Installing the Cell Ranger ARC software on a cluster is identical to installation on a local server. After confirming that the cellranger-arc commands can run in single server mode, configure the job submission template that Cell Ranger ARC uses to submit jobs to the cluster. Assuming Cell Ranger ARC is installed to /opt/cellranger-arc-2.0.2, the process is as follows:

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

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cd /opt/cellranger-arc-2.0.2/external/martian/jobmanagers
ls
config.json  lsf.template.example  sge.template.example  slurm.template.example

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

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cp -v sge.template.example sge.template
`sge.template.example' -> `sge.template'
ls
config.json  lsf.template.example  sge.template  sge.template.example  slurm.template.example

The job submission templates contain a number of special variables that are substituted by the Martian runtime when each stage is submitted. Specifically, the following variables are expanded when a pipeline is submitting jobs to the cluster:

It is critical that the special variables listed as required are present in the final template you create. For more information on how the template should appear for a cluster, consult your cluster administrator or help desk.

Depending on which job scheduler you have, please select a tab below.

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

1. Your research group's queue. For example, #BSUB -q smith_queue
2. The account to which your jobs will charge. For example, #BSUB -P smith_lab

For SGE cluster, you MUST replace <pe_name> within the example template to reflect the name of the cluster's multi-threaded parallel environment. To view a list of the cluster's parallel environments, use the qconf -spl command.

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

1. The research group's queue. For example, #$ -q smith.q
2. The account to which jobs will charge. For example, #$ -A smith_lab

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

1. Your research group's account. For example, #SBATCH -A smith_lab
2. Time limit for the cluster job. For example, #SBATCH -t=24:00:00 to set a 24 hours limit.

To run a Cell Ranger ARC pipeline in cluster mode, add one of --jobmode=lsf, --jobmode=sge or --jobmode=slurm command-line option when using the cellranger-arc commands. It is also possible to use --jobmode=<PATH>, where is the full path to the cluster template file.

To validate that cluster mode is properly configured, follow the same validation instructions given for cellranger-arc in the Installation page and specify the appropriate cluster via --jobmode.

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cellranger-arc mkfastq --run=./tiny-bcl --samplesheet=./tiny-sheet.csv --jobmode=sge

Martian Runtime - 2.0.2

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
...

Once the preflight checks are finished, check the job queue to see stages queuing up:

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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 all.q@cluster.university.edu       1
8675310 0.55500 ID.HAWT7AD jdoe         qw    09/13/2016 12:00:00 all.q@cluster.university.edu       1

In the event of a pipeline failure, an error message is displayed:

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[error] Pipestance failed. Please see log at:
HAWT7ADXX/MAKE_FASTQS_CS/MAKE_FASTQS/MAKE_FASTQS_PREFLIGHT/fork0/chnk0/_errors

Saving diagnostics to HAWT7ADXX/HAWT7ADXX.debug.tgz
For assistance, upload this file to 10x Genomics by running:

uploadto10x <your_email> HAWT7ADXX/HAWT7ADXX.debug.tgz

The _errors file contains a jobcmd error:

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cat HAWT7ADXX/MAKE_FASTQS_CS/MAKE_FASTQS/MAKE_FASTQS_PREFLIGHT/fork0/chnk0/_errors

jobcmd error:
exit status 1

The most likely reason for this failure is an invalid job submission template. This occurs when the job submission via bsub, qsub, or sbatch commands failed.

The "tiny" dataset does not stress the cluster, so it is worthwhile to follow up with a more realistic test using one of our sample datasets

There are two subtle variants of running cellranger-arc pipelines in cluster mode, each with their own pitfalls. Check with your cluster administrator to see which approach is compatible with your institution's setup.

1. Run cellranger-arc with --jobmode=sge on the head node. Cluster mode was originally designed for this use case. However, this approach leaves mrp and mrjob running on the head node for the duration of the pipeline and some clusters impose time limits to prevent long running processes.
2. Use a job script to submit a cellranger-arc command with --jobmode=sge: With this approach, mrp and mrjob run on a cluster mode. However, the cluster must allow jobs to be submitted from a compute node to make this viable.

When cellranger-arc is run in cluster mode, a single library analysis is partitioned into hundreds and potentially thousands of smaller jobs. The underlying Martian pipeline framework launches each stage job using the bsub, qsub or sbatch commands when running on LSF, SGE, or Slurm cluster, respectively. As stage jobs are queued, launched, and completed, the pipeline framework tracks their status using the metadata files that each stage maintains in the pipeline output directory.

Like single server pipelines, cluster-mode pipelines can be restarted after a failure. They maintain the same order of execution for the dependent stages of the pipeline. All executed stage code is identical to single server mode and the quantitative results are identical to the limit of each stage's reproducibility.

In addition, the Cell Ranger ARC 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.

Stages in the Cell Ranger ARC 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 single server mode. The way CPU and memory requests are handled in cluster mode is defined by the following:

• How the __MRO_THREADS__ and __MRO_MEM_GB__ variables are used within the job template.
• How your specific cluster's job manager schedules resources.

Depending on which job scheduler you have, select a tab below:

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,

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cat bsub.template
#BSUB -J __MRO_JOB_NAME__
#BSUB -n __MRO_THREADS__
#BSUB -o __MRO_STDOUT__
#BSUB -e __MRO_STDERR__
#BSUB -R "rusage[mem=__MRO_MEM_MB__]"
#BSUB -R span[hosts=1]

__MRO_CMD__

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:

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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__

__MRO_CMD__

Note that the h_vmem (virtual memory) and mem_free/h_rss (physical memory) represent two different quantities and that Cell Ranger ARC stages' __MRO_MEM_GB__ requests are expressed as physical memory. 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.

Slurm supports job memory requests through the -mem option, but the default units are megabytes, so in order to specify the memory in GB, it's important to keep the trailing 'G' suffix after the __MRO_MEM_GB__ variable, as shown below.

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cat slurm.template
#SBATCH -J __MRO_JOB_NAME__
#SBATCH --export=ALL
#SBATCH --nodes=1 --ntasks-per-node=__MRO_THREADS__
#SBATCH --signal=2
#SBATCH --no-requeue
### Alternatively: --ntasks=1 --cpus-per-task=__MRO_THREADS__
###   Consult with your cluster administrators to find the combination that
###   works best for single-node, multi-threaded applications on your system.
#SBATCH --mem=__MRO_MEM_GB__G
#SBATCH -o __MRO_STDOUT__
#SBATCH -e __MRO_STDERR__

__MRO_CMD__

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 scales up the number of threads requested via the __MRO_THREADS__ variable according to how much memory a stage requires.

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

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

will issue the following resource requests:

• A stage that requires 1 thread and less than 8 GB of memory will pass __MRO_THREADS__ of 1 to the job template.
• A stage that requires 1 thread and 12 GB of memory will pass __MRO_THREADS__ of 2 to the job template because (12 GB) / (8 GB/core) = 2 cores.
• A stage that requires 2 threads and less than 16 GB of memory will pass __MRO_THREADS__ of 2 to the job template.
• A stage that requires 2 threads and 40 GB of memory will pass __MRO_THREADS__ of 5 to the job template because (40 GB) / (8 GB/core) = 5 cores.

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. If you are unsure of how your cluster resource management is configured, contact your cluster administrator or help desk.

Some Cell Ranger ARC 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 these limits or is not shared with other users, you can control how the Martian pipeline runner sends job submissions to the cluster by using the --maxjobs and --jobinterval parameters.

To increase the cap on the number of concurrent jobs to 200, use the --maxjobs parameter:

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cellranger-arc count --id=sample ... --jobmode=sge --maxjobs=200

You can 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:

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cellranger-arc count --id=sample ... --jobmode=sge --jobinterval=5000

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