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Merge branch '18349-fed-request-id'
authorTom Clegg <tom@curii.com>
Wed, 15 Dec 2021 14:26:45 +0000 (09:26 -0500)
committerTom Clegg <tom@curii.com>
Wed, 15 Dec 2021 14:26:45 +0000 (09:26 -0500)
closes #18349

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

32 files changed:
apps/workbench/config/initializers/lograge.rb patch | blob | history
doc/_includes/_container_runtime_constraints.liquid patch | blob | history
doc/admin/upgrading.html.textile.liquid patch | blob | history
doc/api/permission-model.html.textile.liquid patch | blob | history
doc/install/crunch2/install-compute-node-singularity.html.textile.liquid patch | blob | history
go.mod patch | blob | history
go.sum patch | blob | history
lib/config/config.default.yml patch | blob | history
lib/config/export.go patch | blob | history
lib/config/generated_config.go patch | blob | history
lib/crunchrun/crunchrun.go patch | blob | history
lib/crunchrun/crunchrun_test.go patch | blob | history
lib/crunchrun/docker.go patch | blob | history
lib/crunchrun/docker_test.go patch | blob | history
lib/crunchrun/executor.go patch | blob | history
lib/crunchrun/singularity.go patch | blob | history
lib/crunchrun/singularity_test.go patch | blob | history
lib/service/cmd.go patch | blob | history
sdk/go/arvados/config.go patch | blob | history
sdk/go/arvados/container.go patch | blob | history
services/api/app/models/arvados_model.rb patch | blob | history
services/api/config/arvados_config.rb patch | blob | history
services/api/config/initializers/lograge.rb patch | blob | history
services/api/test/functional/arvados/v1/groups_controller_test.rb patch | blob | history
services/api/test/integration/remote_user_test.rb patch | blob | history
services/api/test/unit/permission_test.rb patch | blob | history
services/crunch-dispatch-local/crunch-dispatch-local.go patch | blob | history
services/crunch-dispatch-slurm/crunch-dispatch-slurm.go patch | blob | history
services/keep-web/main.go patch | blob | history
services/keep-web/server.go patch | blob | history
services/keep-web/server_test.go patch | blob | history
services/keepproxy/keepproxy.go patch | blob | history

diff --git a/apps/workbench/config/initializers/lograge.rb b/apps/workbench/config/initializers/lograge.rb
index 6e7f165c135b2132bcaef1e89ccac6890f585ed4..795be7bfc39907ee6590378484b8c04aa9329c3c 100644 (file)
--- a/apps/workbench/config/initializers/lograge.rb
+++ b/apps/workbench/config/initializers/lograge.rb
@@ -7,6 +7,7 @@ ArvadosWorkbench::Application.configure do
   config.lograge.formatter = Lograge::Formatters::Logstash.new
   config.lograge.custom_options = lambda do |event|
     payload = {
+      ClusterID: Rails.configuration.ClusterID,
       request_id: event.payload[:request_id],
     }
     # Also log params (minus the pseudo-params added by Rails). But if
diff --git a/doc/_includes/_container_runtime_constraints.liquid b/doc/_includes/_container_runtime_constraints.liquid
index 7e0c8f18f27910cd146742467a7d38feed39b428..dcdc29cf3f26646d80de501a0431e946d177f431 100644 (file)
--- a/doc/_includes/_container_runtime_constraints.liquid
+++ b/doc/_includes/_container_runtime_constraints.liquid
@@ -14,3 +14,6 @@ table(table table-bordered table-condensed).
 |vcpus|integer|Number of cores to be used to run this process.|Optional. However, a ContainerRequest that is in "Committed" state must provide this.|
 |keep_cache_ram|integer|Number of keep cache bytes to be used to run this process.|Optional.|
 |API|boolean|When set, ARVADOS_API_HOST and ARVADOS_API_TOKEN will be set, and container will have networking enabled to access the Arvados API server.|Optional.|
+|cuda_driver_version|string|Minimum CUDA driver version.|Optional.|
+|cuda_hardware_capability|string|Minimum CUDA hardware capability.|Optional.|
+|cuda_device_count|int|Number of GPUs to request.|Optional.|
diff --git a/doc/admin/upgrading.html.textile.liquid b/doc/admin/upgrading.html.textile.liquid
index 517c2dd0cde0014f44bd03e077048c459a191ef2..411e2ea0ff3cf3d4d4b0e8bd1c7852b336f6ae58 100644 (file)
--- a/doc/admin/upgrading.html.textile.liquid
+++ b/doc/admin/upgrading.html.textile.liquid
@@ -39,6 +39,10 @@ h2(#main). development main (as of 2021-11-10)
 
 "previous: Upgrading from 2.3.0":#v2_3_0
 
+h3. Role groups are visible to all users by default
+
+The permission model has changed such that all role groups are visible to all active users. This enables users to share objects with groups they don't belong to. To preserve the previous behavior, where role groups are only visible to members and admins, add @RoleGroupsVisibleToAll: false@ to the @Users@ section of your configuration file.
+
 h3. Default LSF arguments have changed
 
 If you use LSF and your configuration specifies @Containers.LSF.BsubArgumentsList@, you should update it to include the new arguments (@"-R", "select[mem>=%MMB]", ...@, see "configuration reference":{{site.baseurl}}/admin/config.html). Otherwise, containers that are too big to run on any LSF host will remain in the LSF queue instead of being cancelled.
diff --git a/doc/api/permission-model.html.textile.liquid b/doc/api/permission-model.html.textile.liquid
index a44d2eefa13ac7cc43e89776d9773169f3b5fe4e..faa160248af78a0332f2636e71ea39bf61a9845a 100644 (file)
--- a/doc/api/permission-model.html.textile.liquid
+++ b/doc/api/permission-model.html.textile.liquid
@@ -77,6 +77,7 @@ A "role" is a subtype of Group that is treated in Workbench as a group of users
 * All roles are owned by the system user.
 * The name of a role is unique across a single Arvados cluster.
 * Roles can be both targets (@head_uuid@) and origins (@tail_uuid@) of permission links.
+* By default, all roles are visible to all active users. However, if the configuration entry @Users.RoleGroupsVisibleToAll@ is @false@, visibility is determined by normal permission rules, _i.e._, a role is only visible to users who have that role, and to admins.
 
 h3. Access through Roles
 
diff --git a/doc/install/crunch2/install-compute-node-singularity.html.textile.liquid b/doc/install/crunch2/install-compute-node-singularity.html.textile.liquid
index 8e9db0c4e3d7bcd2a1312f19caeba89ba08da245..14f95e48fb3be044f5cd8d5bb1730d6a32fcfed0 100644 (file)
--- a/doc/install/crunch2/install-compute-node-singularity.html.textile.liquid
+++ b/doc/install/crunch2/install-compute-node-singularity.html.textile.liquid
@@ -54,3 +54,20 @@ Then update @Containers.RuntimeEngine@ in your cluster configuration:
 </notextile>
 
 {% include 'singularity_mksquashfs_configuration' %}
+
+h2(#singularity_loop_device_errors). Singularity loop device errors
+
+With singularity v3.9.1 and earlier, containers may fail intermittently at startup with an error message similar to the following in the container log's @stderr.txt@ (line breaks added):
+
+<notextile>
+<pre><code>FATAL:   container creation failed:
+ mount /proc/self/fd/3->/usr/local/var/singularity/mnt/session/rootfs error:
+ while mounting image /proc/self/fd/3:
+ failed to find loop device:
+ could not attach image file to loop device:
+ failed to set loop flags on loop device:
+ resource temporarily unavailable
+</code></pre>
+</notextile>
+
+This problem is addressed in singularity v3.9.2. For details, please see "Arvados issue #18489":https://dev.arvados.org/issues/18489 and "singularity PR #458":https://github.com/sylabs/singularity/pull/458.
diff --git a/go.mod b/go.mod
index 0ea3dd9169db9ad970a4a985ade5fb525878ee9f..6933d01e30c63b1578757a35905ddff572e000c2 100644 (file)
--- a/go.mod
+++ b/go.mod
@@ -11,22 +11,18 @@ require (
        github.com/Azure/go-autorest/autorest/azure/cli v0.4.4 // indirect
        github.com/Azure/go-autorest/autorest/to v0.4.0
        github.com/Azure/go-autorest/autorest/validation v0.3.0 // indirect
-       github.com/Microsoft/go-winio v0.4.5 // indirect
        github.com/alcortesm/tgz v0.0.0-20161220082320-9c5fe88206d7 // indirect
        github.com/anmitsu/go-shlex v0.0.0-20161002113705-648efa622239 // indirect
        github.com/arvados/cgofuse v1.2.0-arvados1
        github.com/aws/aws-sdk-go v1.25.30
        github.com/aws/aws-sdk-go-v2 v0.23.0
-       github.com/bgentry/speakeasy v0.1.0 // indirect
        github.com/bradleypeabody/godap v0.0.0-20170216002349-c249933bc092
+       github.com/containerd/containerd v1.5.8 // indirect
        github.com/coreos/go-oidc v2.1.0+incompatible
-       github.com/coreos/go-systemd v0.0.0-20180108085132-cc4f39464dc7
+       github.com/coreos/go-systemd v0.0.0-20190321100706-95778dfbb74e
        github.com/creack/pty v1.1.7
-       github.com/dnaeon/go-vcr v1.0.1 // indirect
-       github.com/docker/distribution v2.6.0-rc.1.0.20180105232752-277ed486c948+incompatible // indirect
-       github.com/docker/docker v1.4.2-0.20180109013817-94b8a116fbf1
+       github.com/docker/docker v17.12.0-ce-rc1.0.20210128214336-420b1d36250f+incompatible
        github.com/docker/go-connections v0.3.0 // indirect
-       github.com/docker/go-units v0.3.3-0.20171221200356-d59758554a3d // indirect
        github.com/dustin/go-humanize v1.0.0
        github.com/flynn/go-shlex v0.0.0-20150515145356-3f9db97f8568 // indirect
        github.com/fsnotify/fsnotify v1.4.9
@@ -34,13 +30,12 @@ require (
        github.com/gliderlabs/ssh v0.2.2 // indirect
        github.com/go-asn1-ber/asn1-ber v1.4.1 // indirect
        github.com/go-ldap/ldap v3.0.3+incompatible
-       github.com/gogo/protobuf v1.1.1
+       github.com/gogo/protobuf v1.3.2
        github.com/golang-jwt/jwt/v4 v4.1.0 // indirect
        github.com/google/shlex v0.0.0-20191202100458-e7afc7fbc510
-       github.com/gorilla/context v1.1.1 // indirect
-       github.com/gorilla/mux v1.6.1-0.20180107155708-5bbbb5b2b572
+       github.com/gorilla/mux v1.7.2
        github.com/hashicorp/golang-lru v0.5.1
-       github.com/imdario/mergo v0.3.8-0.20190415133143-5ef87b449ca7
+       github.com/imdario/mergo v0.3.12
        github.com/jbenet/go-context v0.0.0-20150711004518-d14ea06fba99 // indirect
        github.com/jmcvetta/randutil v0.0.0-20150817122601-2bb1b664bcff
        github.com/jmoiron/sqlx v1.2.0
@@ -48,14 +43,13 @@ require (
        github.com/julienschmidt/httprouter v1.2.0
        github.com/kevinburke/ssh_config v0.0.0-20171013211458-802051befeb5 // indirect
        github.com/lib/pq v1.10.2
+       github.com/morikuni/aec v1.0.0 // indirect
        github.com/msteinert/pam v0.0.0-20190215180659-f29b9f28d6f9
-       github.com/opencontainers/go-digest v1.0.0-rc1 // indirect
-       github.com/opencontainers/image-spec v1.0.1-0.20171125024018-577479e4dc27 // indirect
        github.com/pelletier/go-buffruneio v0.2.0 // indirect
        github.com/pquerna/cachecontrol v0.0.0-20180517163645-1555304b9b35 // indirect
-       github.com/prometheus/client_golang v1.2.1
-       github.com/prometheus/client_model v0.0.0-20190812154241-14fe0d1b01d4
-       github.com/prometheus/common v0.7.0
+       github.com/prometheus/client_golang v1.7.1
+       github.com/prometheus/client_model v0.2.0
+       github.com/prometheus/common v0.10.0
        github.com/satori/go.uuid v1.2.1-0.20180103174451-36e9d2ebbde5 // indirect
        github.com/sergi/go-diff v1.0.0 // indirect
        github.com/sirupsen/logrus v1.8.1
@@ -63,18 +57,17 @@ require (
        github.com/xanzy/ssh-agent v0.1.0 // indirect
        golang.org/x/crypto v0.0.0-20211117183948-ae814b36b871
        golang.org/x/net v0.0.0-20211112202133-69e39bad7dc2
-       golang.org/x/oauth2 v0.0.0-20190604053449-0f29369cfe45
+       golang.org/x/oauth2 v0.0.0-20200107190931-bf48bf16ab8d
        golang.org/x/sys v0.0.0-20210809222454-d867a43fc93e
        golang.org/x/tools v0.1.7 // indirect
-       google.golang.org/api v0.13.0
+       google.golang.org/api v0.20.0
        gopkg.in/asn1-ber.v1 v1.0.0-20181015200546-f715ec2f112d // indirect
-       gopkg.in/check.v1 v1.0.0-20161208181325-20d25e280405
-       gopkg.in/square/go-jose.v2 v2.3.1
+       gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15
+       gopkg.in/square/go-jose.v2 v2.5.1
        gopkg.in/src-d/go-billy.v4 v4.0.1
        gopkg.in/src-d/go-git-fixtures.v3 v3.5.0 // indirect
        gopkg.in/src-d/go-git.v4 v4.0.0
        gopkg.in/warnings.v0 v0.1.2 // indirect
-       gopkg.in/yaml.v2 v2.2.4 // indirect
        rsc.io/getopt v0.0.0-20170811000552-20be20937449
 )
 
diff --git a/go.sum b/go.sum
index 28ff3dadc9b9fe03785932b474a865e7e09075db..1f8fabbfdaaaff266553c13d2d2b54c488bdddb8 100644 (file)
--- a/go.sum
+++ b/go.sum
@@ -1,14 +1,41 @@
+bazil.org/fuse v0.0.0-20160811212531-371fbbdaa898/go.mod h1:Xbm+BRKSBEpa4q4hTSxohYNQpsxXPbPry4JJWOB3LB8=
 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 h1:ROfEUZz+Gh5pa62DJWXSaonyu3StP6EA6lPEXPI6mCo=
 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 h1:3ithwDMr7/3vpAMXiH+ZQnYbuIsh+OPhUPMFC9enmn0=
+cloud.google.com/go v0.54.0/go.mod h1:1rq2OEkV3YMf6n/9ZvGWI3GWw0VoqH/1x2nd8Is/bPc=
+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/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/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=
+dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU=
+github.com/Azure/azure-sdk-for-go v16.2.1+incompatible/go.mod h1:9XXNKU+eRnpl9moKnB4QOLf1HestfXbmab5FXxiDBjc=
 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 v0.0.0-20170929234023-d6e3b3328b78 h1:w+iIsaOQNcT7OZ575w+acHgRric5iCyQh+xv+KJ4HB8=
+github.com/Azure/go-ansiterm v0.0.0-20170929234023-d6e3b3328b78/go.mod h1:LmzpDX56iTiv29bbRTIsUNlaFfuhWRQBWjQdVyAevI8=
+github.com/Azure/go-autorest v10.8.1+incompatible/go.mod h1:r+4oMnoxhatjLLJ6zxSWATqVooLgysK6ZNox3g/xq24=
 github.com/Azure/go-autorest v14.2.0+incompatible h1:V5VMDjClD3GiElqLWO7mz2MxNAK/vTfRHdAubSIPRgs=
 github.com/Azure/go-autorest v14.2.0+incompatible/go.mod h1:r+4oMnoxhatjLLJ6zxSWATqVooLgysK6ZNox3g/xq24=
+github.com/Azure/go-autorest/autorest v0.11.1/go.mod h1:JFgpikqFJ/MleTTxwepExTKnFUKKszPS8UavbQYUMuw=
 github.com/Azure/go-autorest/autorest v0.11.19/go.mod h1:dSiJPy22c3u0OtOKDNttNgqpNFY/GeWa7GH/Pz56QRA=
 github.com/Azure/go-autorest/autorest v0.11.22 h1:bXiQwDjrRmBQOE67bwlvUKAC1EU1yZTPQ38c+bstZws=
 github.com/Azure/go-autorest/autorest v0.11.22/go.mod h1:BAWYUWGPEtKPzjVkp0Q6an0MJcJDsoh5Z1BFAEFs4Xs=
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 github.com/Azure/go-autorest/autorest/adal v0.9.5/go.mod h1:B7KF7jKIeC9Mct5spmyCB/A8CG/sEz1vwIRGv/bbw7A=
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@@ -314,40 +944,152 @@ golang.org/x/xerrors v0.0.0-20191011141410-1b5146add898/go.mod h1:I/5z698sn9Ka8T
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+k8s.io/api v0.20.4/go.mod h1:++lNL1AJMkDymriNniQsWRkMDzRaX2Y/POTUi8yvqYQ=
+k8s.io/api v0.20.6/go.mod h1:X9e8Qag6JV/bL5G6bU8sdVRltWKmdHsFUGS3eVndqE8=
+k8s.io/apimachinery v0.20.1/go.mod h1:WlLqWAHZGg07AeltaI0MV5uk1Omp8xaN0JGLY6gkRpU=
+k8s.io/apimachinery v0.20.4/go.mod h1:WlLqWAHZGg07AeltaI0MV5uk1Omp8xaN0JGLY6gkRpU=
+k8s.io/apimachinery v0.20.6/go.mod h1:ejZXtW1Ra6V1O5H8xPBGz+T3+4gfkTCeExAHKU57MAc=
+k8s.io/apiserver v0.20.1/go.mod h1:ro5QHeQkgMS7ZGpvf4tSMx6bBOgPfE+f52KwvXfScaU=
+k8s.io/apiserver v0.20.4/go.mod h1:Mc80thBKOyy7tbvFtB4kJv1kbdD0eIH8k8vianJcbFM=
+k8s.io/apiserver v0.20.6/go.mod h1:QIJXNt6i6JB+0YQRNcS0hdRHJlMhflFmsBDeSgT1r8Q=
+k8s.io/client-go v0.20.1/go.mod h1:/zcHdt1TeWSd5HoUe6elJmHSQ6uLLgp4bIJHVEuy+/Y=
+k8s.io/client-go v0.20.4/go.mod h1:LiMv25ND1gLUdBeYxBIwKpkSC5IsozMMmOOeSJboP+k=
+k8s.io/client-go v0.20.6/go.mod h1:nNQMnOvEUEsOzRRFIIkdmYOjAZrC8bgq0ExboWSU1I0=
+k8s.io/component-base v0.20.1/go.mod h1:guxkoJnNoh8LNrbtiQOlyp2Y2XFCZQmrcg2n/DeYNLk=
+k8s.io/component-base v0.20.4/go.mod h1:t4p9EdiagbVCJKrQ1RsA5/V4rFQNDfRlevJajlGwgjI=
+k8s.io/component-base v0.20.6/go.mod h1:6f1MPBAeI+mvuts3sIdtpjljHWBQ2cIy38oBIWMYnrM=
+k8s.io/cri-api v0.17.3/go.mod h1:X1sbHmuXhwaHs9xxYffLqJogVsnI+f6cPRcgPel7ywM=
+k8s.io/cri-api v0.20.1/go.mod h1:2JRbKt+BFLTjtrILYVqQK5jqhI+XNdF6UiGMgczeBCI=
+k8s.io/cri-api v0.20.4/go.mod h1:2JRbKt+BFLTjtrILYVqQK5jqhI+XNdF6UiGMgczeBCI=
+k8s.io/cri-api v0.20.6/go.mod h1:ew44AjNXwyn1s0U4xCKGodU7J1HzBeZ1MpGrpa5r8Yc=
+k8s.io/gengo v0.0.0-20200413195148-3a45101e95ac/go.mod h1:ezvh/TsK7cY6rbqRK0oQQ8IAqLxYwwyPxAX1Pzy0ii0=
+k8s.io/klog/v2 v2.0.0/go.mod h1:PBfzABfn139FHAV07az/IF9Wp1bkk3vpT2XSJ76fSDE=
+k8s.io/klog/v2 v2.4.0/go.mod h1:Od+F08eJP+W3HUb4pSrPpgp9DGU4GzlpG/TmITuYh/Y=
+k8s.io/kube-openapi v0.0.0-20201113171705-d219536bb9fd/go.mod h1:WOJ3KddDSol4tAGcJo0Tvi+dK12EcqSLqcWsryKMpfM=
+k8s.io/kubernetes v1.13.0/go.mod h1:ocZa8+6APFNC2tX1DZASIbocyYT5jHzqFVsY5aoB7Jk=
+k8s.io/utils v0.0.0-20201110183641-67b214c5f920/go.mod h1:jPW/WVKK9YHAvNhRxK0md/EJ228hCsBRufyofKtW8HA=
+rsc.io/binaryregexp v0.2.0/go.mod h1:qTv7/COck+e2FymRvadv62gMdZztPaShugOCi3I+8D8=
 rsc.io/getopt v0.0.0-20170811000552-20be20937449 h1:UukjJOsjQH0DIuyyrcod6CXHS6cdaMMuJmrt+SN1j4A=
 rsc.io/getopt v0.0.0-20170811000552-20be20937449/go.mod h1:dhCdeqAxkyt5u3/sKRkUXuHaMXUu1Pt13GTQAM2xnig=
+rsc.io/quote/v3 v3.1.0/go.mod h1:yEA65RcK8LyAZtP9Kv3t0HmxON59tX3rD+tICJqUlj0=
+rsc.io/sampler v1.3.0/go.mod h1:T1hPZKmBbMNahiBKFy5HrXp6adAjACjK9JXDnKaTXpA=
+sigs.k8s.io/apiserver-network-proxy/konnectivity-client v0.0.14/go.mod h1:LEScyzhFmoF5pso/YSeBstl57mOzx9xlU9n85RGrDQg=
+sigs.k8s.io/apiserver-network-proxy/konnectivity-client v0.0.15/go.mod h1:LEScyzhFmoF5pso/YSeBstl57mOzx9xlU9n85RGrDQg=
+sigs.k8s.io/structured-merge-diff/v4 v4.0.2/go.mod h1:bJZC9H9iH24zzfZ/41RGcq60oK1F7G282QMXDPYydCw=
+sigs.k8s.io/structured-merge-diff/v4 v4.0.3/go.mod h1:bJZC9H9iH24zzfZ/41RGcq60oK1F7G282QMXDPYydCw=
+sigs.k8s.io/yaml v1.1.0/go.mod h1:UJmg0vDUVViEyp3mgSv9WPwZCDxu4rQW1olrI1uml+o=
+sigs.k8s.io/yaml v1.2.0/go.mod h1:yfXDCHCao9+ENCvLSE62v9VSji2MKu5jeNfTrofGhJc=
diff --git a/lib/config/config.default.yml b/lib/config/config.default.yml
index a84dc5d31673b58b152645f3b73f3efa514ea767..7f859822537dfe440ebf7c8064400d11193a9cbe 100644 (file)
--- a/lib/config/config.default.yml
+++ b/lib/config/config.default.yml
@@ -319,6 +319,14 @@ Clusters:
         Thanks,
         Your Arvados administrator.
 
+      # If RoleGroupsVisibleToAll is true, all role groups are visible
+      # to all active users.
+      #
+      # If false, users must be granted permission to role groups in
+      # order to see them. This is more appropriate for a multi-tenant
+      # cluster.
+      RoleGroupsVisibleToAll: true
+
     AuditLogs:
       # Time to keep audit logs, in seconds. (An audit log is a row added
       # to the "logs" table in the PostgreSQL database each time an
diff --git a/lib/config/export.go b/lib/config/export.go
index 4c4e341f5a34c8608e554f407aab4869da88a8f6..cfc4cb6272d522d0505c909a82906c2723fea323 100644 (file)
--- a/lib/config/export.go
+++ b/lib/config/export.go
@@ -234,6 +234,7 @@ var whitelist = map[string]bool{
        "Users.UserNotifierEmailBcc":                          false,
        "Users.UserProfileNotificationAddress":                false,
        "Users.UserSetupMailText":                             false,
+       "Users.RoleGroupsVisibleToAll":                        false,
        "Volumes":                                             true,
        "Volumes.*":                                           true,
        "Volumes.*.*":                                         false,
diff --git a/lib/config/generated_config.go b/lib/config/generated_config.go
index 567ac30a9b7d855cfabdc10374dcf55b8f9694c7..485273e1b0ed0409f07f058959c45a8f739b5f08 100644 (file)
--- a/lib/config/generated_config.go
+++ b/lib/config/generated_config.go
@@ -325,6 +325,14 @@ Clusters:
         Thanks,
         Your Arvados administrator.
 
+      # If RoleGroupsVisibleToAll is true, all role groups are visible
+      # to all active users.
+      #
+      # If false, users must be granted permission to role groups in
+      # order to see them. This is more appropriate for a multi-tenant
+      # cluster.
+      RoleGroupsVisibleToAll: true
+
     AuditLogs:
       # Time to keep audit logs, in seconds. (An audit log is a row added
       # to the "logs" table in the PostgreSQL database each time an
diff --git a/lib/crunchrun/crunchrun.go b/lib/crunchrun/crunchrun.go
index dd0169025bb3cba58049dcdc9151738ea7b48463..7e68dcd3314685bf4132739bb17ff0ad2e9ba7b8 100644 (file)
--- a/lib/crunchrun/crunchrun.go
+++ b/lib/crunchrun/crunchrun.go
@@ -986,20 +986,33 @@ func (runner *ContainerRunner) CreateContainer(imageID string, bindmounts map[st
        runner.executorStdin = stdin
        runner.executorStdout = stdout
        runner.executorStderr = stderr
+
+       cudaDeviceCount := 0
+       if runner.Container.RuntimeConstraints.CUDADriverVersion != "" ||
+               runner.Container.RuntimeConstraints.CUDAHardwareCapability != "" ||
+               runner.Container.RuntimeConstraints.CUDADeviceCount != 0 {
+               // if any of these are set, enable CUDA GPU support
+               cudaDeviceCount = runner.Container.RuntimeConstraints.CUDADeviceCount
+               if cudaDeviceCount == 0 {
+                       cudaDeviceCount = 1
+               }
+       }
+
        return runner.executor.Create(containerSpec{
-               Image:         imageID,
-               VCPUs:         runner.Container.RuntimeConstraints.VCPUs,
-               RAM:           ram,
-               WorkingDir:    workdir,
-               Env:           env,
-               BindMounts:    bindmounts,
-               Command:       runner.Container.Command,
-               EnableNetwork: enableNetwork,
-               NetworkMode:   runner.networkMode,
-               CgroupParent:  runner.setCgroupParent,
-               Stdin:         stdin,
-               Stdout:        stdout,
-               Stderr:        stderr,
+               Image:           imageID,
+               VCPUs:           runner.Container.RuntimeConstraints.VCPUs,
+               RAM:             ram,
+               WorkingDir:      workdir,
+               Env:             env,
+               BindMounts:      bindmounts,
+               Command:         runner.Container.Command,
+               EnableNetwork:   enableNetwork,
+               CUDADeviceCount: cudaDeviceCount,
+               NetworkMode:     runner.networkMode,
+               CgroupParent:    runner.setCgroupParent,
+               Stdin:           stdin,
+               Stdout:          stdout,
+               Stderr:          stderr,
        })
 }
 
diff --git a/lib/crunchrun/crunchrun_test.go b/lib/crunchrun/crunchrun_test.go
index c28cf73cbe0cfc694f81464eae65350c703238f8..67b18857b0ea3cf5321e529a8984ed5e89017628 100644 (file)
--- a/lib/crunchrun/crunchrun_test.go
+++ b/lib/crunchrun/crunchrun_test.go
@@ -715,6 +715,7 @@ func (s *TestSuite) TestFullRunHello(c *C) {
                c.Check(s.executor.created.RAM, Equals, int64(1000000))
                c.Check(s.executor.created.NetworkMode, Equals, "default")
                c.Check(s.executor.created.EnableNetwork, Equals, false)
+               c.Check(s.executor.created.CUDADeviceCount, Equals, 0)
                fmt.Fprintln(s.executor.created.Stdout, "hello world")
        })
 
@@ -982,6 +983,42 @@ func (s *TestSuite) TestFullRunSetOutputStorageClasses(c *C) {
        c.Check(s.testContainerKeepClient.StorageClasses, DeepEquals, []string{"foo", "bar"})
 }
 
+func (s *TestSuite) TestEnableCUDADeviceCount(c *C) {
+       s.fullRunHelper(c, `{
+    "command": ["pwd"],
+    "container_image": "`+arvadostest.DockerImage112PDH+`",
+    "cwd": "/bin",
+    "environment": {},
+    "mounts": {"/tmp": {"kind": "tmp"} },
+    "output_path": "/tmp",
+    "priority": 1,
+    "runtime_constraints": {"cuda_device_count": 2},
+    "state": "Locked",
+    "output_storage_classes": ["foo", "bar"]
+}`, nil, 0, func() {
+               fmt.Fprintln(s.executor.created.Stdout, "ok")
+       })
+       c.Check(s.executor.created.CUDADeviceCount, Equals, 2)
+}
+
+func (s *TestSuite) TestEnableCUDAHardwareCapability(c *C) {
+       s.fullRunHelper(c, `{
+    "command": ["pwd"],
+    "container_image": "`+arvadostest.DockerImage112PDH+`",
+    "cwd": "/bin",
+    "environment": {},
+    "mounts": {"/tmp": {"kind": "tmp"} },
+    "output_path": "/tmp",
+    "priority": 1,
+    "runtime_constraints": {"cuda_hardware_capability": "foo"},
+    "state": "Locked",
+    "output_storage_classes": ["foo", "bar"]
+}`, nil, 0, func() {
+               fmt.Fprintln(s.executor.created.Stdout, "ok")
+       })
+       c.Check(s.executor.created.CUDADeviceCount, Equals, 1)
+}
+
 func (s *TestSuite) TestStopOnSignal(c *C) {
        s.executor.runFunc = func() {
                s.executor.created.Stdout.Write([]byte("foo\n"))
diff --git a/lib/crunchrun/docker.go b/lib/crunchrun/docker.go
index 07f79bbcc2d11f0239a6231288a94d84a89f87fb..ab00273ef3a8eda38fccfc67b2a6e0b3c00659d3 100644 (file)
--- a/lib/crunchrun/docker.go
+++ b/lib/crunchrun/docker.go
@@ -71,7 +71,7 @@ func (e *dockerExecutor) LoadImage(imageID string, imageTarballPath string, cont
        return nil
 }
 
-func (e *dockerExecutor) Create(spec containerSpec) error {
+func (e *dockerExecutor) config(spec containerSpec) (dockercontainer.Config, dockercontainer.HostConfig) {
        e.logf("Creating Docker container")
        cfg := dockercontainer.Config{
                Image:        spec.Image,
@@ -106,6 +106,13 @@ func (e *dockerExecutor) Create(spec containerSpec) error {
                        KernelMemory: spec.RAM, // kernel portion
                },
        }
+       if spec.CUDADeviceCount != 0 {
+               hostCfg.Resources.DeviceRequests = append(hostCfg.Resources.DeviceRequests, dockercontainer.DeviceRequest{
+                       Driver:       "nvidia",
+                       Count:        spec.CUDADeviceCount,
+                       Capabilities: [][]string{[]string{"gpu", "nvidia", "compute"}},
+               })
+       }
        for path, mount := range spec.BindMounts {
                bind := mount.HostPath + ":" + path
                if mount.ReadOnly {
@@ -116,7 +123,11 @@ func (e *dockerExecutor) Create(spec containerSpec) error {
        if spec.EnableNetwork {
                hostCfg.NetworkMode = dockercontainer.NetworkMode(spec.NetworkMode)
        }
+       return cfg, hostCfg
+}
 
+func (e *dockerExecutor) Create(spec containerSpec) error {
+       cfg, hostCfg := e.config(spec)
        created, err := e.dockerclient.ContainerCreate(context.TODO(), &cfg, &hostCfg, nil, e.containerUUID)
        if err != nil {
                return fmt.Errorf("While creating container: %v", err)
diff --git a/lib/crunchrun/docker_test.go b/lib/crunchrun/docker_test.go
index 28eb59546a69ea36ecfbabf2a7bad8dc4ebb69e3..9a1573193b6801d7ffd1c32ae73a2d7a9c188784 100644 (file)
--- a/lib/crunchrun/docker_test.go
+++ b/lib/crunchrun/docker_test.go
@@ -8,6 +8,7 @@ import (
        "os/exec"
        "time"
 
+       dockercontainer "github.com/docker/docker/api/types/container"
        . "gopkg.in/check.v1"
 )
 
@@ -29,3 +30,35 @@ func (s *dockerSuite) SetUpSuite(c *C) {
                c.Assert(err, IsNil)
        }
 }
+
+var _ = Suite(&dockerStubSuite{})
+
+// dockerStubSuite tests don't really connect to the docker service,
+// so we can run them even if docker is not installed.
+type dockerStubSuite struct{}
+
+func (s *dockerStubSuite) TestDockerContainerConfig(c *C) {
+       e, err := newDockerExecutor("zzzzz-zzzzz-zzzzzzzzzzzzzzz", c.Logf, time.Second/2)
+       c.Assert(err, IsNil)
+       cfg, hostCfg := e.config(containerSpec{
+               VCPUs:           4,
+               RAM:             123123123,
+               WorkingDir:      "/WorkingDir",
+               Env:             map[string]string{"FOO": "bar"},
+               BindMounts:      map[string]bindmount{"/mnt": {HostPath: "/hostpath", ReadOnly: true}},
+               EnableNetwork:   false,
+               CUDADeviceCount: 3,
+       })
+       c.Check(cfg.WorkingDir, Equals, "/WorkingDir")
+       c.Check(cfg.Env, DeepEquals, []string{"FOO=bar"})
+       c.Check(hostCfg.NetworkMode, Equals, dockercontainer.NetworkMode("none"))
+       c.Check(hostCfg.Resources.NanoCPUs, Equals, int64(4000000000))
+       c.Check(hostCfg.Resources.Memory, Equals, int64(123123123))
+       c.Check(hostCfg.Resources.MemorySwap, Equals, int64(123123123))
+       c.Check(hostCfg.Resources.KernelMemory, Equals, int64(123123123))
+       c.Check(hostCfg.Resources.DeviceRequests, DeepEquals, []dockercontainer.DeviceRequest{{
+               Driver:       "nvidia",
+               Count:        3,
+               Capabilities: [][]string{{"gpu", "nvidia", "compute"}},
+       }})
+}
diff --git a/lib/crunchrun/executor.go b/lib/crunchrun/executor.go
index b7c341f3186b1af319780d19777d892be082a1cc..dc1bc20b7c3a110269d1f95441a6c7e75af48ace 100644 (file)
--- a/lib/crunchrun/executor.go
+++ b/lib/crunchrun/executor.go
@@ -16,19 +16,20 @@ type bindmount struct {
 }
 
 type containerSpec struct {
-       Image         string
-       VCPUs         int
-       RAM           int64
-       WorkingDir    string
-       Env           map[string]string
-       BindMounts    map[string]bindmount
-       Command       []string
-       EnableNetwork bool
-       NetworkMode   string // docker network mode, normally "default"
-       CgroupParent  string
-       Stdin         io.Reader
-       Stdout        io.Writer
-       Stderr        io.Writer
+       Image           string
+       VCPUs           int
+       RAM             int64
+       WorkingDir      string
+       Env             map[string]string
+       BindMounts      map[string]bindmount
+       Command         []string
+       EnableNetwork   bool
+       CUDADeviceCount int
+       NetworkMode     string // docker network mode, normally "default"
+       CgroupParent    string
+       Stdin           io.Reader
+       Stdout          io.Writer
+       Stderr          io.Writer
 }
 
 // containerExecutor is an interface to a container runtime
diff --git a/lib/crunchrun/singularity.go b/lib/crunchrun/singularity.go
index 5af023a83dc2dc61506818c88ccfadc5b0c22514..cda10aa611b7cf8d3d1d03822495f91a9ee0f8d6 100644 (file)
--- a/lib/crunchrun/singularity.go
+++ b/lib/crunchrun/singularity.go
@@ -241,11 +241,16 @@ func (e *singularityExecutor) Create(spec containerSpec) error {
        return nil
 }
 
-func (e *singularityExecutor) Start() error {
-       args := []string{"singularity", "exec", "--containall", "--cleanenv", "--pwd", e.spec.WorkingDir}
+func (e *singularityExecutor) execCmd(path string) *exec.Cmd {
+       args := []string{path, "exec", "--containall", "--cleanenv", "--pwd", e.spec.WorkingDir}
        if !e.spec.EnableNetwork {
                args = append(args, "--net", "--network=none")
        }
+
+       if e.spec.CUDADeviceCount != 0 {
+               args = append(args, "--nv")
+       }
+
        readonlyflag := map[bool]string{
                false: "rw",
                true:  "ro",
@@ -282,11 +287,7 @@ func (e *singularityExecutor) Start() error {
        args = append(args, e.imageFilename)
        args = append(args, e.spec.Command...)
 
-       path, err := exec.LookPath(args[0])
-       if err != nil {
-               return err
-       }
-       child := &exec.Cmd{
+       return &exec.Cmd{
                Path:   path,
                Args:   args,
                Env:    env,
@@ -294,6 +295,14 @@ func (e *singularityExecutor) Start() error {
                Stdout: e.spec.Stdout,
                Stderr: e.spec.Stderr,
        }
+}
+
+func (e *singularityExecutor) Start() error {
+       path, err := exec.LookPath("singularity")
+       if err != nil {
+               return err
+       }
+       child := e.execCmd(path)
        err = child.Start()
        if err != nil {
                return err
diff --git a/lib/crunchrun/singularity_test.go b/lib/crunchrun/singularity_test.go
index a1263da3215ad6d07d7fcf2db444c06528d7dd72..cdeafee88242b3330adcf2c5ae7550fdcb104f46 100644 (file)
--- a/lib/crunchrun/singularity_test.go
+++ b/lib/crunchrun/singularity_test.go
@@ -27,3 +27,26 @@ func (s *singularitySuite) SetUpSuite(c *C) {
                c.Assert(err, IsNil)
        }
 }
+
+var _ = Suite(&singularityStubSuite{})
+
+// singularityStubSuite tests don't really invoke singularity, so we
+// can run them even if singularity is not installed.
+type singularityStubSuite struct{}
+
+func (s *singularityStubSuite) TestSingularityExecArgs(c *C) {
+       e, err := newSingularityExecutor(c.Logf)
+       c.Assert(err, IsNil)
+       err = e.Create(containerSpec{
+               WorkingDir:      "/WorkingDir",
+               Env:             map[string]string{"FOO": "bar"},
+               BindMounts:      map[string]bindmount{"/mnt": {HostPath: "/hostpath", ReadOnly: true}},
+               EnableNetwork:   false,
+               CUDADeviceCount: 3,
+       })
+       c.Check(err, IsNil)
+       e.imageFilename = "/fake/image.sif"
+       cmd := e.execCmd("./singularity")
+       c.Check(cmd.Args, DeepEquals, []string{"./singularity", "exec", "--containall", "--cleanenv", "--pwd", "/WorkingDir", "--net", "--network=none", "--nv", "--bind", "/hostpath:/mnt:ro", "/fake/image.sif"})
+       c.Check(cmd.Env, DeepEquals, []string{"SINGULARITYENV_FOO=bar"})
+}
diff --git a/lib/service/cmd.go b/lib/service/cmd.go
index 880799b348b57b2e9d485711c2b49ccd2f1757e4..dbafc89fe4792d90b30e5fa70ec18b43a0c5107d 100644 (file)
--- a/lib/service/cmd.go
+++ b/lib/service/cmd.go
@@ -105,7 +105,8 @@ func (c *command) RunCommand(prog string, args []string, stdin io.Reader, stdout
        // logger with a new one according to the logging config.
        log = ctxlog.New(stderr, cluster.SystemLogs.Format, cluster.SystemLogs.LogLevel)
        logger := log.WithFields(logrus.Fields{
-               "PID": os.Getpid(),
+               "PID":       os.Getpid(),
+               "ClusterID": cluster.ClusterID,
        })
        ctx := ctxlog.Context(c.ctx, logger)
 
diff --git a/sdk/go/arvados/config.go b/sdk/go/arvados/config.go
index 474ce33b0ee4e9b2262bbe1b16f9ed36c0c2af38..6d5156e765c07cb580f695b3e83b03bf996172be 100644 (file)
--- a/sdk/go/arvados/config.go
+++ b/sdk/go/arvados/config.go
@@ -241,6 +241,7 @@ type Cluster struct {
                UserProfileNotificationAddress        string
                PreferDomainForUsername               string
                UserSetupMailText                     string
+               RoleGroupsVisibleToAll                bool
        }
        StorageClasses map[string]StorageClassConfig
        Volumes        map[string]Volume
diff --git a/sdk/go/arvados/container.go b/sdk/go/arvados/container.go
index 7c68bdb20222f59067b5c5f1d89bad8ea6fef5fe..27afc1a3abbb31f380a20fdfb6110a5300168afb 100644 (file)
--- a/sdk/go/arvados/container.go
+++ b/sdk/go/arvados/container.go
@@ -96,10 +96,13 @@ type Mount struct {
 // RuntimeConstraints specify a container's compute resources (RAM,
 // CPU) and network connectivity.
 type RuntimeConstraints struct {
-       API          bool  `json:"API"`
-       RAM          int64 `json:"ram"`
-       VCPUs        int   `json:"vcpus"`
-       KeepCacheRAM int64 `json:"keep_cache_ram"`
+       API                    bool   `json:"API"`
+       RAM                    int64  `json:"ram"`
+       VCPUs                  int    `json:"vcpus"`
+       KeepCacheRAM           int64  `json:"keep_cache_ram"`
+       CUDADriverVersion      string `json:"cuda_driver_version,omitempty"`
+       CUDAHardwareCapability string `json:"cuda_hardware_capability,omitempty"`
+       CUDADeviceCount        int    `json:"cuda_device_count,omitempty"`
 }
 
 // SchedulingParameters specify a container's scheduling parameters
diff --git a/services/api/app/models/arvados_model.rb b/services/api/app/models/arvados_model.rb
index af226cde821399a0d115fdddfc698ec57b39ace9..54b1394ffd06245e6d7fc7c7fd97f004abbde3b4 100644 (file)
--- a/services/api/app/models/arvados_model.rb
+++ b/services/api/app/models/arvados_model.rb
@@ -384,6 +384,14 @@ class ArvadosModel < ApplicationRecord
         direct_check = " OR " + direct_check
       end
 
+      if Rails.configuration.Users.RoleGroupsVisibleToAll &&
+         sql_table == "groups" &&
+         users_list.select { |u| u.is_active }.any?
+        # All role groups are readable (but we still need the other
+        # direct_check clauses to handle non-role groups).
+        direct_check += " OR #{sql_table}.group_class = 'role'"
+      end
+
       links_cond = ""
       if sql_table == "links"
         # 1) Match permission links incoming or outgoing on the
diff --git a/services/api/config/arvados_config.rb b/services/api/config/arvados_config.rb
index 49865039c4649a8a8b7270682b97fd073b742504..c5db6e6b9e443a54550a577db32594e71194afc8 100644 (file)
--- a/services/api/config/arvados_config.rb
+++ b/services/api/config/arvados_config.rb
@@ -100,6 +100,7 @@ arvcfg.declare_config "Users.UserNotifierEmailFrom", String, :user_notifier_emai
 arvcfg.declare_config "Users.UserNotifierEmailBcc", Hash
 arvcfg.declare_config "Users.NewUserNotificationRecipients", Hash, :new_user_notification_recipients, ->(cfg, k, v) { arrayToHash cfg, "Users.NewUserNotificationRecipients", v }
 arvcfg.declare_config "Users.NewInactiveUserNotificationRecipients", Hash, :new_inactive_user_notification_recipients, method(:arrayToHash)
+arvcfg.declare_config "Users.RoleGroupsVisibleToAll", Boolean
 arvcfg.declare_config "Login.LoginCluster", String
 arvcfg.declare_config "Login.TrustedClients", Hash
 arvcfg.declare_config "Login.RemoteTokenRefresh", ActiveSupport::Duration
diff --git a/services/api/config/initializers/lograge.rb b/services/api/config/initializers/lograge.rb
index 9b422462b193a400a58375bc31cf76486132d023..9c0f76691535eade936fa1712c06ea1657031c47 100644 (file)
--- a/services/api/config/initializers/lograge.rb
+++ b/services/api/config/initializers/lograge.rb
@@ -9,6 +9,7 @@ Server::Application.configure do
   config.lograge.formatter = Lograge::Formatters::Logstash.new
   config.lograge.custom_options = lambda do |event|
     payload = {
+      ClusterID: Rails.configuration.ClusterID,
       request_id: event.payload[:request_id],
       client_ipaddr: event.payload[:client_ipaddr],
       client_auth: event.payload[:client_auth],
diff --git a/services/api/test/functional/arvados/v1/groups_controller_test.rb b/services/api/test/functional/arvados/v1/groups_controller_test.rb
index 4dbccc5eb24edd07cdb09e6f2e400faa9c4f0c81..0819c2306717f08cfac634494d1e55a1e6a677d4 100644 (file)
--- a/services/api/test/functional/arvados/v1/groups_controller_test.rb
+++ b/services/api/test/functional/arvados/v1/groups_controller_test.rb
@@ -6,12 +6,19 @@ require 'test_helper'
 
 class Arvados::V1::GroupsControllerTest < ActionController::TestCase
 
-  test "attempt to delete group without read or write access" do
+  test "attempt to delete group that cannot be seen" do
+    Rails.configuration.Users.RoleGroupsVisibleToAll = false
     authorize_with :active
     post :destroy, params: {id: groups(:empty_lonely_group).uuid}
     assert_response 404
   end
 
+  test "attempt to delete group without read or write access" do
+    authorize_with :active
+    post :destroy, params: {id: groups(:empty_lonely_group).uuid}
+    assert_response 403
+  end
+
   test "attempt to delete group without write access" do
     authorize_with :active
     post :destroy, params: {id: groups(:all_users).uuid}
@@ -553,6 +560,30 @@ class Arvados::V1::GroupsControllerTest < ActionController::TestCase
     end
   end
 
+  [
+    [false, :inactive, :private_role, false],
+    [false, :spectator, :private_role, false],
+    [false, :admin, :private_role, true],
+    [true, :inactive, :private_role, false],
+    [true, :spectator, :private_role, true],
+    [true, :admin, :private_role, true],
+    # project (non-role) groups are invisible even when RoleGroupsVisibleToAll is true
+    [true, :inactive, :private, false],
+    [true, :spectator, :private, false],
+    [true, :admin, :private, true],
+  ].each do |visibleToAll, userFixture, groupFixture, visible|
+    test "with RoleGroupsVisibleToAll=#{visibleToAll}, #{groupFixture} group is #{visible ? '' : 'in'}visible to #{userFixture} user" do
+      Rails.configuration.Users.RoleGroupsVisibleToAll = visibleToAll
+      authorize_with userFixture
+      get :show, params: {id: groups(groupFixture).uuid, format: :json}
+      if visible
+        assert_response :success
+      else
+        assert_response 404
+      end
+    end
+  end
+
   ### trashed project tests ###
 
   #
diff --git a/services/api/test/integration/remote_user_test.rb b/services/api/test/integration/remote_user_test.rb
index 568d5088d9d708fdc166dc04564106d81b27f108..179d30f3cbf3c255a1570ba3227b732603dd8ef9 100644 (file)
--- a/services/api/test/integration/remote_user_test.rb
+++ b/services/api/test/integration/remote_user_test.rb
@@ -304,6 +304,7 @@ class RemoteUsersTest < ActionDispatch::IntegrationTest
   end
 
   test "list readable groups with salted token" do
+    Rails.configuration.Users.RoleGroupsVisibleToAll = false
     salted_token = salt_token(fixture: :active, remote: 'zbbbb')
     get '/arvados/v1/groups',
       params: {
diff --git a/services/api/test/unit/permission_test.rb b/services/api/test/unit/permission_test.rb
index 128d0ebaa6f6f255ce54add5e8aac9b39ecca208..647139d9ec9d38d4d5570a19e658b866bd609544 100644 (file)
--- a/services/api/test/unit/permission_test.rb
+++ b/services/api/test/unit/permission_test.rb
@@ -218,6 +218,7 @@ class PermissionTest < ActiveSupport::TestCase
   end
 
   test "manager user gets permission to minions' articles via can_manage link" do
+    Rails.configuration.Users.RoleGroupsVisibleToAll = false
     Rails.configuration.Users.ActivatedUsersAreVisibleToOthers = false
     manager = create :active_user, first_name: "Manage", last_name: "Er"
     minion = create :active_user, first_name: "Min", last_name: "Ion"
diff --git a/services/crunch-dispatch-local/crunch-dispatch-local.go b/services/crunch-dispatch-local/crunch-dispatch-local.go
index c9cbdd01fec15ca340d0e9342f8a1e24c42f1942..968b556a27e720d100abb705e3b704cb2b237299 100644 (file)
--- a/services/crunch-dispatch-local/crunch-dispatch-local.go
+++ b/services/crunch-dispatch-local/crunch-dispatch-local.go
@@ -35,11 +35,11 @@ var (
 )
 
 func main() {
-       logger := logrus.StandardLogger()
+       baseLogger := logrus.StandardLogger()
        if os.Getenv("DEBUG") != "" {
-               logger.SetLevel(logrus.DebugLevel)
+               baseLogger.SetLevel(logrus.DebugLevel)
        }
-       logger.Formatter = &logrus.JSONFormatter{
+       baseLogger.Formatter = &logrus.JSONFormatter{
                TimestampFormat: "2006-01-02T15:04:05.000000000Z07:00",
        }
 
@@ -70,7 +70,7 @@ func main() {
                return
        }
 
-       loader := config.NewLoader(nil, logger)
+       loader := config.NewLoader(nil, baseLogger)
        cfg, err := loader.Load()
        if err != nil {
                fmt.Fprintf(os.Stderr, "error loading config: %s\n", err)
@@ -82,6 +82,7 @@ func main() {
                os.Exit(1)
        }
 
+       logger := baseLogger.WithField("ClusterID", cluster.ClusterID)
        logger.Printf("crunch-dispatch-local %s started", version)
 
        runningCmds = make(map[string]*exec.Cmd)
diff --git a/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go b/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go
index ff1077fae63ace1703e8c66ad95e54bb32d5a49a..84105e1fc77e5315df0ab1a7d3ba8d6b219f9b99 100644 (file)
--- a/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go
+++ b/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go
@@ -114,6 +114,8 @@ func (disp *Dispatcher) configure(prog string, args []string) error {
                return fmt.Errorf("config error: %s", err)
        }
 
+       disp.logger = disp.logger.WithField("ClusterID", disp.cluster.ClusterID)
+
        disp.Client.APIHost = disp.cluster.Services.Controller.ExternalURL.Host
        disp.Client.AuthToken = disp.cluster.SystemRootToken
        disp.Client.Insecure = disp.cluster.TLS.Insecure
diff --git a/services/keep-web/main.go b/services/keep-web/main.go
index aa97a18ad899af1a49897e72e6c63ec439dbe35b..208b23b93b5206c0e55cea5a8eab74849a54855f 100644 (file)
--- a/services/keep-web/main.go
+++ b/services/keep-web/main.go
@@ -5,6 +5,7 @@
 package main
 
 import (
+       "context"
        "flag"
        "fmt"
        "mime"
@@ -13,6 +14,7 @@ import (
        "git.arvados.org/arvados.git/lib/cmd"
        "git.arvados.org/arvados.git/lib/config"
        "git.arvados.org/arvados.git/sdk/go/arvados"
+       "git.arvados.org/arvados.git/sdk/go/ctxlog"
        "github.com/coreos/go-systemd/daemon"
        "github.com/ghodss/yaml"
        "github.com/sirupsen/logrus"
@@ -97,16 +99,17 @@ func configure(logger log.FieldLogger, args []string) (*Config, error) {
 }
 
 func main() {
-       logger := log.New()
-
+       initLogger := log.StandardLogger()
+       logger := initLogger.WithField("PID", os.Getpid())
        cfg, err := configure(logger, os.Args)
        if err != nil {
-               logger.Fatal(err)
+               log.Fatal(err)
        } else if cfg == nil {
                return
        }
-
-       log.Printf("keep-web %s started", version)
+       logger = logger.WithField("ClusterID", cfg.cluster.ClusterID)
+       logger.Printf("keep-web %s started", version)
+       ctx := ctxlog.Context(context.Background(), logger)
 
        if ext := ".txt"; mime.TypeByExtension(ext) == "" {
                log.Warnf("cannot look up MIME type for %q -- this probably means /etc/mime.types is missing -- clients will see incorrect content types", ext)
@@ -114,14 +117,14 @@ func main() {
 
        os.Setenv("ARVADOS_API_HOST", cfg.cluster.Services.Controller.ExternalURL.Host)
        srv := &server{Config: cfg}
-       if err := srv.Start(logrus.StandardLogger()); err != nil {
-               log.Fatal(err)
+       if err := srv.Start(ctx, initLogger); err != nil {
+               logger.Fatal(err)
        }
        if _, err := daemon.SdNotify(false, "READY=1"); err != nil {
-               log.Printf("Error notifying init daemon: %v", err)
+               logger.Printf("Error notifying init daemon: %v", err)
        }
-       log.Println("Listening at", srv.Addr)
+       logger.Println("Listening at", srv.Addr)
        if err := srv.Wait(); err != nil {
-               log.Fatal(err)
+               logger.Fatal(err)
        }
 }
diff --git a/services/keep-web/server.go b/services/keep-web/server.go
index 586f6b805736e23437357dbc8eb1a8cf4b5a5cc7..24f1b77be238bd188b482a9beb678e1b7dfc812f 100644 (file)
--- a/services/keep-web/server.go
+++ b/services/keep-web/server.go
@@ -10,7 +10,6 @@ import (
        "net/http"
 
        "git.arvados.org/arvados.git/sdk/go/arvados"
-       "git.arvados.org/arvados.git/sdk/go/ctxlog"
        "git.arvados.org/arvados.git/sdk/go/httpserver"
        "github.com/prometheus/client_golang/prometheus"
        "github.com/sirupsen/logrus"
@@ -21,7 +20,7 @@ type server struct {
        Config *Config
 }
 
-func (srv *server) Start(logger *logrus.Logger) error {
+func (srv *server) Start(ctx context.Context, logger *logrus.Logger) error {
        h := &handler{Config: srv.Config}
        reg := prometheus.NewRegistry()
        h.Config.Cache.registry = reg
@@ -33,7 +32,7 @@ func (srv *server) Start(logger *logrus.Logger) error {
        mh := httpserver.Instrument(reg, logger, httpserver.AddRequestIDs(httpserver.LogRequests(h)))
        h.MetricsAPI = mh.ServeAPI(h.Config.cluster.ManagementToken, http.NotFoundHandler())
        srv.Handler = mh
-       srv.BaseContext = func(net.Listener) context.Context { return ctxlog.Context(context.Background(), logger) }
+       srv.BaseContext = func(net.Listener) context.Context { return ctx }
        var listen arvados.URL
        for listen = range srv.Config.cluster.Services.WebDAV.InternalURLs {
                break
diff --git a/services/keep-web/server_test.go b/services/keep-web/server_test.go
index 54e9ddf3704d606a14c2b8965c1bf611cacb76bd..2d28dbc5d7175fe78149487f532d4b6b5f4a08ac 100644 (file)
--- a/services/keep-web/server_test.go
+++ b/services/keep-web/server_test.go
@@ -6,6 +6,7 @@ package main
 
 import (
        "bytes"
+       "context"
        "crypto/md5"
        "encoding/json"
        "fmt"
@@ -447,7 +448,9 @@ func (s *IntegrationSuite) SetUpTest(c *check.C) {
        cfg.cluster.Users.AnonymousUserToken = arvadostest.AnonymousToken
        s.ArvConfig = arvCfg
        s.testServer = &server{Config: cfg}
-       err = s.testServer.Start(ctxlog.TestLogger(c))
+       logger := ctxlog.TestLogger(c)
+       ctx := ctxlog.Context(context.Background(), logger)
+       err = s.testServer.Start(ctx, logger)
        c.Assert(err, check.Equals, nil)
 }
 
diff --git a/services/keepproxy/keepproxy.go b/services/keepproxy/keepproxy.go
index 7c1360ad71a2e945b2aaee72d4f6aadabaf664ba..c2760a2a4fb462e193f833ac97f59167871c7065 100644 (file)
--- a/services/keepproxy/keepproxy.go
+++ b/services/keepproxy/keepproxy.go
@@ -5,6 +5,7 @@
 package main
 
 import (
+       "context"
        "errors"
        "flag"
        "fmt"
@@ -23,6 +24,7 @@ import (
        "git.arvados.org/arvados.git/lib/config"
        "git.arvados.org/arvados.git/sdk/go/arvados"
        "git.arvados.org/arvados.git/sdk/go/arvadosclient"
+       "git.arvados.org/arvados.git/sdk/go/ctxlog"
        "git.arvados.org/arvados.git/sdk/go/health"
        "git.arvados.org/arvados.git/sdk/go/httpserver"
        "git.arvados.org/arvados.git/sdk/go/keepclient"
@@ -30,7 +32,7 @@ import (
        "github.com/ghodss/yaml"
        "github.com/gorilla/mux"
        lru "github.com/hashicorp/golang-lru"
-       log "github.com/sirupsen/logrus"
+       "github.com/sirupsen/logrus"
 )
 
 var version = "dev"
@@ -42,13 +44,19 @@ var (
 
 const rfc3339NanoFixed = "2006-01-02T15:04:05.000000000Z07:00"
 
-func configure(logger log.FieldLogger, args []string) (*arvados.Cluster, error) {
+func configure(args []string) (*arvados.Cluster, logrus.FieldLogger, error) {
        prog := args[0]
        flags := flag.NewFlagSet(prog, flag.ContinueOnError)
 
        dumpConfig := flags.Bool("dump-config", false, "write current configuration to stdout and exit")
        getVersion := flags.Bool("version", false, "Print version information and exit.")
 
+       initLogger := logrus.New()
+       initLogger.Formatter = &logrus.JSONFormatter{
+               TimestampFormat: rfc3339NanoFixed,
+       }
+       var logger logrus.FieldLogger = initLogger
+
        loader := config.NewLoader(os.Stdin, logger)
        loader.SetupFlags(flags)
        args = loader.MungeLegacyConfigArgs(logger, args[1:], "-legacy-keepproxy-config")
@@ -57,55 +65,56 @@ func configure(logger log.FieldLogger, args []string) (*arvados.Cluster, error)
                os.Exit(code)
        } else if *getVersion {
                fmt.Printf("keepproxy %s\n", version)
-               return nil, nil
+               return nil, logger, nil
        }
 
        cfg, err := loader.Load()
        if err != nil {
-               return nil, err
+               return nil, logger, err
        }
        cluster, err := cfg.GetCluster("")
        if err != nil {
-               return nil, err
+               return nil, logger, err
        }
 
+       logger = ctxlog.New(os.Stderr, cluster.SystemLogs.Format, cluster.SystemLogs.LogLevel).WithFields(logrus.Fields{
+               "ClusterID": cluster.ClusterID,
+               "PID":       os.Getpid(),
+       })
+
        if *dumpConfig {
                out, err := yaml.Marshal(cfg)
                if err != nil {
-                       return nil, err
+                       return nil, logger, err
                }
                if _, err := os.Stdout.Write(out); err != nil {
-                       return nil, err
+                       return nil, logger, err
                }
-               return nil, nil
+               return nil, logger, nil
        }
-       return cluster, nil
+
+       return cluster, logger, nil
 }
 
 func main() {
-       logger := log.New()
-       logger.Formatter = &log.JSONFormatter{
-               TimestampFormat: rfc3339NanoFixed,
-       }
-
-       cluster, err := configure(logger, os.Args)
+       cluster, logger, err := configure(os.Args)
        if err != nil {
-               log.Fatal(err)
+               logger.Fatal(err)
        }
        if cluster == nil {
                return
        }
 
-       log.Printf("keepproxy %s started", version)
+       logger.Printf("keepproxy %s started", version)
 
        if err := run(logger, cluster); err != nil {
-               log.Fatal(err)
+               logger.Fatal(err)
        }
 
-       log.Println("shutting down")
+       logger.Println("shutting down")
 }
 
-func run(logger log.FieldLogger, cluster *arvados.Cluster) error {
+func run(logger logrus.FieldLogger, cluster *arvados.Cluster) error {
        client, err := arvados.NewClientFromConfig(cluster)
        if err != nil {
                return err
@@ -124,7 +133,7 @@ func run(logger log.FieldLogger, cluster *arvados.Cluster) error {
        }
 
        if cluster.SystemLogs.LogLevel == "debug" {
-               keepclient.DebugPrintf = log.Printf
+               keepclient.DebugPrintf = logger.Printf
        }
        kc, err := keepclient.MakeKeepClient(arv)
        if err != nil {
@@ -148,16 +157,16 @@ func run(logger log.FieldLogger, cluster *arvados.Cluster) error {
        }
 
        if _, err := daemon.SdNotify(false, "READY=1"); err != nil {
-               log.Printf("Error notifying init daemon: %v", err)
+               logger.Printf("Error notifying init daemon: %v", err)
        }
-       log.Println("listening at", listener.Addr())
+       logger.Println("listening at", listener.Addr())
 
        // Shut down the server gracefully (by closing the listener)
        // if SIGTERM is received.
        term := make(chan os.Signal, 1)
        go func(sig <-chan os.Signal) {
                s := <-sig
-               log.Println("caught signal:", s)
+               logger.Println("caught signal:", s)
                listener.Close()
        }(term)
        signal.Notify(term, syscall.SIGTERM)
@@ -168,7 +177,13 @@ func run(logger log.FieldLogger, cluster *arvados.Cluster) error {
        if err != nil {
                return err
        }
-       return http.Serve(listener, httpserver.AddRequestIDs(httpserver.LogRequests(router)))
+       server := http.Server{
+               Handler: httpserver.AddRequestIDs(httpserver.LogRequests(router)),
+               BaseContext: func(net.Listener) context.Context {
+                       return ctxlog.Context(context.Background(), logger)
+               },
+       }
+       return server.Serve(listener)
 }
 
 type TokenCacheEntry struct {
@@ -267,7 +282,7 @@ func (h *proxyHandler) CheckAuthorizationHeader(req *http.Request) (pass bool, t
                }
        }
        if err != nil {
-               log.Printf("%s: CheckAuthorizationHeader error: %v", GetRemoteAddress(req), err)
+               ctxlog.FromContext(req.Context()).Printf("%s: CheckAuthorizationHeader error: %v", GetRemoteAddress(req), err)
                return false, "", nil
        }
 
@@ -309,13 +324,13 @@ type proxyHandler struct {
        *APITokenCache
        timeout   time.Duration
        transport *http.Transport
-       logger    log.FieldLogger
+       logger    logrus.FieldLogger
        cluster   *arvados.Cluster
 }
 
 // MakeRESTRouter returns an http.Handler that passes GET and PUT
 // requests to the appropriate handlers.
-func MakeRESTRouter(kc *keepclient.KeepClient, timeout time.Duration, cluster *arvados.Cluster, logger log.FieldLogger) (http.Handler, error) {
+func MakeRESTRouter(kc *keepclient.KeepClient, timeout time.Duration, cluster *arvados.Cluster, logger logrus.FieldLogger) (http.Handler, error) {
        rest := mux.NewRouter()
 
        transport := defaultTransport
@@ -390,12 +405,12 @@ func SetCorsHeaders(resp http.ResponseWriter) {
 type InvalidPathHandler struct{}
 
 func (InvalidPathHandler) ServeHTTP(resp http.ResponseWriter, req *http.Request) {
-       log.Printf("%s: %s %s unroutable", GetRemoteAddress(req), req.Method, req.URL.Path)
+       ctxlog.FromContext(req.Context()).Printf("%s: %s %s unroutable", GetRemoteAddress(req), req.Method, req.URL.Path)
        http.Error(resp, "Bad request", http.StatusBadRequest)
 }
 
 func (h *proxyHandler) Options(resp http.ResponseWriter, req *http.Request) {
-       log.Printf("%s: %s %s", GetRemoteAddress(req), req.Method, req.URL.Path)
+       ctxlog.FromContext(req.Context()).Printf("%s: %s %s", GetRemoteAddress(req), req.Method, req.URL.Path)
        SetCorsHeaders(resp)
 }
 
@@ -419,7 +434,7 @@ func (h *proxyHandler) Get(resp http.ResponseWriter, req *http.Request) {
        var proxiedURI = "-"
 
        defer func() {
-               log.Println(GetRemoteAddress(req), req.Method, req.URL.Path, status, expectLength, responseLength, proxiedURI, err)
+               h.logger.Println(GetRemoteAddress(req), req.Method, req.URL.Path, status, expectLength, responseLength, proxiedURI, err)
                if status != http.StatusOK {
                        http.Error(resp, err.Error(), status)
                }
@@ -470,7 +485,7 @@ func (h *proxyHandler) Get(resp http.ResponseWriter, req *http.Request) {
        }
 
        if expectLength == -1 {
-               log.Println("Warning:", GetRemoteAddress(req), req.Method, proxiedURI, "Content-Length not provided")
+               h.logger.Println("Warning:", GetRemoteAddress(req), req.Method, proxiedURI, "Content-Length not provided")
        }
 
        switch respErr := err.(type) {
@@ -518,7 +533,7 @@ func (h *proxyHandler) Put(resp http.ResponseWriter, req *http.Request) {
        var locatorOut string = "-"
 
        defer func() {
-               log.Println(GetRemoteAddress(req), req.Method, req.URL.Path, status, expectLength, kc.Want_replicas, wroteReplicas, locatorOut, err)
+               h.logger.Println(GetRemoteAddress(req), req.Method, req.URL.Path, status, expectLength, kc.Want_replicas, wroteReplicas, locatorOut, err)
                if status != http.StatusOK {
                        http.Error(resp, err.Error(), status)
                }