...
-h1. Crunch setup
-
The dispatcher normally runs on the same host/VM as the API server.
-h4. Perl SDK dependencies
+h2. Perl SDK dependencies
-* @apt-get install libjson-perl libwww-perl libio-socket-ssl-perl libipc-system-simple-perl@
+Install the Perl SDK on the controller.
-h4. Python SDK dependencies
+* See "Perl SDK":{{site.baseurl}}/sdk/perl/index.html page for details.
-On controller and all compute nodes:
+h2. Python SDK dependencies
-* @apt-get install python-pip@
-* @pip install --upgrade virtualenv arvados-python-client@
+Install the Python SDK and CLI tools on controller and all compute nodes.
-h4. Likely crunch job dependencies
+* See "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html page for details.
-On compute nodes:
+h2(#slurm). Set up SLURM
-* @pip install --upgrade pyvcf@
+On the API server, install SLURM and munge, and generate a munge key.
-h4. Redis
+On Debian-based systems:
-On controller:
+<notextile>
+<pre><code>~$ <span class="userinput">sudo /usr/bin/apt-get install slurm-llnl munge</span>
+~$ <span class="userinput">sudo /usr/sbin/create-munge-key</span>
+</code></pre>
+</notextile>
-* @apt-get install redis-server@
+On Red Hat-based systems, "install SLURM and munge from source following their installation guide":https://computing.llnl.gov/linux/slurm/quickstart_admin.html.
-h4. Crunch user account
+Now we need to give SLURM a configuration file in @/etc/slurm-llnl/slurm.conf@. Here's an example:
-On compute nodes and controller:
+<notextile>
+<pre>
+ControlMachine=uuid_prefix.your.domain
+SlurmctldPort=6817
+SlurmdPort=6818
+AuthType=auth/munge
+StateSaveLocation=/tmp
+SlurmdSpoolDir=/tmp/slurmd
+SwitchType=switch/none
+MpiDefault=none
+SlurmctldPidFile=/var/run/slurmctld.pid
+SlurmdPidFile=/var/run/slurmd.pid
+ProctrackType=proctrack/pgid
+CacheGroups=0
+ReturnToService=2
+TaskPlugin=task/affinity
+#
+# TIMERS
+SlurmctldTimeout=300
+SlurmdTimeout=300
+InactiveLimit=0
+MinJobAge=300
+KillWait=30
+Waittime=0
+#
+# SCHEDULING
+SchedulerType=sched/backfill
+SchedulerPort=7321
+SelectType=select/cons_res
+SelectTypeParameters=CR_CPU_Memory
+FastSchedule=1
+#
+# LOGGING
+SlurmctldDebug=3
+#SlurmctldLogFile=
+SlurmdDebug=3
+#SlurmdLogFile=
+JobCompType=jobcomp/none
+#JobCompLoc=
+JobAcctGatherType=jobacct_gather/none
+#
+# COMPUTE NODES
+NodeName=DEFAULT
+PartitionName=DEFAULT MaxTime=INFINITE State=UP
+PartitionName=compute Default=YES Shared=yes
+
+NodeName=compute[0-255]
+
+PartitionName=compute Nodes=compute[0-255]
+</pre>
+</notextile>
-* @adduser crunch@
+Please make sure to update the value of the @ControlMachine@ parameter to the hostname of your dispatcher (API server).
-The crunch user should have the same UID, GID, and home directory on all compute nodes and on the controller.
+h2. Enable SLURM job dispatch
-h4. Repositories
+In your API server's @application.yml@ configuration file, add the line @crunch_job_wrapper: :slurm_immediate@ under the appropriate section. (The second colon is not a typo. It denotes a Ruby symbol.)
-Crunch scripts must be in git repositories in @/var/cache/git/*/.git@ (or whatever is configured in @services/api/config/environments/production.rb@).
+h2. Crunch user account
-h4. Importing commits
+Run @sudo adduser crunch@. The crunch user should have the same UID, GID, and home directory on all compute nodes and on the dispatcher (API server).
-@services/api/script/import_commits.rb production@ must run periodically. Example @/var/service/arvados_import_commits/run@ script for daemontools or runit:
+h2. Git Repositories
-<pre>
-#!/bin/sh
-set -e
-while sleep 60
-do
- cd /path/to/arvados/services/api
- setuidgid www-data env RAILS_ENV=production /usr/local/rvm/bin/rvm 2.0.0 do bundle exec ./script/import_commits.rb 2>&1
-done
-</pre>
+Crunch scripts must be in Git repositories in the directory configured as @git_repositories_dir@/*.git (see the "API server installation":install-api-server.html#git_repositories_dir).
-Once you have imported some commits, you should be able to create a new job:
+Once you have a repository with commits -- and you have read access to the repository -- you should be able to create a new job:
<pre>
read -rd $'\000' newjob <<EOF; arv job create --job "$newjob"
{"script_parameters":{"input":"f815ec01d5d2f11cb12874ab2ed50daa"},
"script_version":"master",
- "script":"hash"}
+ "script":"hash",
+ "repository":"arvados"}
EOF
</pre>
ArgumentError: Specified script_version does not resolve to a commit
</pre>
-h4. Running jobs
+h2. Running jobs
* @services/api/script/crunch-dispatch.rb@ must be running.
* @crunch-dispatch.rb@ needs @services/crunch/crunch-job@ in its @PATH@.
-* @crunch-job@ needs @sdk/perl/lib@ and @warehouse-apps/libwarehouse-perl/lib@ in its @PERLLIB@
-* @crunch-job@ needs @ARVADOS_API_HOST@ (and, if necessary in a development environment, @ARVADOS_API_HOST_INSECURE@)
+* @crunch-job@ needs the installation path of the Perl SDK in its @PERLLIB@.
+* @crunch-job@ needs the @ARVADOS_API_HOST@ (and, if necessary in a development environment, @ARVADOS_API_HOST_INSECURE@) environment variable set.
Example @/var/service/arvados_crunch_dispatch/run@ script:
<pre>
#!/bin/sh
set -e
+
+rvmexec=""
+## uncomment this line if you use rvm:
+#rvmexec="/usr/local/rvm/bin/rvm-exec 2.1.1"
+
export PATH="$PATH":/path/to/arvados/services/crunch
-export PERLLIB=/path/to/arvados/sdk/perl/lib:/path/to/warehouse-apps/libwarehouse-perl/lib
export ARVADOS_API_HOST={{ site.arvados_api_host }}
export CRUNCH_DISPATCH_LOCKFILE=/var/lock/crunch-dispatch
+# This is the path to docker on your compute nodes. You might need to
+# change it to "docker", "/opt/bin/docker", etc.
+export CRUNCH_JOB_DOCKER_BIN=docker.io
+
fuser -TERM -k $CRUNCH_DISPATCH_LOCKFILE || true
## Only if your SSL cert is unverifiable:
# export ARVADOS_API_HOST_INSECURE=yes
cd /path/to/arvados/services/api
-RAILS_ENV=production /usr/local/rvm/bin/rvm 2.0.0 do bundle exec ./script/crunch-dispatch.rb 2>&1
+export RAILS_ENV=production
+exec $rvmexec bundle exec ./script/crunch-dispatch.rb 2>&1
</pre>
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