HPC slurm example

Example SLURM job script for Wilkes2 (Cambridge HPC GPUs)

Thanks to Huiyuan Xie of the NLIP Group for sharing this example script. Please see the HPC documentation for latest instructions on job submission.

Link back to How to use GPUs.

#!/bin/bash
#!
#! Example SLURM job script for Wilkes2 (Broadwell, ConnectX-4, P100)
#! Last updated: Mon 13 Nov 12:06:57 GMT 2017
#!
#!#############################################################
#!#### Modify the options in this section as appropriate ######
#!#############################################################


#! sbatch directives begin here ###############################
#! Name of the job:
#SBATCH -J ice-ex-oneshape
#! Which project should be charged (NB Wilkes2 projects end in '-GPU'):
#SBATCH -A COMPUTERLAB-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=1
#! 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 3 cpus per GPU.
#SBATCH --gres=gpu:1
#! How much wallclock time will be required?
#SBATCH --time=15:00:00
#! What types of email messages do you wish to receive?
#SBATCH --mail-type=FAIL
#! Uncomment this to prevent the job from being requeued (e.g. if
#! interrupted by node failure or system downtime):
##SBATCH --no-requeue

#! Do not change:
#SBATCH -p pascal

#! 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 rhel7/default-gpu              # REQUIRED - loads the basic environment

#! Insert additional module load commands after this line if needed:
source /home/hx255/miniconda3/bin/activate ice

#! Full path to application executable: 
application="python /home/hx255/ice/train_network.py"

#! Run options for the application:
data_dir="/home/hx255/ShapeWorld/ice_data"
log_dir="/home/hx255/ice/log"
cnn_ckpt="/home/hx255/ice/models/cnn/factor/"
exp_tag="existential-oneshape"

options="--data_dir $data_dir --log_dir $log_dir --dtype agreement --name existential --variant oneshape --parse_type shape_color --exp_tag $exp_tag --cnn_ckpt $cnn_ckpt --batch_size 64 --num_shards 50 --num_epochs 35 --record_loss_every_10k 1000 --record_loss_every 10000 --save_ckpt_every_10k 1000 --save_ckpt_every 10000"

#! 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 12:
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 "Start 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 

echo "End time: `date`"

source /home/hx255/miniconda3/bin/deactivate