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Refine_DLC_GPU_submit.sh
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Refine_DLC_GPU_submit.sh
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#!/bin/bash
#!
#! Example SLURM job script for Wilkes3 (AMD EPYC 7763, ConnectX-6, A100)
#! Last updated: Fri 30 Jul 11:07:58 BST 2021
#!
#!#############################################################
#!#### Modify the options in this section as appropriate ######
#!#############################################################
#! sbatch directives begin here ###############################
#! Name of the job:
#SBATCH -J DLC-gpu-training
#! Which project should be charged (NB Wilkes2 projects end in '-GPU'):
#SBATCH -A merkle-Sl2-gpu
#! How many whole nodes should be allocated?
#SBATCH --nodes=1
#! How many (MPI) tasks will there be in total?
#! Note probably this should not exceed the total number of GPUs in use.
#SBATCH --ntasks=4
#! Specify the number of GPUs per node (between 1 and 4; must be 4 if nodes>1).
#! Note that the job submission script will enforce no more than 32 cpus per GPU.
#SBATCH --gres=gpu:4
#! How much wallclock time will be required?
#SBATCH --time=12:00:00
#! What types of email messages do you wish to receive?
#SBATCH --mail-type=ALL
#! Uncomment this to prevent the job from being requeued (e.g. if
#! interrupted by node failure or system downtime):
##SBATCH --no-requeue
#SBATCH [email protected]
#! Do not change:
#SBATCH -p ampere
#! sbatch directives end here (put any additional directives above this line)
#! Notes:
#! Charging is determined by GPU number*walltime.
#! Number of nodes and tasks per node allocated by SLURM (do not change):
numnodes=$SLURM_JOB_NUM_NODES
numtasks=$SLURM_NTASKS
mpi_tasks_per_node=$(echo "$SLURM_TASKS_PER_NODE" | sed -e 's/^\([0-9][0-9]*\).*$/\1/')
#! ############################################################
#! Modify the settings below to specify the application's environment, location
#! and launch method:
#! Optionally modify the environment seen by the application
#! (note that SLURM reproduces the environment at submission irrespective of ~/.bashrc):
. /etc/profile.d/modules.sh # Leave this line (enables the module command)
module purge # Removes all modules still loaded
module load rhel8/default-amp # REQUIRED - loads the basic environment
module load cuda/11.2 cudnn/8.1_cuda-11.2 #load cuda drivers for GPU
module load python/3.6 cuda/10.0 cudnn/7.5_cuda-10.0 #load more cuda drivers for GPU
module load ffmpeg #load codec for video conversion
#! Insert additional module load commands after this line if needed:
export DLClight=True
#! Full path to application executable:
source /home/ech66/rds/hpc-work/miniconda3/bin/activate &&
application="conda activate DeepLabCut && python3 /rds/user/ech66/hpc-work/scripts/Refine_deeplabcut.py"
#! Run options for the application:
options=""
#! Work directory (i.e. where the job will run):
workdir="$SLURM_SUBMIT_DIR" # The value of SLURM_SUBMIT_DIR sets workdir to the directory
# in which sbatch is run.
#! Are you using OpenMP (NB this is unrelated to OpenMPI)? If so increase this
#! safe value to no more than 128:
export OMP_NUM_THREADS=1
#! Number of MPI tasks to be started by the application per node and in total (do not change):
np=$[${numnodes}*${mpi_tasks_per_node}]
#! Choose this for a pure shared-memory OpenMP parallel program on a single node:
#! (OMP_NUM_THREADS threads will be created):
CMD="$application $options"
#! Choose this for a MPI code using OpenMPI:
#CMD="mpirun -npernode $mpi_tasks_per_node -np $np $application $options"
###############################################################
### You should not have to change anything below this line ####
###############################################################
cd $workdir
echo -e "Changed directory to `pwd`.\n"
JOBID=$SLURM_JOB_ID
echo -e "JobID: $JOBID\n======"
echo "Time: `date`"
echo "Running on master node: `hostname`"
echo "Current directory: `pwd`"
if [ "$SLURM_JOB_NODELIST" ]; then
#! Create a machine file:
export NODEFILE=`generate_pbs_nodefile`
cat $NODEFILE | uniq > machine.file.$JOBID
echo -e "\nNodes allocated:\n================"
echo `cat machine.file.$JOBID | sed -e 's/\..*$//g'`
fi
echo -e "\nnumtasks=$numtasks, numnodes=$numnodes, mpi_tasks_per_node=$mpi_tasks_per_node (OMP_NUM_THREADS=$OMP_NUM_THREADS)"
echo -e "\nExecuting command:\n==================\n$CMD\n"
eval $CMD