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{% include 'notebox_begin_warning' %}
-arvados-dispatch-lsf is only relevant for on premises clusters that will spool jobs to LSF. Skip this section if you are installing a cloud cluster.
+@arvados-dispatch-lsf@ is only relevant for on premises clusters that will spool jobs to LSF. Skip this section if you use Slurm or if you are installing a cloud cluster.
{% include 'notebox_end' %}
-Containers can be dispatched to an LSF cluster. The dispatcher sends work to the cluster using LSF's @bsub@ command, so it works in a variety of LSF configurations.
-
-*LSF support is currently considered experimental.*
+h2(#overview). Overview
-Limitations include:
-* Arvados container priority is not propagated to LSF job priority. This can cause inefficient use of compute resources, and even deadlock if there are fewer compute nodes than concurrent Arvados workflows.
-* Combining LSF with docker may not work, depending on LSF configuration and user/group IDs (if LSF only sets up the configured user's primary group ID when executing the crunch-run process on a compute node, it may not have permission to connect to the docker daemon).
+Containers can be dispatched to an LSF cluster. The dispatcher sends work to the cluster using LSF's @bsub@ command, so it works in a variety of LSF configurations.
In order to run containers, you must choose a user that has permission to set up FUSE mounts and run Singularity/Docker containers on each compute node. This install guide refers to this user as the @crunch@ user. We recommend you create this user on each compute node with the same UID and GID, and add it to the @fuse@ and @docker@ system groups to grant it the necessary permissions. However, you can run the dispatcher under any account with sufficient permissions across the cluster.
-Set up all of your compute nodes "as you would for a SLURM cluster":../crunch2-slurm/install-compute-node.html.
+Set up all of your compute nodes with "Docker":../crunch2/install-compute-node-singularity.html or "Singularity":../crunch2/install-compute-node-docker.html.
+*Current limitations*:
+* Arvados container priority is not propagated to LSF job priority. This can cause inefficient use of compute resources, and even deadlock if there are fewer compute nodes than concurrent Arvados workflows.
+* Combining LSF with docker may not work, depending on LSF configuration and user/group IDs (if LSF only sets up the configured user's primary group ID when executing the crunch-run process on a compute node, it may not have permission to connect to the docker daemon).
h2(#update-config). Update config.yml
Arvados-dispatch-lsf reads the common configuration file at @/etc/arvados/config.yml@.
-Review the following configuration parameters and adjust as needed.
+Add a DispatchLSF entry to the Services section, using the hostname where @arvados-dispatch-lsf@ will run, and an available port:
+
+<notextile>
+<pre> Services:
+ DispatchLSF:
+ InternalURLs:
+ "http://<code class="userinput">hostname.zzzzz.arvadosapi.com:9007</code>": {}</pre>
+</notextile>
+Review the following configuration parameters and adjust as needed.
h3(#BsubSudoUser). Containers.LSF.BsubSudoUser
-arvados-dispatch-lsf uses @sudo@ to execute @bsub@, for example @sudo -E -u crunch bsub [...]@. To use a user account other than @crunch@, configure @BsubSudoUser@:
+arvados-dispatch-lsf uses @sudo@ to execute @bsub@, for example @sudo -E -u crunch bsub [...]@. This means the @crunch@ account must exist on the hosts where LSF jobs run ("execution hosts"), as well as on the host where you are installing the Arvados LSF dispatcher (the "submission host"). To use a user account other than @crunch@, configure @BsubSudoUser@:
<notextile>
<pre> Containers:
h3(#SbatchArguments). Containers.LSF.BsubArgumentsList
-When arvados-dispatch-lsf invokes @bsub@, you can add arguments to the command by specifying @BsubArgumentsList@. You can use this to send the jobs to specific cluster partitions or add resource requests. Set @BsubArgumentsList@ to an array of strings. For example:
+When arvados-dispatch-lsf invokes @bsub@, you can add arguments to the command by specifying @BsubArgumentsList@. You can use this to send the jobs to specific cluster partitions or add resource requests. Set @BsubArgumentsList@ to an array of strings.
+
+Template variables starting with % will be substituted as follows:
+
+%U uuid
+%C number of VCPUs
+%M memory in MB
+%T tmp in MB
+%G number of GPU devices (@runtime_constraints.cuda.device_count@)
+
+Use %% to express a literal %. The %%J in the default will be changed to %J, which is interpreted by @bsub@ itself.
+
+For example:
<notextile>
<pre> Containers:
LSF:
- <code class="userinput">BsubArgumentsList: <b>["-C", "0"]</b></code>
+ <code class="userinput">BsubArgumentsList: <b>["-o", "/tmp/crunch-run.%%J.out", "-e", "/tmp/crunch-run.%%J.err", "-J", "%U", "-n", "%C", "-D", "%MMB", "-R", "rusage[mem=%MMB:tmp=%TMB] span[hosts=1]", "-R", "select[mem>=%MMB]", "-R", "select[tmp>=%TMB]", "-R", "select[ncpus>=%C]"]</b></code>
</pre>
</notextile>
+Note that the default value for @BsubArgumentsList@ uses the @-o@ and @-e@ arguments to write stdout/stderr data to files in @/tmp@ on the compute nodes, which is helpful for troubleshooting installation/configuration problems. Ensure you have something in place to delete old files from @/tmp@, or adjust these arguments accordingly.
+
+h3(#SbatchArguments). Containers.LSF.BsubCUDAArguments
+
+If the container requests access to GPUs (@runtime_constraints.cuda.device_count@ of the container request is greater than zero), the command line arguments in @BsubCUDAArguments@ will be added to the command line _after_ @BsubArgumentsList@. This should consist of the additional @bsub@ flags your site requires to schedule the job on a node with GPU support. Set @BsubCUDAArguments@ to an array of strings. For example:
+
+<notextile>
+<pre> Containers:
+ LSF:
+ <code class="userinput">BsubCUDAArguments: <b>["-gpu", "num=%G"]</b></code>
+</pre>
+</notextile>
h3(#PollPeriod). Containers.PollInterval
projects / arvados.git / blobdiff