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.
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
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 with Docker or Singularity.
Arvados-dispatch-lsf reads the common configuration file at
Add a DispatchLSF entry to the Services section, using the hostname where
arvados-dispatch-lsf will run, and an available port:
Services: DispatchLSF: InternalURLs: "http://
Review the following configuration parameters and adjust as needed.
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
Alternatively, you can arrange for the arvados-dispatch-lsf process to run as an unprivileged user that has a corresponding account on all compute nodes, and disable the use of
sudo by specifying an empty string:
Containers: LSF: # Don't use sudo
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:
%C number of VCPUs
%M memory in MB
%T tmp in MB
%G number of GPU devices (
Use %% to express a literal %. The %%J in the default will be changed to %J, which is interpreted by
BsubArgumentsList: ["-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]"]
Note that the default value for
BsubArgumentsList uses the
-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.
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:
BsubCUDAArguments: ["-gpu", "num=%G"]
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
h. For example:
Extra RAM to reserve (in bytes) on each LSF job submitted by Arvados, which is added to the amount specified in the container’s
runtime_constraints. If not provided, the default value is zero.
KB is 103,
KiB is 210,
MB is 106,
MiB is 220 and so forth).
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.
CrunchRunArgumentsList: - "-container-enable-networking=always" - "-container-network-mode=host"
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.
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
# yum install arvados-dispatch-lsf
# apt-get install arvados-dispatch-lsf
# systemctl enable --now arvados-dispatch-lsf # systemctl status arvados-dispatch-lsf [...]
systemctl status indicates it is not running, use
journalctl to check logs for errors:
# journalctl -n12 --unit arvados-dispatch-lsf
Make sure the cluster config file is up to date on the API server host then restart the API server and controller processes to ensure the configuration changes are visible to the whole cluster.
# systemctl restart nginx arvados-controller # arvados-server check
On the dispatch node, start monitoring the arvados-dispatch-lsf logs:
# journalctl -o cat -fu arvados-dispatch-lsf.service
In another terminal window, use the diagnostics tool to run a simple container.
# arvados-client sudo diagnostics 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
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.
The content of this documentation is licensed under the
Commons Attribution-Share Alike 3.0 United States licence.
Code samples in this documentation are licensed under the Apache License, Version 2.0.