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Chromium Single Cell Immune Profiling

Using Cell Ranger with SGE and LSF

The Cell Ranger pipelines support launching stages on SGE- and LSF-based clusters. This cluster mode allows highly parallelizable stages to utilize hundreds or thousands of cores concurrently, dramatically reducing time to solution.

Running pipelines in cluster mode requires the following:

  1. Cell Ranger is installed in the same location on all nodes of the cluster (e.g., /opt/cellranger-2.2.0 or /net/apps/cellranger-2.2.0)
  2. Cell Ranger pipelines will be run on a shared file system that is accessible to all nodes of the cluster. NFS-mounted directories are are the most common solution to this requirement.
  3. The cluster will accept both single-core and multithreaded (shared-memory) jobs.

Configuring Cluster Integration

Installing the Cell Ranger software on a cluster is identical to the installation procedure for local-mode (non-cluster) operation. After you have confirmed that the cellranger pipelines can run in local mode, you must configure the job submission template that Cell Ranger will use to submit jobs to your cluster. Assuming you installed Cell Ranger to /opt/cellranger-2.2.0, the process is as follows.

Step 1. Navigate to the Martian runtime's jobmanagers/ directory which contains example jobmanager templates.

$ cd /opt/cellranger-2.2.0/martian-cs/v2.3.3/jobmanagers
$ ls
bsub.template.example  config.json  sge.template.example

Step 2. Make a copy of your cluster's example template (SGE or LSF) to either sge.template or lsf.template in this jobmanagers/ directory.

$ cp -v sge.template.example sge.template
`sge.template.example' -> `sge.template'
$ ls
bsub.template.example  config.json  sge.template  sge.template.example

Step 3. Edit this template file and make the necessary modifications that may be required by your specific cluster.

$ nano sge.template
$ cat sge.template
#$ -N __MRO_JOB_NAME__
#$ -V
#$ -pe threads __MRO_THREADS__
#$ -l mem_free=__MRO_MEM_GB__G
#$ -cwd
#$ -o __MRO_STDOUT__
#$ -e __MRO_STDERR__

If you are using an SGE cluster, you MUST modify the #$ -pe <pe_name> line of the example template to reflect the name of your cluster's multithreaded parallel environment (e.g., threads in the above example). You can view a list of your cluster's parallel environments using the qconf -spl command.

The most common modifications to the job submission template include adding additional lines to specify:

These job submission templates contain a number of special variables, contained within double underscores, that are substituted by the Martian runtime when each stage is being submitted. Specifically, the following variables will be expanded when a pipeline is submitting jobs to the cluster:

VariableMust be present?Description
__MRO_JOB_NAME__YesJob name composed of the sample ID and stage being executed
__MRO_THREADS__NoNumber of threads required by the stage
NoAmount of memory (in GB or MB) required by the stage
NoAmount of memory (in GB or MB) required per thread in multi-threaded stages.
YesPaths to the _stdout and _stderr metadata files for the stage
__MRO_CMD__YesBourne shell command to run the stage code

It is critical that the special variables listed as required are present in the final template you create. If you are unsure of how this template should appear for your cluster, consult your cluster's administrator or help desk.

Validating Template Configuration

To run a Cell Ranger pipeline in cluster mode, simply add the --jobmode=sge or --jobmode=lsf command-line option when using the cellranger commands. The pipeline orchestration will still occur on your local machine, but individual stages will be submitted to your cluster as they become eligible to execute.

To validate that cluster mode is properly configured, you can follow the same validation instructions given for cellranger in the Installation page but add --jobmode=sge or --jobmode=lsf.

$ cellranger mkfastq --run=./tiny-bcl --samplesheet=./tiny-sheet.csv --jobmode=sge
Martian Runtime - 2.2.0
Running preflight checks (please wait)...
2016-09-13 12:00:00 [runtime] (ready)           ID.HAWT7ADXX.MAKE_FASTQS_CS.MAKE_FASTQS.PREPARE_SAMPLESHEET
2016-09-13 12:00:00 [runtime] (split_complete)  ID.HAWT7ADXX.MAKE_FASTQS_CS.MAKE_FASTQS.PREPARE_SAMPLESHEET

If you check your job queue, you will begin to see stages queuing up:

$ qstat
job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID
8675309 0.56000 ID.HAWT7AD jdoe         qw    09/13/2016 12:00:00 [email protected]       1
8675310 0.55500 ID.HAWT7AD jdoe         qw    09/13/2016 12:00:00 [email protected]       1

If you encounter a pipeline failure:

[error] Pipestance failed. Please see log at:
Saving diagnostics to HAWT7ADXX/HAWT7ADXX.debug.tgz
For assistance, upload this file to 10x by running:
uploadto10x <your_email> HAWT7ADXX/HAWT7ADXX.debug.tgz

And the _errors file contains a jobcmd error:

jobcmd error:
exit status 1

You likely have an invalid job submission template. This jobcmd error occurs when the job submission via qsub or bsub commands failed.

Cluster Mode Mechanics

After configuring Cell Ranger for cluster mode, the cellranger pipelines can be run with --jobmode=sge or --jobmode=lsf. This will make the underlying Martian pipeline framework launch each stage through the qsub or bsub commands when running in SGE or LSF modes, respectively. As stages' jobs are queued, launched, and completed, the pipeline framework will track their states using the metadata files that each stage maintains in the pipeline output directory.

Just as with local-mode pipelines, cluster-mode pipelines can be restarted after failure and maintain the same order of execution for dependent subsections of the pipeline. All of the stage code that is executed is identical to that of local mode, and the quantitative results will be identical to the limit of each stage's reproducibility.

In addition, the Cell Ranger UI can still be used with cluster mode. Because the Martian pipeline framework runs on the node from which the command was issued, the UI will also run from that node.

Memory Requests and Consumption

Stages in the Cell Ranger pipelines each request a specific number of cores and memory to aid with resource management. These values are used to prevent oversubscription of the computing system when running pipelines in local (non-cluster) mode, but the way in which CPU and memory requests are handled in cluster mode is defined by (1) how the __MRO_THREADS__ and __MRO_MEM_GB__ variables are used within the job template and (2) how your specific cluster's job manager schedules resources.

SGE / Grid Engine

SGE supports requesting memory via the mem_free resource natively, although your cluster may have another mechanism for requesting memory. To pass each stage's memory request through to SGE, add an additional line to your sge.template that requests mem_free, h_vmem, h_rss, or the custom memory resource defined by your cluster:

$ cat sge.template
#$ -N __MRO_JOB_NAME__
#$ -V
#$ -pe threads __MRO_THREADS__
#$ -l mem_free=__MRO_MEM_GB__G
#$ -cwd
#$ -o __MRO_STDOUT__
#$ -e __MRO_STDERR__

Note that the h_vmem (virtual memory) and mem_free/h_rss (physical memory) represent two different quantities, and that Cell Ranger stages' __MRO_MEM_GB__ requests are expressed as physical memory. As such, using h_vmem in your job template may cause certain stages to be unduly killed if their virtual memory consumption is substantially larger than their physical memory consumption. It follows that we do not recommend using h_vmem.

Platform LSF

LSF supports job memory requests through the -M and -R [mem=...] options, but these requests generally must be expressed in MB, not GB. As such, your LSF job template should use the __MRO_MEM_MB__ variable rather than __MRO_MEM_GB__. For example,

$ cat bsub.template
#BSUB -R "rusage[mem=__MRO_MEM_MB__]"
#BSUB -R span[hosts=1]

Requesting Memory via Cores

For clusters whose job managers do not support memory requests, it is possible to request memory in the form of cores via the --mempercore command-line option. This option will scale up the number of threads requested via the __MRO_THREADS__ variable according to how much memory a stage requires when given to the ratio of memory on your nodes.

For example, given a cluster whose nodes have 16 cores and 128 GB of memory (8 GB per core), the following pipeline invocation command

$ cellranger mkfastq --run=./tiny-bcl --samplesheet=./tiny-sheet.csv --jobmode=sge --mempercore=8

will issue the following resource requests:

As the final bullet point illustrates, this mode can result in wasted CPU cycles and is only provided for clusters that cannot allocate memory as an independent resource.

Every cluster configuration is different, so if you are unsure of how your cluster resource management is configured, please contact your cluster administrator or help desk.

Rate Limiting Job Submissions

Some Cell Ranger pipeline stages are divided into hundreds of jobs. By default, the rate at which these jobs are submitted to the cluster is throttled to at most 64 at a time and at least 100ms between each submission to avoid running into limits on clusters which impose quotas on the total number of pending jobs a user can submit.

If your cluster does not have such limits or is not shared with other users, you can control how the Martian pipeline runner sends job submissions to your cluster by using the --maxjobs and --jobinterval parameters.

You can increase the cap on the number of concurrent jobs to 200 with the --maxjobs parameter:

$ cellranger vdj --id=sample ... --jobmode=sge --maxjobs=200

You may also change the rate limit on how often the Martian pipeline runner sends submissions to the cluster. To add a five-second pause between job submissions, use the --jobinterval parameter:

$ cellranger vdj --id=sample ... --jobmode=sge --jobinterval=5000

The job interval parameter is in milliseconds. The minimum allowable value is 1.