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Best practices for submitting jobs to compG, excluding compG000 and compG001.

Note that if you intend to, or are using compG, it is strongly advised that you join the BMRC GPU user mailing list: rescomp-users-gpu@well.ox.ac.uk. Simply email a request to be included to bmrc-help@medsci.ox.ac.uk.

Much of the following information has been taken from the bmrc website (see below).

Available GPU Resources

Information taken from the bmrc website on 24/10/2019.

Server compG00? GPUtype Number of GPUs GPU memory (GB) Cuda Version OS Role Access
0 k80 8 12 8+ CentOS 6.8 Strubi cryosparc jobs open
1 TitanX 1 12 8+ Strubi cryosparc jobs restricted
2 v100 1 16 9+ currently offline open
3 p100 4 16 8+ CentOS 6.8 Queued GPU jobs open
4 p100 4 16 8+ CentOS 6.8 Queued GPU jobs open
5 1080Ti 4 12 8+ Prototyping and development open
6 1080Ti 4 12 8+ Prototyping and development open
7 1080Ti 4 12 8+ Prototyping and development open
8 1080Ti 4 12 8+ Prototyping and development open
9 p100-os7 4 CentOS 7.3 Queued GPU jobs open
10 p100-os7 4 CentOS 7.3 Queued GPU jobs restricted
11 p100-os7 4 CentOS 7.3 Queued GPU jobs restricted

Note that users can use NVidia DGX-1V (8 x V100) hosted by ARC, run by the IT services upon request. Contact bmrc-help@medsci.ox.ac.uk.

Submitting Jobs

The 1080Ti cards are gaming cards that are a bit slower and cheaper than the HPC-grade P100 cards. To make access as fair as possible, please submit any large jobs to the queue system.

#################EXAMPLE SUBMISSION SCRIPT. Many thanks to Rob Stass ###################

#!/bin/bash


# Name of the job
#$ -N motioncor2_job


# Job log file (optional)
#$ -o motioncor2-$JOB_ID.log


#queue information

#$ -cwd -V
#$ -j y
#$ -P strubi.prjc
#$ -q gpu8.q
#$ -l gpu=1
#$ -l gputype=p100

# or can request gputype=p100

#load cuda
module unload cuda

#If you want to use an older version of motioncor2 uncomment/comment the lines to load cuda/7.5 instead.
#module load cuda/7.5
module load cuda/8.0

num_gpu=`echo $SGE_HGR_gpu | wc -w`

gpu_identifiers=`seq -s " " 0 1 $(($num_gpu-1))`

/apps/strubi/motioncorr/20170130/MotionCor2-01-30-2017  -Gpu $gpu_identifiers <other_motioncor2_parameters>

 

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For more information head to:

Note that the following website may only be accessed via your rescomp login credentials.

https://help.bmrc.ox.ac.uk/tutorials

https://rescomp.well.ox.ac.uk/wiki/Using_the_Rescomp_GPU_resources