Review the following configuration parameters and adjust as needed.
+{% include 'hpc_max_gateway_tunnels' %}
+
h3(#BsubSudoUser). Containers.LSF.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>
-h3(#SbatchArguments). Containers.LSF.BsubArgumentsList
+h3(#BsubArgumentsList). 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.
+
+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@)
+%W maximum job run time in minutes, suitable for use with @-W@ or @-We@ flags (see MaxRunTimeOverhead MaxRunTimeDefault below)
+
+Use %% to express a literal %. The %%J in the default will be changed to %J, which is interpreted by @bsub@ itself.
-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:
+For example:
<notextile>
<pre> Containers:
LSF:
- <code class="userinput">BsubArgumentsList: <b>["-C", "0", "-o", "/tmp/crunch-run.%J.out", "-e", "/tmp/crunch-run.%J.err"]</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]", "-We", "%W"]</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(#BsubCUDAArguments). 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(#MaxRunTimeOverhead). Containers.LSF.MaxRunTimeOverhead
+
+Extra time to add to each container's @scheduling_parameters.max_run_time@ value when substituting for @%W@ in @BsubArgumentsList@, to account for time spent setting up the container image, copying output files, etc.
+
+h3(#MaxRunTimeDefault). Containers.LSF.MaxRunTimeDefault
-h3(#PollPeriod). Containers.PollInterval
+Default @max_run_time@ value to use for containers that do not specify one in @scheduling_parameters.max_run_time@. If this is zero, and @BsubArgumentsList@ contains @"-W", "%W"@ or @"-We", "%W"@, those arguments will be dropped when submitting containers that do not specify @scheduling_parameters.max_run_time@.
+
+h3(#PollInterval). Containers.PollInterval
arvados-dispatch-lsf polls the API server periodically for new containers to run. The @PollInterval@ option controls how often this poll happens. Set this to a string of numbers suffixed with one of the time units @s@, @m@, or @h@. For example:
</notextile>
-h3(#CrunchRunCommand-network). Containers.CrunchRunArgumentList: Using host networking for containers
+h3(#CrunchRunArgumentList). Containers.CrunchRunArgumentList: Using host networking for containers
Older Linux kernels (prior to 3.18) have bugs in network namespace handling which can lead to compute node lockups. This by is indicated by blocked kernel tasks in "Workqueue: netns cleanup_net". If you are experiencing this problem, as a workaround you can disable use of network namespaces by Docker across the cluster. Be aware this reduces container isolation, which may be a security risk.
</pre>
</notextile>
+
+h3(#InstanceTypes). InstanceTypes: Avoid submitting jobs with unsatisfiable resource constraints
+
+LSF does not provide feedback when a submitted job's RAM, CPU, or disk space constraints cannot be satisfied by any node: the job will wait in the queue indefinitely with "pending" status, reported by Arvados as "queued".
+
+As a workaround, you can configure @InstanceTypes@ with your LSF cluster's compute node sizes. Arvados will use these sizes to determine when a container is impossible to run, and cancel it instead of submitting an LSF job.
+
+Apart from detecting non-runnable containers, the configured instance types will not have any effect on scheduling.
+
+<notextile>
+<pre> InstanceTypes:
+ most-ram:
+ VCPUs: 8
+ RAM: 640GiB
+ IncludedScratch: 640GB
+ most-cpus:
+ VCPUs: 32
+ RAM: 256GiB
+ IncludedScratch: 640GB
+ gpu:
+ VCPUs: 8
+ RAM: 256GiB
+ IncludedScratch: 640GB
+ CUDA:
+ DriverVersion: "11.4"
+ HardwareCapability: "7.5"
+ DeviceCount: 1
+</pre>
+</notextile>
+
+
{% assign arvados_component = 'arvados-dispatch-lsf' %}
{% include 'install_packages' %}
{% include 'start_service' %}
{% include 'restart_api' %}
+
+h2(#confirm-working). Confirm working installation
+
+On the dispatch node, start monitoring the arvados-dispatch-lsf logs:
+
+<notextile>
+<pre><code># <span class="userinput">journalctl -o cat -fu arvados-dispatch-lsf.service</span>
+</code></pre>
+</notextile>
+
+In another terminal window, use the diagnostics tool to run a simple container.
+
+<notextile>
+<pre><code># <span class="userinput">arvados-client sudo diagnostics</span>
+INFO 5: running health check (same as `arvados-server check`)
+INFO 10: getting discovery document from https://zzzzz.arvadosapi.com/discovery/v1/apis/arvados/v1/rest
+...
+INFO 160: running a container
+INFO ... container request submitted, waiting up to 10m for container to run
+</code></pre>
+</notextile>
+
+After performing a number of other quick tests, this will submit a new container request and wait for it to finish.
+
+While the diagnostics tool is waiting, the @arvados-dispatch-lsf@ logs will show details about submitting an LSF job to run the container.
projects / arvados.git / blobdiff