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docker-fah-client

Running the Folding@home client inside a docker image.

The jchodera/docker-fah-client docker image has a copy of the Folding@home linux client inside the /fah directory.

Running on hal.cbio.mskcc.org

Note that you must first request to be added to the docker access group by posting to the hal GitHub issue tracker.

Install the docker-fah-client conda package:

conda install -c choderalab docker-fah-client

Then, you can run the fah-client command-line helper:

[chodera@mskcc-ln1 ~/docker-fah-client]$ scripts/fah-client --help
usage: fah-client [-h] [--project PROJECT] [--number NUMBER]
                  [--maxworkers MAXWORKERS] [--walltime WALLTIME]
                  [--jobname JOBNAME] [--verbose]

Spin up a specified number of FAHClient instances pointed out designated
INTERNAL project inside of docker containers. 

optional arguments:
  -h, --help            show this help message and exit
  --project PROJECT     the internal project number (required)
  --number NUMBER       number of work units to process (default: 1)
  --maxworkers MAXWORKERS
                        maximum number of simultaneous wokers (default: 1)
  --walltime WALLTIME   walltime limit (default: 12:00:00)
  --jobname JOBNAME     job name (default: docker-fah-client)
  --verbose             print debug output (default: False)

For example, to launch 4 workers to test project 10495, you would use

fah-client --project=10495 --number=4 --maxworkers=4

If you want to grind through 100 work units running at most 10 workers at a time, you would use

fah-client --project=10495 --number=100 --maxworkers=10

Running via Torque/Moab scripts

Sample submit-torque-docker-fah-client.sh Torque/Moab script:

#!/bin/bash
#
# Set low priority
#PBS -p -1024
#
# Array job: Run 10 WUs total, allowing 2 to run at a time.
#PBS -t 1-10%2
#
# Set a maximum wall time greater than the time per WU (or else no WUs will finish)
#PBS -l walltime=12:00:00
#
# Use the GPU queue
#PBS -q gpu
#
# Reserve one GPU
#PBS -l nodes=1:ppn=1:gpus=1:exclusive

# Set the project key here.
export PROJECT_KEY=10495

# Change to working directory
cd "$PBS_O_WORKDIR"

# Set CUDA_VISIBLE_DEVICES
export CUDA_VISIBLE_DEVICES=`cat $PBS_GPUFILE | awk -F"-gpu" '{ printf A$2;A=","}'`

# Run exactly one work unit
docker run --device /dev/nvidiactl:/dev/nvidiactl --device /dev/nvidia-uvm:/dev/nvidia-uvm --device /dev/nvidia${CUDA_VISIBLE_DEVICES}:/dev/nvidia0 jchodera/docker-fah-client /bin/sh -c 'cd fah && ./FAHClient --client-type=INTERNAL --project-key=$PROJECT_KEY --max-units=1'

Testing in an interactive shell

You can drop into an interactive shell using

qsub -I -l walltime=04:00:00 -l nodes=1:ppn=1:gpus=1:exclusive -l mem=4G -q active

Assuming CUDA_VISIBLE_DEVICES is set correctly by Torque/Moab, you can run docker using

docker run -it --device /dev/nvidiactl:/dev/nvidiactl --device /dev/nvidia-uvm:/dev/nvidia-uvm --device /dev/nvidia${CUDA_VISIBLE_DEVICES}:/dev/nvidia0 jchodera/docker-fah-client /bin/sh -c 'cd fah && ./FAHClient --client-type=INTERNAL --project-key=$PROJECT_KEY --max-units=1'

Manifest

  • Dockerfile - dockerfile for jchodera/docker-fah-client
  • scripts/ - useful scripts

Dockerbot stats

FAHClient currently runs with the dockerbot@choderalab.org user.

Dockerbot FAH stats and certificate.

Acknowledgments

The jchodera/docker-fah-client image is based on the excellent kaixhin/cuda CUDA-enabled docker instance.

Thanks to Patrick Grinaway for discovering it was possible to run a Folding@home client inside a docker instance.

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jchodera
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