0-7][0-7])', lambda m: chr(int(m.group(1), 8)), path)
+ return re.sub(r'\\([0-3][0-7][0-7])', lambda m: chr(int(m.group(1), 8)), path)
@synchronized
def _import_manifest(self, manifest_text):
cfg = {}
with open(config_file, "r") as f:
for config_line in f:
- if re.match('^\s*$', config_line):
- continue
- if re.match('^\s*#', config_line):
+ if re.match(r'^\s*(?:#|$)', config_line):
continue
var, val = config_line.rstrip().split('=', 2)
cfg[var] = val
os.unlink(os.path.join(path, '.locator'))
for f in CollectionReader(tarball).all_files():
- if re.search('\.(tbz|tar.bz2)$', f.name()):
+ f_name = f.name()
+ if f_name.endswith(('.tbz', '.tar.bz2')):
p = tar_extractor(path, 'j')
- elif re.search('\.(tgz|tar.gz)$', f.name()):
+ elif f_name.endswith(('.tgz', '.tar.gz')):
p = tar_extractor(path, 'z')
- elif re.search('\.tar$', f.name()):
+ elif f_name.endswith('.tar'):
p = tar_extractor(path, '')
else:
raise arvados.errors.AssertionError(
os.unlink(os.path.join(path, '.locator'))
for f in CollectionReader(zipball).all_files():
- if not re.search('\.zip$', f.name()):
+ if not f.name().endswith('.zip'):
raise arvados.errors.NotImplementedError(
"zipball_extract cannot handle filename %s" % f.name())
zip_filename = os.path.join(path, os.path.basename(f.name()))
import glob
import httplib2
import os
-import pipes
import random
import re
+import shlex
import shutil
import signal
import socket
resdir = subprocess.check_output(['bundle', 'exec', 'passenger-config', 'about', 'resourcesdir']).decode().rstrip()
with open(resdir + '/templates/standalone/config.erb') as f:
template = f.read()
- newtemplate = re.sub('http {', 'http {\n passenger_stat_throttle_rate 0;', template)
+ newtemplate = re.sub(r'http \{', 'http {\n passenger_stat_throttle_rate 0;', template)
if newtemplate == template:
raise "template edit failed"
with open('tmp/passenger-nginx.conf.erb', 'w') as f:
host = os.environ['ARVADOS_API_HOST']
if args.auth is not None:
token = auth_token(args.auth)
- print("export ARVADOS_API_TOKEN={}".format(pipes.quote(token)))
- print("export ARVADOS_API_HOST={}".format(pipes.quote(host)))
+ print("export ARVADOS_API_TOKEN={}".format(shlex.quote(token)))
+ print("export ARVADOS_API_HOST={}".format(shlex.quote(host)))
print("export ARVADOS_API_HOST_INSECURE=true")
else:
print(host)
def test_get_block(self):
# Get raw data using a block locator
- blk = re.search(' (acbd18\S+\+A\S+) ', self.col_manifest).group(1)
+ blk = re.search(r' (acbd18\S+\+A\S+) ', self.col_manifest).group(1)
r = self.run_get([blk, '-'])
self.assertEqual(0, r)
self.assertEqual(b'foo', self.stdout.getvalue())
# Ensure stripped_manifest() doesn't mangle our manifest in
# any way other than stripping hints.
self.assertEqual(
- re.sub('\+[^\d\s\+]+', '', nonnormal),
+ re.sub(r'\+[^\d\s\+]+', '', nonnormal),
reader.stripped_manifest())
# Ensure stripped_manifest() didn't mutate our reader.
self.assertEqual(nonnormal, reader.manifest_text())
fpm_depends+=('git >= 1.7.10')
case "$TARGET" in
- centos*)
+ centos*|rocky*)
fpm_depends+=(libcurl-devel postgresql-devel bison make automake gcc gcc-c++ postgresql shared-mime-info)
;;
ubuntu1804)
+++ /dev/null
-crunchstat
+++ /dev/null
-// Copyright (C) The Arvados Authors. All rights reserved.
-//
-// SPDX-License-Identifier: AGPL-3.0
-
-package main
-
-import (
- "bufio"
- "flag"
- "fmt"
- "io"
- "log"
- "os"
- "os/exec"
- "os/signal"
- "syscall"
- "time"
-
- "git.arvados.org/arvados.git/lib/cmd"
- "git.arvados.org/arvados.git/lib/crunchstat"
-)
-
-const MaxLogLine = 1 << 14 // Child stderr lines >16KiB will be split
-
-var (
- signalOnDeadPPID int = 15
- ppidCheckInterval = time.Second
- version = "dev"
-)
-
-type logger interface {
- Printf(string, ...interface{})
-}
-
-func main() {
- reporter := crunchstat.Reporter{
- Logger: log.New(os.Stderr, "crunchstat: ", 0),
- }
-
- flags := flag.NewFlagSet(os.Args[0], flag.ExitOnError)
- flags.StringVar(&reporter.CgroupRoot, "cgroup-root", "", "Root of cgroup tree")
- flags.StringVar(&reporter.CgroupParent, "cgroup-parent", "", "Name of container parent under cgroup")
- flags.StringVar(&reporter.CIDFile, "cgroup-cid", "", "Path to container id file")
- flags.IntVar(&signalOnDeadPPID, "signal-on-dead-ppid", signalOnDeadPPID, "Signal to send child if crunchstat's parent process disappears (0 to disable)")
- flags.DurationVar(&ppidCheckInterval, "ppid-check-interval", ppidCheckInterval, "Time between checks for parent process disappearance")
- pollMsec := flags.Int64("poll", 1000, "Reporting interval, in milliseconds")
- getVersion := flags.Bool("version", false, "Print version information and exit.")
-
- if ok, code := cmd.ParseFlags(flags, os.Args[0], os.Args[1:], "program [args ...]", os.Stderr); !ok {
- os.Exit(code)
- } else if *getVersion {
- fmt.Printf("crunchstat %s\n", version)
- return
- } else if flags.NArg() == 0 {
- fmt.Fprintf(os.Stderr, "missing required argument: program (try -help)\n")
- os.Exit(2)
- }
-
- reporter.Logger.Printf("crunchstat %s started", version)
-
- if reporter.CgroupRoot == "" {
- reporter.Logger.Printf("error: must provide -cgroup-root")
- os.Exit(2)
- } else if signalOnDeadPPID < 0 {
- reporter.Logger.Printf("-signal-on-dead-ppid=%d is invalid (use a positive signal number, or 0 to disable)", signalOnDeadPPID)
- os.Exit(2)
- }
- reporter.PollPeriod = time.Duration(*pollMsec) * time.Millisecond
-
- reporter.Start()
- err := runCommand(flags.Args(), reporter.Logger)
- reporter.Stop()
-
- if err, ok := err.(*exec.ExitError); ok {
- // The program has exited with an exit code != 0
-
- // This works on both Unix and Windows. Although
- // package syscall is generally platform dependent,
- // WaitStatus is defined for both Unix and Windows and
- // in both cases has an ExitStatus() method with the
- // same signature.
- if status, ok := err.Sys().(syscall.WaitStatus); ok {
- os.Exit(status.ExitStatus())
- } else {
- reporter.Logger.Printf("ExitError without WaitStatus: %v", err)
- os.Exit(1)
- }
- } else if err != nil {
- reporter.Logger.Printf("error running command: %v", err)
- os.Exit(1)
- }
-}
-
-func runCommand(argv []string, logger logger) error {
- cmd := exec.Command(argv[0], argv[1:]...)
-
- logger.Printf("Running %v", argv)
-
- // Child process will use our stdin and stdout pipes
- // (we close our copies below)
- cmd.Stdin = os.Stdin
- cmd.Stdout = os.Stdout
-
- // Forward SIGINT and SIGTERM to child process
- sigChan := make(chan os.Signal, 1)
- go func(sig <-chan os.Signal) {
- catch := <-sig
- if cmd.Process != nil {
- cmd.Process.Signal(catch)
- }
- logger.Printf("notice: caught signal: %v", catch)
- }(sigChan)
- signal.Notify(sigChan, syscall.SIGTERM)
- signal.Notify(sigChan, syscall.SIGINT)
-
- // Kill our child proc if our parent process disappears
- if signalOnDeadPPID != 0 {
- go sendSignalOnDeadPPID(ppidCheckInterval, signalOnDeadPPID, os.Getppid(), cmd, logger)
- }
-
- // Funnel stderr through our channel
- stderrPipe, err := cmd.StderrPipe()
- if err != nil {
- logger.Printf("error in StderrPipe: %v", err)
- return err
- }
-
- // Run subprocess
- if err := cmd.Start(); err != nil {
- logger.Printf("error in cmd.Start: %v", err)
- return err
- }
-
- // Close stdin/stdout in this (parent) process
- os.Stdin.Close()
- os.Stdout.Close()
-
- err = copyPipeToChildLog(stderrPipe, log.New(os.Stderr, "", 0))
- if err != nil {
- cmd.Process.Kill()
- return err
- }
-
- return cmd.Wait()
-}
-
-func sendSignalOnDeadPPID(intvl time.Duration, signum, ppidOrig int, cmd *exec.Cmd, logger logger) {
- ticker := time.NewTicker(intvl)
- for range ticker.C {
- ppid := os.Getppid()
- if ppid == ppidOrig {
- continue
- }
- if cmd.Process == nil {
- // Child process isn't running yet
- continue
- }
- logger.Printf("notice: crunchstat ppid changed from %d to %d -- killing child pid %d with signal %d", ppidOrig, ppid, cmd.Process.Pid, signum)
- err := cmd.Process.Signal(syscall.Signal(signum))
- if err != nil {
- logger.Printf("error: sending signal: %s", err)
- continue
- }
- ticker.Stop()
- break
- }
-}
-
-func copyPipeToChildLog(in io.ReadCloser, logger logger) error {
- reader := bufio.NewReaderSize(in, MaxLogLine)
- var prefix string
- for {
- line, isPrefix, err := reader.ReadLine()
- if err == io.EOF {
- break
- } else if err != nil {
- return fmt.Errorf("error reading child stderr: %w", err)
- }
- var suffix string
- if isPrefix {
- suffix = "[...]"
- }
- logger.Printf("%s%s%s", prefix, string(line), suffix)
- // Set up prefix for following line
- if isPrefix {
- prefix = "[...]"
- } else {
- prefix = ""
- }
- }
- return in.Close()
-}
+++ /dev/null
-// Copyright (C) The Arvados Authors. All rights reserved.
-//
-// SPDX-License-Identifier: AGPL-3.0
-
-package main
-
-import (
- "bufio"
- "bytes"
- "fmt"
- "io"
- "io/ioutil"
- "log"
- "math/rand"
- "os"
- "os/exec"
- "sync"
- "syscall"
- "testing"
- "time"
-)
-
-// Test that CopyPipeToChildLog works even on lines longer than
-// bufio.MaxScanTokenSize.
-func TestCopyPipeToChildLogLongLines(t *testing.T) {
- logger, logBuf := bufLogger()
-
- pipeIn, pipeOut := io.Pipe()
- copied := make(chan bool)
- go func() {
- copyPipeToChildLog(pipeIn, logger)
- close(copied)
- }()
-
- sentBytes := make([]byte, bufio.MaxScanTokenSize+MaxLogLine+(1<<22))
- go func() {
- pipeOut.Write([]byte("before\n"))
-
- for i := range sentBytes {
- // Some bytes that aren't newlines:
- sentBytes[i] = byte((rand.Int() & 0xff) | 0x80)
- }
- sentBytes[len(sentBytes)-1] = '\n'
- pipeOut.Write(sentBytes)
-
- pipeOut.Write([]byte("after"))
- pipeOut.Close()
- }()
-
- if before, err := logBuf.ReadBytes('\n'); err != nil || string(before) != "before\n" {
- t.Fatalf("\"before\n\" not received (got \"%s\", %s)", before, err)
- }
-
- var receivedBytes []byte
- done := false
- for !done {
- line, err := logBuf.ReadBytes('\n')
- if err != nil {
- t.Fatal(err)
- }
- if len(line) >= 5 && string(line[0:5]) == "[...]" {
- if receivedBytes == nil {
- t.Fatal("Beginning of line reported as continuation")
- }
- line = line[5:]
- }
- if len(line) >= 6 && string(line[len(line)-6:]) == "[...]\n" {
- line = line[:len(line)-6]
- } else {
- done = true
- }
- receivedBytes = append(receivedBytes, line...)
- }
- if bytes.Compare(receivedBytes, sentBytes) != 0 {
- t.Fatalf("sent %d bytes, got %d different bytes", len(sentBytes), len(receivedBytes))
- }
-
- if after, err := logBuf.ReadBytes('\n'); err != nil || string(after) != "after\n" {
- t.Fatalf("\"after\n\" not received (got \"%s\", %s)", after, err)
- }
-
- select {
- case <-time.After(time.Second):
- t.Fatal("Timeout")
- case <-copied:
- // Done.
- }
-}
-
-func bufLogger() (*log.Logger, *bufio.Reader) {
- r, w := io.Pipe()
- logger := log.New(w, "", 0)
- return logger, bufio.NewReader(r)
-}
-
-func TestSignalOnDeadPPID(t *testing.T) {
- if !testDeadParent(t, 0) {
- t.Fatal("child should still be alive after parent dies")
- }
- if testDeadParent(t, 15) {
- t.Fatal("child should have been killed when parent died")
- }
-}
-
-// testDeadParent returns true if crunchstat's child proc is still
-// alive after its parent dies.
-func testDeadParent(t *testing.T, signum int) bool {
- var err error
- var bin, childlockfile, parentlockfile *os.File
- for _, f := range []**os.File{&bin, &childlockfile, &parentlockfile} {
- *f, err = ioutil.TempFile("", "crunchstat_")
- if err != nil {
- t.Fatal(err)
- }
- defer (*f).Close()
- defer os.Remove((*f).Name())
- }
-
- bin.Close()
- err = exec.Command("go", "build", "-o", bin.Name()).Run()
- if err != nil {
- t.Fatal(err)
- }
-
- err = syscall.Flock(int(parentlockfile.Fd()), syscall.LOCK_EX)
- if err != nil {
- t.Fatal(err)
- }
-
- cmd := exec.Command("bash", "-c", `
-set -e
-"$BINFILE" -cgroup-root=/none -ppid-check-interval=10ms -signal-on-dead-ppid="$SIGNUM" bash -c '
- set -e
- unlock() {
- flock --unlock "$CHILDLOCKFD"
- kill %1
- }
- trap unlock TERM
- flock --exclusive "$CHILDLOCKFD"
- echo -n "$$" > "$CHILDLOCKFILE"
- flock --unlock "$PARENTLOCKFD"
- sleep 20 </dev/null >/dev/null 2>/dev/null &
- wait %1
- unlock
-' &
-
-# wait for inner bash to start, to ensure $BINFILE has seen this bash proc as its initial PPID
-flock --exclusive "$PARENTLOCKFILE" true
-`)
- cmd.Env = append(os.Environ(),
- "SIGNUM="+fmt.Sprintf("%d", signum),
- "PARENTLOCKFD=3",
- "PARENTLOCKFILE="+parentlockfile.Name(),
- "CHILDLOCKFD=4",
- "CHILDLOCKFILE="+childlockfile.Name(),
- "BINFILE="+bin.Name())
- cmd.ExtraFiles = []*os.File{parentlockfile, childlockfile}
- stderr, err := cmd.StderrPipe()
- if err != nil {
- t.Fatal(err)
- }
- stdout, err := cmd.StdoutPipe()
- if err != nil {
- t.Fatal(err)
- }
- cmd.Start()
- defer cmd.Wait()
-
- var wg sync.WaitGroup
- wg.Add(2)
- defer wg.Wait()
- for _, rdr := range []io.ReadCloser{stderr, stdout} {
- go func(rdr io.ReadCloser) {
- defer wg.Done()
- buf := make([]byte, 1024)
- for {
- n, err := rdr.Read(buf)
- if n > 0 {
- t.Logf("%s", buf[:n])
- }
- if err != nil {
- return
- }
- }
- }(rdr)
- }
-
- // Wait until inner bash process releases parentlockfile
- // (which means it has locked childlockfile and written its
- // PID)
- err = exec.Command("flock", "--exclusive", parentlockfile.Name(), "true").Run()
- if err != nil {
- t.Fatal(err)
- }
-
- childDone := make(chan bool)
- go func() {
- // Notify the main thread when the inner bash process
- // releases its lock on childlockfile (which means
- // either its sleep process ended or it received a
- // TERM signal).
- t0 := time.Now()
- err = exec.Command("flock", "--exclusive", childlockfile.Name(), "true").Run()
- if err != nil {
- t.Fatal(err)
- }
- t.Logf("child done after %s", time.Since(t0))
- close(childDone)
- }()
-
- select {
- case <-time.After(500 * time.Millisecond):
- // Inner bash process is still alive after the timeout
- // period. Kill it now, so our stdout and stderr pipes
- // can finish and we don't leave a mess of child procs
- // behind.
- buf, err := ioutil.ReadFile(childlockfile.Name())
- if err != nil {
- t.Fatal(err)
- }
- var childPID int
- _, err = fmt.Sscanf(string(buf), "%d", &childPID)
- if err != nil {
- t.Fatal(err)
- }
- child, err := os.FindProcess(childPID)
- if err != nil {
- t.Fatal(err)
- }
- child.Signal(syscall.Signal(15))
- return true
-
- case <-childDone:
- // Inner bash process ended soon after its grandparent
- // ended.
- return false
- }
-}
Installing under your user account
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-This method lets you install the package without root access.
-However, other users on the same system won't be able to use it.
+This method lets you install the package without root access. However,
+other users on the same system will need to reconfigure their shell in order
+to be able to use it. Run the following to install the package in an
+environment at ``~/arvclients``::
-1. Run ``pip install --user arvados_fuse``.
+ python3 -m venv ~/arvclients
+ ~/arvclients/bin/pip install arvados_fuse
-2. In your shell configuration, make sure you add ``$HOME/.local/bin``
- to your PATH environment variable. For example, you could add the
- command ``PATH=$PATH:$HOME/.local/bin`` to your ``.bashrc`` file.
+Command line tools will be installed under ``~/arvclients/bin``. You can
+test one by running::
-3. Reload your shell configuration. For example, bash users could run
- ``source ~/.bashrc``.
+ ~/arvclients/bin/arv-mount --version
+
+You can run these tools by specifying the full path every time, or you can
+add the directory to your shell's search path by running::
+
+ export PATH="$PATH:$HOME/arvclients/bin"
+
+You can make this search path change permanent by adding this command to
+your shell's configuration, for example ``~/.bashrc`` if you're using bash.
+You can test the change by running::
+
+ arv-mount --version
Installing on Debian systems
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Match any character which FUSE or Linux cannot accommodate as part
# of a filename. (If present in a collection filename, they will
# appear as underscores in the fuse mount.)
-_disallowed_filename_characters = re.compile('[\x00/]')
+_disallowed_filename_characters = re.compile(r'[\x00/]')
class Directory(FreshBase):
fpm_depends+=(fuse)
case "$TARGET" in
- centos*)
+ centos*|rocky*)
fpm_depends+=(fuse-libs)
;;
debian* | ubuntu*)
import multiprocessing
import os
from . import run_test_server
+import shlex
import tempfile
import unittest
from .integration_test import workerPool
-try:
- from shlex import quote
-except:
- from pipes import quote
-
def try_exec(mnt, cmd):
try:
os.environ['KEEP_LOCAL_STORE'] = tempfile.mkdtemp()
def test_exec(self):
workerPool().apply(try_exec, (self.mnt, [
- 'sh', '-c',
- 'echo -n foo >{}; cp {} {}'.format(
- quote(os.path.join(self.mnt, 'zzz', 'foo.txt')),
- quote(os.path.join(self.mnt, 'zzz', '.arvados#collection')),
- quote(os.path.join(self.okfile)))]))
+ 'sh', '-c', 'echo -n foo >{}; cp {} {}'.format(
+ shlex.quote(os.path.join(self.mnt, 'zzz', 'foo.txt')),
+ shlex.quote(os.path.join(self.mnt, 'zzz', '.arvados#collection')),
+ shlex.quote(os.path.join(self.okfile)),
+ )]))
with open(self.okfile) as f:
assertRegex(
self,
import (
"errors"
"net/http"
+ "sort"
"sync"
- "sync/atomic"
"time"
"git.arvados.org/arvados.git/sdk/go/arvados"
"git.arvados.org/arvados.git/sdk/go/arvadosclient"
"git.arvados.org/arvados.git/sdk/go/keepclient"
- lru "github.com/hashicorp/golang-lru"
"github.com/prometheus/client_golang/prometheus"
"github.com/sirupsen/logrus"
)
logger logrus.FieldLogger
registry *prometheus.Registry
metrics cacheMetrics
- sessions *lru.TwoQueueCache
+ sessions map[string]*cachedSession
setupOnce sync.Once
+ mtx sync.Mutex
chPruneSessions chan struct{}
}
}
type cachedSession struct {
+ cache *cache
expire time.Time
- fs atomic.Value
client *arvados.Client
arvadosclient *arvadosclient.ArvadosClient
keepclient *keepclient.KeepClient
- user atomic.Value
+
+ // Each session uses a system of three mutexes (plus the
+ // cache-wide mutex) to enable the following semantics:
+ //
+ // - There are never multiple sessions in use for a given
+ // token.
+ //
+ // - If the cached in-memory filesystems/user records are
+ // older than the configured cache TTL when a request starts,
+ // the request will use new ones.
+ //
+ // - Unused sessions are garbage-collected.
+ //
+ // In particular, when it is necessary to reset a session's
+ // filesystem/user record (to save memory or respect the
+ // configured cache TTL), any operations that are already
+ // using the existing filesystem/user record are allowed to
+ // finish before the new filesystem is constructed.
+ //
+ // The locks must be acquired in the following order:
+ // cache.mtx, session.mtx, session.refresh, session.inuse.
+
+ // mtx is RLocked while session is not safe to evict from
+ // cache -- i.e., a checkout() has decided to use it, and its
+ // caller is not finished with it. When locking or rlocking
+ // this mtx, the cache mtx MUST already be held.
+ //
+ // This mutex enables pruneSessions to detect when it is safe
+ // to completely remove the session entry from the cache.
+ mtx sync.RWMutex
+ // refresh must be locked in order to read or write the
+ // fs/user/userLoaded/lastuse fields. This mutex enables
+ // GetSession and pruneSessions to remove/replace fs and user
+ // values safely.
+ refresh sync.Mutex
+ // inuse must be RLocked while the session is in use by a
+ // caller. This mutex enables pruneSessions() to wait for all
+ // existing usage to finish by calling inuse.Lock().
+ inuse sync.RWMutex
+
+ fs arvados.CustomFileSystem
+ user arvados.User
+ userLoaded bool
+ lastuse time.Time
+}
+
+func (sess *cachedSession) Release() {
+ sess.inuse.RUnlock()
+ sess.mtx.RUnlock()
+ select {
+ case sess.cache.chPruneSessions <- struct{}{}:
+ default:
+ }
}
func (c *cache) setup() {
var err error
- c.sessions, err = lru.New2Q(c.cluster.Collections.WebDAVCache.MaxSessions)
+ c.sessions = map[string]*cachedSession{}
if err != nil {
panic(err)
}
}
func (c *cache) updateGauges() {
- c.metrics.collectionBytes.Set(float64(c.collectionBytes()))
- c.metrics.sessionEntries.Set(float64(c.sessions.Len()))
+ n, size := c.sessionsSize()
+ c.metrics.collectionBytes.Set(float64(size))
+ c.metrics.sessionEntries.Set(float64(n))
}
var selectPDH = map[string]interface{}{
"select": []string{"portable_data_hash"},
}
-// ResetSession unloads any potentially stale state. Should be called
-// after write operations, so subsequent reads don't return stale
-// data.
-func (c *cache) ResetSession(token string) {
- c.setupOnce.Do(c.setup)
- c.sessions.Remove(token)
-}
-
-// Get a long-lived CustomFileSystem suitable for doing a read operation
-// with the given token.
-func (c *cache) GetSession(token string) (arvados.CustomFileSystem, *cachedSession, *arvados.User, error) {
+func (c *cache) checkout(token string) (*cachedSession, error) {
c.setupOnce.Do(c.setup)
- now := time.Now()
- ent, _ := c.sessions.Get(token)
- sess, _ := ent.(*cachedSession)
- expired := false
+ c.mtx.Lock()
+ defer c.mtx.Unlock()
+ sess := c.sessions[token]
if sess == nil {
- c.metrics.sessionMisses.Inc()
- sess = &cachedSession{
- expire: now.Add(c.cluster.Collections.WebDAVCache.TTL.Duration()),
- }
- var err error
- sess.client, err = arvados.NewClientFromConfig(c.cluster)
+ client, err := arvados.NewClientFromConfig(c.cluster)
if err != nil {
- return nil, nil, nil, err
+ return nil, err
}
- sess.client.AuthToken = token
- sess.client.Timeout = time.Minute
+ client.AuthToken = token
+ client.Timeout = time.Minute
// A non-empty origin header tells controller to
// prioritize our traffic as interactive, which is
// true most of the time.
origin := c.cluster.Services.WebDAVDownload.ExternalURL
- sess.client.SendHeader = http.Header{"Origin": {origin.Scheme + "://" + origin.Host}}
- sess.arvadosclient, err = arvadosclient.New(sess.client)
+ client.SendHeader = http.Header{"Origin": {origin.Scheme + "://" + origin.Host}}
+ arvadosclient, err := arvadosclient.New(client)
if err != nil {
- return nil, nil, nil, err
+ return nil, err
}
- sess.keepclient = keepclient.New(sess.arvadosclient)
- c.sessions.Add(token, sess)
- } else if sess.expire.Before(now) {
- c.metrics.sessionMisses.Inc()
- expired = true
- } else {
- c.metrics.sessionHits.Inc()
- }
- select {
- case c.chPruneSessions <- struct{}{}:
- default:
+ sess = &cachedSession{
+ cache: c,
+ client: client,
+ arvadosclient: arvadosclient,
+ keepclient: keepclient.New(arvadosclient),
+ }
+ c.sessions[token] = sess
}
+ sess.mtx.RLock()
+ return sess, nil
+}
- fs, _ := sess.fs.Load().(arvados.CustomFileSystem)
- if fs == nil || expired {
- fs = sess.client.SiteFileSystem(sess.keepclient)
- fs.ForwardSlashNameSubstitution(c.cluster.Collections.ForwardSlashNameSubstitution)
- sess.fs.Store(fs)
+// Get a long-lived CustomFileSystem suitable for doing a read or
+// write operation with the given token.
+//
+// If the returned error is nil, the caller must call Release() on the
+// returned session when finished using it.
+func (c *cache) GetSession(token string) (arvados.CustomFileSystem, *cachedSession, *arvados.User, error) {
+ sess, err := c.checkout(token)
+ if err != nil {
+ return nil, nil, nil, err
}
+ sess.refresh.Lock()
+ defer sess.refresh.Unlock()
+ now := time.Now()
+ sess.lastuse = now
+ refresh := sess.expire.Before(now)
+ if sess.fs == nil || !sess.userLoaded || refresh {
+ // Wait for all active users to finish (otherwise they
+ // might make changes to an old fs after we start
+ // using the new fs).
+ sess.inuse.Lock()
+ if !sess.userLoaded || refresh {
+ err := sess.client.RequestAndDecode(&sess.user, "GET", "/arvados/v1/users/current", nil, nil)
+ if he := errorWithHTTPStatus(nil); errors.As(err, &he) && he.HTTPStatus() == http.StatusForbidden {
+ // token is OK, but "get user id" api is out
+ // of scope -- use existing/expired info if
+ // any, or leave empty for unknown user
+ } else if err != nil {
+ sess.inuse.Unlock()
+ sess.mtx.RUnlock()
+ return nil, nil, nil, err
+ }
+ sess.userLoaded = true
+ }
- user, _ := sess.user.Load().(*arvados.User)
- if user == nil || expired {
- user = new(arvados.User)
- err := sess.client.RequestAndDecode(user, "GET", "/arvados/v1/users/current", nil, nil)
- if he := errorWithHTTPStatus(nil); errors.As(err, &he) && he.HTTPStatus() == http.StatusForbidden {
- // token is OK, but "get user id" api is out
- // of scope -- return nil, signifying unknown
- // user
- } else if err != nil {
- return nil, nil, nil, err
+ if sess.fs == nil || refresh {
+ sess.fs = sess.client.SiteFileSystem(sess.keepclient)
+ sess.fs.ForwardSlashNameSubstitution(c.cluster.Collections.ForwardSlashNameSubstitution)
+ sess.expire = now.Add(c.cluster.Collections.WebDAVCache.TTL.Duration())
+ c.metrics.sessionMisses.Inc()
+ } else {
+ c.metrics.sessionHits.Inc()
}
- sess.user.Store(user)
+ sess.inuse.Unlock()
+ } else {
+ c.metrics.sessionHits.Inc()
}
+ sess.inuse.RLock()
+ return sess.fs, sess, &sess.user, nil
+}
- return fs, sess, user, nil
+type sessionSnapshot struct {
+ token string
+ sess *cachedSession
+ lastuse time.Time
+ fs arvados.CustomFileSystem
+ size int64
+ prune bool
}
-// Remove all expired session cache entries, then remove more entries
-// until approximate remaining size <= maxsize/2
+// Remove all expired idle session cache entries, and remove in-memory
+// filesystems until approximate remaining size <= maxsize
func (c *cache) pruneSessions() {
now := time.Now()
- keys := c.sessions.Keys()
- sizes := make([]int64, len(keys))
+ c.mtx.Lock()
+ snaps := make([]sessionSnapshot, 0, len(c.sessions))
+ for token, sess := range c.sessions {
+ snaps = append(snaps, sessionSnapshot{
+ token: token,
+ sess: sess,
+ })
+ }
+ c.mtx.Unlock()
+
+ // Load lastuse/fs/expire data from sessions. Note we do this
+ // after unlocking c.mtx because sess.refresh.Lock sometimes
+ // waits for another goroutine to finish "[re]fetch user
+ // record".
+ for i := range snaps {
+ snaps[i].sess.refresh.Lock()
+ snaps[i].lastuse = snaps[i].sess.lastuse
+ snaps[i].fs = snaps[i].sess.fs
+ snaps[i].prune = snaps[i].sess.expire.Before(now)
+ snaps[i].sess.refresh.Unlock()
+ }
+
+ // Sort sessions with oldest first.
+ sort.Slice(snaps, func(i, j int) bool {
+ return snaps[i].lastuse.Before(snaps[j].lastuse)
+ })
+
+ // Add up size of sessions that aren't already marked for
+ // pruning based on expire time.
var size int64
- for i, token := range keys {
- ent, ok := c.sessions.Peek(token)
- if !ok {
- continue
+ for i, snap := range snaps {
+ if !snap.prune && snap.fs != nil {
+ size := snap.fs.MemorySize()
+ snaps[i].size = size
+ size += size
+ }
+ }
+ // Mark more sessions for deletion until reaching desired
+ // memory size limit, starting with the oldest entries.
+ for i, snap := range snaps {
+ if size <= c.cluster.Collections.WebDAVCache.MaxCollectionBytes {
+ break
}
- s := ent.(*cachedSession)
- if s.expire.Before(now) {
- c.sessions.Remove(token)
+ if snap.prune {
continue
}
- if fs, ok := s.fs.Load().(arvados.CustomFileSystem); ok {
- sizes[i] = fs.MemorySize()
- size += sizes[i]
+ snaps[i].prune = true
+ size -= snap.size
+ }
+
+ // Mark more sessions for deletion until reaching desired
+ // session count limit.
+ mustprune := len(snaps) - c.cluster.Collections.WebDAVCache.MaxSessions
+ for i := range snaps {
+ if snaps[i].prune {
+ mustprune--
}
}
- // Remove tokens until reaching size limit, starting with the
- // least frequently used entries (which Keys() returns last).
- for i := len(keys) - 1; i >= 0 && size > c.cluster.Collections.WebDAVCache.MaxCollectionBytes; i-- {
- if sizes[i] > 0 {
- c.sessions.Remove(keys[i])
- size -= sizes[i]
+ for i := range snaps {
+ if mustprune < 1 {
+ break
+ } else if !snaps[i].prune {
+ snaps[i].prune = true
+ mustprune--
}
}
-}
-// collectionBytes returns the approximate combined memory size of the
-// collection cache and session filesystem cache.
-func (c *cache) collectionBytes() uint64 {
- var size uint64
- for _, token := range c.sessions.Keys() {
- ent, ok := c.sessions.Peek(token)
- if !ok {
+ c.mtx.Lock()
+ defer c.mtx.Unlock()
+ for _, snap := range snaps {
+ if !snap.prune {
continue
}
- if fs, ok := ent.(*cachedSession).fs.Load().(arvados.CustomFileSystem); ok {
- size += uint64(fs.MemorySize())
+ sess := snap.sess
+ if sess.mtx.TryLock() {
+ delete(c.sessions, snap.token)
+ continue
+ }
+ // We can't remove a session that's been checked out
+ // -- that would allow another session to be created
+ // for the same token using a different in-memory
+ // filesystem. Instead, we wait for active requests to
+ // finish and then "unload" it. After this, either the
+ // next GetSession will reload fs/user, or a
+ // subsequent pruneSessions will remove the session.
+ go func() {
+ // Ensure nobody is mid-GetSession() (note we
+ // already know nobody is mid-checkout()
+ // because we have c.mtx locked)
+ sess.refresh.Lock()
+ defer sess.refresh.Unlock()
+ // Wait for current usage to finish (i.e.,
+ // anyone who has decided to use the current
+ // values of sess.fs and sess.user, and hasn't
+ // called Release() yet)
+ sess.inuse.Lock()
+ defer sess.inuse.Unlock()
+ // Release memory
+ sess.fs = nil
+ // Next GetSession will make a new fs
+ }()
+ }
+}
+
+// sessionsSize returns the number and approximate total memory size
+// of all cached sessions.
+func (c *cache) sessionsSize() (n int, size int64) {
+ c.mtx.Lock()
+ n = len(c.sessions)
+ sessions := make([]*cachedSession, 0, n)
+ for _, sess := range c.sessions {
+ sessions = append(sessions, sess)
+ }
+ c.mtx.Unlock()
+ for _, sess := range sessions {
+ sess.refresh.Lock()
+ fs := sess.fs
+ sess.refresh.Unlock()
+ if fs != nil {
+ size += fs.MemorySize()
}
}
- return size
+ return
}
# SPDX-License-Identifier: AGPL-3.0
case "$TARGET" in
- centos*)
+ centos*|rocky*)
fpm_depends+=(mailcap)
;;
debian* | ubuntu*)
"strconv"
"strings"
"sync"
+ "time"
"git.arvados.org/arvados.git/lib/cmd"
"git.arvados.org/arvados.git/lib/webdavfs"
Cache cache
Cluster *arvados.Cluster
setupOnce sync.Once
+
+ lockMtx sync.Mutex
+ lock map[string]*sync.RWMutex
+ lockTidied time.Time
}
var urlPDHDecoder = strings.NewReplacer(" ", "+", "-", "+")
// collection id is outside scope of supplied
// token
tokenScopeProblem = true
+ sess.Release()
continue
} else if os.IsNotExist(err) {
// collection does not exist or is not
// readable using this token
+ sess.Release()
continue
} else if err != nil {
http.Error(w, err.Error(), http.StatusInternalServerError)
+ sess.Release()
return
}
defer f.Close()
+ defer sess.Release()
collectionDir, sessionFS, session, tokenUser = f, fs, sess, user
break
}
h.logUploadOrDownload(r, session.arvadosclient, sessionFS, fsprefix+strings.Join(targetPath, "/"), nil, tokenUser)
- if writeMethod[r.Method] {
+ writing := writeMethod[r.Method]
+ locker := h.collectionLock(collectionID, writing)
+ defer locker.Unlock()
+
+ if writing {
// Save the collection only if/when all
// webdav->filesystem operations succeed --
// and send a 500 error if the modified
return nil, ""
}
+var lockTidyInterval = time.Minute * 10
+
+// Lock the specified collection for reading or writing. Caller must
+// call Unlock() on the returned Locker when the operation is
+// finished.
+func (h *handler) collectionLock(collectionID string, writing bool) sync.Locker {
+ h.lockMtx.Lock()
+ defer h.lockMtx.Unlock()
+ if time.Since(h.lockTidied) > lockTidyInterval {
+ // Periodically delete all locks that aren't in use.
+ h.lockTidied = time.Now()
+ for id, locker := range h.lock {
+ if locker.TryLock() {
+ locker.Unlock()
+ delete(h.lock, id)
+ }
+ }
+ }
+ locker := h.lock[collectionID]
+ if locker == nil {
+ locker = new(sync.RWMutex)
+ if h.lock == nil {
+ h.lock = map[string]*sync.RWMutex{}
+ }
+ h.lock[collectionID] = locker
+ }
+ if writing {
+ locker.Lock()
+ return locker
+ } else {
+ locker.RLock()
+ return locker.RLocker()
+ }
+}
+
func ServeCORSPreflight(w http.ResponseWriter, header http.Header) bool {
method := header.Get("Access-Control-Request-Method")
if method == "" {
"path/filepath"
"regexp"
"strings"
+ "sync"
"time"
"git.arvados.org/arvados.git/lib/config"
}
}
}
+
+func (s *IntegrationSuite) TestConcurrentWrites(c *check.C) {
+ s.handler.Cluster.Collections.WebDAVCache.TTL = arvados.Duration(time.Second * 2)
+ lockTidyInterval = time.Second
+ client := arvados.NewClientFromEnv()
+ client.AuthToken = arvadostest.ActiveTokenV2
+ // Start small, and increase concurrency (2^2, 4^2, ...)
+ // only until hitting failure. Avoids unnecessarily long
+ // failure reports.
+ for n := 2; n < 16 && !c.Failed(); n = n * 2 {
+ c.Logf("%s: n=%d", c.TestName(), n)
+
+ var coll arvados.Collection
+ err := client.RequestAndDecode(&coll, "POST", "arvados/v1/collections", nil, nil)
+ c.Assert(err, check.IsNil)
+ defer client.RequestAndDecode(&coll, "DELETE", "arvados/v1/collections/"+coll.UUID, nil, nil)
+
+ var wg sync.WaitGroup
+ for i := 0; i < n && !c.Failed(); i++ {
+ i := i
+ wg.Add(1)
+ go func() {
+ defer wg.Done()
+ u := mustParseURL(fmt.Sprintf("http://%s.collections.example.com/i=%d", coll.UUID, i))
+ resp := httptest.NewRecorder()
+ req, err := http.NewRequest("MKCOL", u.String(), nil)
+ c.Assert(err, check.IsNil)
+ req.Header.Set("Authorization", "Bearer "+client.AuthToken)
+ s.handler.ServeHTTP(resp, req)
+ c.Assert(resp.Code, check.Equals, http.StatusCreated)
+ for j := 0; j < n && !c.Failed(); j++ {
+ j := j
+ wg.Add(1)
+ go func() {
+ defer wg.Done()
+ content := fmt.Sprintf("i=%d/j=%d", i, j)
+ u := mustParseURL("http://" + coll.UUID + ".collections.example.com/" + content)
+
+ resp := httptest.NewRecorder()
+ req, err := http.NewRequest("PUT", u.String(), strings.NewReader(content))
+ c.Assert(err, check.IsNil)
+ req.Header.Set("Authorization", "Bearer "+client.AuthToken)
+ s.handler.ServeHTTP(resp, req)
+ c.Check(resp.Code, check.Equals, http.StatusCreated)
+
+ time.Sleep(time.Second)
+ resp = httptest.NewRecorder()
+ req, err = http.NewRequest("GET", u.String(), nil)
+ c.Assert(err, check.IsNil)
+ req.Header.Set("Authorization", "Bearer "+client.AuthToken)
+ s.handler.ServeHTTP(resp, req)
+ c.Check(resp.Code, check.Equals, http.StatusOK)
+ c.Check(resp.Body.String(), check.Equals, content)
+ }()
+ }
+ }()
+ }
+ wg.Wait()
+ for i := 0; i < n; i++ {
+ u := mustParseURL(fmt.Sprintf("http://%s.collections.example.com/i=%d", coll.UUID, i))
+ resp := httptest.NewRecorder()
+ req, err := http.NewRequest("PROPFIND", u.String(), &bytes.Buffer{})
+ c.Assert(err, check.IsNil)
+ req.Header.Set("Authorization", "Bearer "+client.AuthToken)
+ s.handler.ServeHTTP(resp, req)
+ c.Assert(resp.Code, check.Equals, http.StatusMultiStatus)
+ }
+ }
+}
s3ErrorResponse(w, InternalError, err.Error(), r.URL.Path, http.StatusInternalServerError)
return true
}
+ defer sess.Release()
readfs := fs
if writeMethod[r.Method] {
// Create a FileSystem for this request, to avoid
http.Error(w, "invalid continuation token", http.StatusBadRequest)
return
}
+ // marker and start-after perform the same function,
+ // but we keep them separate so we can repeat them
+ // back to the client in the response.
params.marker = string(marker)
params.startAfter = r.FormValue("start-after")
switch r.FormValue("encoding-type") {
return
}
} else {
+ // marker is functionally equivalent to start-after.
params.marker = r.FormValue("marker")
}
+ // startAfter is params.marker or params.startAfter, whichever
+ // comes last.
+ startAfter := params.startAfter
+ if startAfter < params.marker {
+ startAfter = params.marker
+ }
+
bucketdir := "by_id/" + bucket
// walkpath is the directory (relative to bucketdir) we need
// to walk: the innermost directory that is guaranteed to
ContinuationToken: r.FormValue("continuation-token"),
StartAfter: params.startAfter,
}
+
+ // nextMarker will be the last path we add to either
+ // resp.Contents or commonPrefixes. It will be included in
+ // the response as NextMarker or NextContinuationToken if
+ // needed.
nextMarker := ""
commonPrefixes := map[string]bool{}
+ full := false
err := walkFS(fs, strings.TrimSuffix(bucketdir+"/"+walkpath, "/"), true, func(path string, fi os.FileInfo) error {
if path == bucketdir {
return nil
path += "/"
filesize = 0
}
- if len(path) <= len(params.prefix) {
- if path > params.prefix[:len(path)] {
- // with prefix "foobar", walking "fooz" means we're done
- return errDone
- }
- if path < params.prefix[:len(path)] {
- // with prefix "foobar", walking "foobag" is pointless
- return filepath.SkipDir
- }
- if fi.IsDir() && !strings.HasPrefix(params.prefix+"/", path) {
- // with prefix "foo/bar", walking "fo"
- // is pointless (but walking "foo" or
- // "foo/bar" is necessary)
- return filepath.SkipDir
- }
- if len(path) < len(params.prefix) {
- // can't skip anything, and this entry
- // isn't in the results, so just
- // continue descent
- return nil
- }
- } else {
- if path[:len(params.prefix)] > params.prefix {
- // with prefix "foobar", nothing we
- // see after "foozzz" is relevant
- return errDone
- }
- }
- if path < params.marker || path < params.prefix || path <= params.startAfter {
+ if strings.HasPrefix(params.prefix, path) && params.prefix != path {
+ // Descend into subtree until we reach desired prefix
return nil
+ } else if path < params.prefix {
+ // Not an ancestor or descendant of desired
+ // prefix, therefore none of its descendants
+ // can be either -- skip
+ return filepath.SkipDir
+ } else if path > params.prefix && !strings.HasPrefix(path, params.prefix) {
+ // We must have traversed everything under
+ // desired prefix
+ return errDone
+ } else if path == startAfter {
+ // Skip startAfter itself, just descend into
+ // subtree
+ return nil
+ } else if strings.HasPrefix(startAfter, path) {
+ // Descend into subtree in case it contains
+ // something after startAfter
+ return nil
+ } else if path < startAfter {
+ // Skip ahead until we reach startAfter
+ return filepath.SkipDir
}
if fi.IsDir() && !h.Cluster.Collections.S3FolderObjects {
// Note we don't add anything to
// finding a regular file inside it.
return nil
}
- if len(resp.Contents)+len(commonPrefixes) >= params.maxKeys {
- resp.IsTruncated = true
- if params.delimiter != "" || params.v2 {
- nextMarker = path
- }
- return errDone
- }
if params.delimiter != "" {
idx := strings.Index(path[len(params.prefix):], params.delimiter)
if idx >= 0 {
// "z", when we hit "foobar/baz", we
// add "/baz" to commonPrefixes and
// stop descending.
- commonPrefixes[path[:len(params.prefix)+idx+1]] = true
- return filepath.SkipDir
+ prefix := path[:len(params.prefix)+idx+1]
+ if prefix == startAfter {
+ return nil
+ } else if prefix < startAfter && !strings.HasPrefix(startAfter, prefix) {
+ return nil
+ } else if full {
+ resp.IsTruncated = true
+ return errDone
+ } else {
+ commonPrefixes[prefix] = true
+ nextMarker = prefix
+ full = len(resp.Contents)+len(commonPrefixes) >= params.maxKeys
+ return filepath.SkipDir
+ }
}
}
+ if full {
+ resp.IsTruncated = true
+ return errDone
+ }
resp.Contents = append(resp.Contents, s3Key{
Key: path,
LastModified: fi.ModTime().UTC().Format("2006-01-02T15:04:05.999") + "Z",
Size: filesize,
})
+ nextMarker = path
+ full = len(resp.Contents)+len(commonPrefixes) >= params.maxKeys
return nil
})
if err != nil && err != errDone {
http.Error(w, err.Error(), http.StatusInternalServerError)
return
}
+ if params.delimiter == "" && !params.v2 || !resp.IsTruncated {
+ nextMarker = ""
+ }
if params.delimiter != "" {
resp.CommonPrefixes = make([]commonPrefix, 0, len(commonPrefixes))
for prefix := range commonPrefixes {
"net/url"
"os"
"os/exec"
+ "sort"
"strings"
"sync"
"time"
s.testS3PutObjectSuccess(c, stage.projbucket, stage.coll.Name+"/", stage.coll.UUID)
}
func (s *IntegrationSuite) testS3PutObjectSuccess(c *check.C, bucket *s3.Bucket, prefix string, collUUID string) {
+ // We insert a delay between test cases to ensure we exercise
+ // rollover of expired sessions.
+ sleep := time.Second / 100
+ s.handler.Cluster.Collections.WebDAVCache.TTL = arvados.Duration(sleep * 3)
+
for _, trial := range []struct {
path string
size int
contentType: "application/x-directory",
},
} {
+ time.Sleep(sleep)
c.Logf("=== %v", trial)
objname := prefix + trial.path
var markers int
for markers, s.handler.Cluster.Collections.S3FolderObjects = range []bool{false, true} {
- dirs := 2
- filesPerDir := 1001
+ dirs := 2000
+ filesPerDir := 2
stage.writeBigDirs(c, dirs, filesPerDir)
// Total # objects is:
// 2 file entries from s3setup (emptyfile and sailboat.txt)
// +filesPerDir*dirs file entries from writeBigDirs (dir0/file0.txt, etc.)
s.testS3List(c, stage.collbucket, "", 4000, markers+2+(filesPerDir+markers)*dirs)
s.testS3List(c, stage.collbucket, "", 131, markers+2+(filesPerDir+markers)*dirs)
+ s.testS3List(c, stage.collbucket, "", 51, markers+2+(filesPerDir+markers)*dirs)
s.testS3List(c, stage.collbucket, "dir0/", 71, filesPerDir+markers)
}
}
break
}
for _, key := range resp.Contents {
+ if _, dup := gotKeys[key.Key]; dup {
+ c.Errorf("got duplicate key %q on page %d", key.Key, pages)
+ }
gotKeys[key.Key] = key
if strings.Contains(key.Key, "sailboat.txt") {
c.Check(key.Size, check.Equals, int64(4))
}
nextMarker = resp.NextMarker
}
- c.Check(len(gotKeys), check.Equals, expectFiles)
+ if !c.Check(len(gotKeys), check.Equals, expectFiles) {
+ var sorted []string
+ for k := range gotKeys {
+ sorted = append(sorted, k)
+ }
+ sort.Strings(sorted)
+ for _, k := range sorted {
+ c.Logf("got %s", k)
+ }
+ }
}
func (s *IntegrationSuite) TestS3CollectionListRollup(c *check.C) {
{"dir0", "", ""},
{"dir0/", "", ""},
{"dir0/f", "", ""},
- {"dir0", "/", "dir0/file14.txt"}, // no commonprefixes
+ {"dir0", "/", "dir0/file14.txt"}, // one commonprefix, "dir0/"
+ {"dir0", "/", "dir0/zzzzfile.txt"}, // no commonprefixes
{"", "", "dir0/file14.txt"}, // middle page, skip walking dir1
{"", "", "dir1/file14.txt"}, // middle page, skip walking dir0
{"", "", "dir1/file498.txt"}, // last page of results
var expectTruncated bool
for _, key := range allfiles {
full := len(expectKeys)+len(expectPrefixes) >= maxKeys
- if !strings.HasPrefix(key, trial.prefix) || key < trial.marker {
+ if !strings.HasPrefix(key, trial.prefix) || key <= trial.marker {
continue
} else if idx := strings.Index(key[len(trial.prefix):], trial.delimiter); trial.delimiter != "" && idx >= 0 {
prefix := key[:len(trial.prefix)+idx+1]
if len(expectPrefixes) > 0 && expectPrefixes[len(expectPrefixes)-1] == prefix {
// same prefix as previous key
} else if full {
- expectNextMarker = key
expectTruncated = true
} else {
expectPrefixes = append(expectPrefixes, prefix)
+ expectNextMarker = prefix
}
} else if full {
- if trial.delimiter != "" {
- expectNextMarker = key
- }
expectTruncated = true
break
} else {
expectKeys = append(expectKeys, key)
+ if trial.delimiter != "" {
+ expectNextMarker = key
+ }
}
}
+ if !expectTruncated {
+ expectNextMarker = ""
+ }
var gotKeys []string
for _, key := range resp.Contents {
}
}
+func (s *IntegrationSuite) TestS3ListObjectsV2ManySubprojects(c *check.C) {
+ stage := s.s3setup(c)
+ defer stage.teardown(c)
+ projects := 50
+ collectionsPerProject := 2
+ for i := 0; i < projects; i++ {
+ var subproj arvados.Group
+ err := stage.arv.RequestAndDecode(&subproj, "POST", "arvados/v1/groups", nil, map[string]interface{}{
+ "group": map[string]interface{}{
+ "owner_uuid": stage.subproj.UUID,
+ "group_class": "project",
+ "name": fmt.Sprintf("keep-web s3 test subproject %d", i),
+ },
+ })
+ c.Assert(err, check.IsNil)
+ for j := 0; j < collectionsPerProject; j++ {
+ err = stage.arv.RequestAndDecode(nil, "POST", "arvados/v1/collections", nil, map[string]interface{}{"collection": map[string]interface{}{
+ "owner_uuid": subproj.UUID,
+ "name": fmt.Sprintf("keep-web s3 test collection %d", j),
+ "manifest_text": ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:emptyfile\n./emptydir d41d8cd98f00b204e9800998ecf8427e+0 0:0:.\n",
+ }})
+ c.Assert(err, check.IsNil)
+ }
+ }
+ c.Logf("setup complete")
+
+ sess := aws_session.Must(aws_session.NewSession(&aws_aws.Config{
+ Region: aws_aws.String("auto"),
+ Endpoint: aws_aws.String(s.testServer.URL),
+ Credentials: aws_credentials.NewStaticCredentials(url.QueryEscape(arvadostest.ActiveTokenV2), url.QueryEscape(arvadostest.ActiveTokenV2), ""),
+ S3ForcePathStyle: aws_aws.Bool(true),
+ }))
+ client := aws_s3.New(sess)
+ ctx := context.Background()
+ params := aws_s3.ListObjectsV2Input{
+ Bucket: aws_aws.String(stage.proj.UUID),
+ Delimiter: aws_aws.String("/"),
+ Prefix: aws_aws.String("keep-web s3 test subproject/"),
+ MaxKeys: aws_aws.Int64(int64(projects / 2)),
+ }
+ for page := 1; ; page++ {
+ t0 := time.Now()
+ result, err := client.ListObjectsV2WithContext(ctx, ¶ms)
+ if !c.Check(err, check.IsNil) {
+ break
+ }
+ c.Logf("got page %d in %v with len(Contents) == %d, len(CommonPrefixes) == %d", page, time.Since(t0), len(result.Contents), len(result.CommonPrefixes))
+ if !*result.IsTruncated {
+ break
+ }
+ params.ContinuationToken = result.NextContinuationToken
+ *params.MaxKeys = *params.MaxKeys/2 + 1
+ }
+}
+
func (s *IntegrationSuite) TestS3ListObjectsV2(c *check.C) {
stage := s.s3setup(c)
defer stage.teardown(c)
"aws_access_key": "",
"aws_profile": "",
"aws_secret_key": "",
- "aws_source_ami": "ami-031283ff8a43b021c",
+ "aws_source_ami": "ami-0a9d5908c7201e91d",
"aws_ebs_autoscale": "",
"aws_associate_public_ip_address": "",
"aws_ena_support": "",
$SUDO mkdir -p /etc/arvados/docker-cleaner
$SUDO echo -e "{\n \"Quota\": \"10G\",\n \"RemoveStoppedContainers\": \"always\"\n}" > /etc/arvados/docker-cleaner/docker-cleaner.json
-# Enable cgroup accounting
-$SUDO sed -i 's/GRUB_CMDLINE_LINUX=""/GRUB_CMDLINE_LINUX="cgroup_enable=memory swapaccount=1"/g' /etc/default/grub
+# Enable cgroup accounting (forcing cgroups v1)
+$SUDO echo 'GRUB_CMDLINE_LINUX="$GRUB_CMDLINE_LINUX cgroup_enable=memory swapaccount=1 systemd.unified_cgroup_hierarchy=0"' >> /etc/default/grub
$SUDO update-grub
# Make sure user_allow_other is set in fuse.conf
projects / arvados.git / commitdiff
