Openpose issue: srv/beegfs

HPC Support HPC issues
1

Primary informations

Username: kojovic
Cluster: $baobab

Description

Openpose gives an error when run on videos from the /srv/beegfs/scratch/shares/schaer2 but no such error is shown if i give it videos from my home folder.

Steps to Reproduce

/var/spool/slurmd/job6031123/slurm_script: line 55: 2493603 Aborted                 (core dumped) apptainer run --nv --pwd /openpose-master /home/kojovic/openpose_orchestrator/openpose.simg build/examples/openpose/openpose.bin --no_display --net_resolution '-1x368' --scale_number 4 --scale_gap 0.25 --video /srv/beegfs/scratch/shares/schaer2/saranew/2023/XXXX_T1a_ADOS.mp4 --disable_blending --write_coco_json /srv/beegfs/scratch/shares/schaer2/saranew/2023/OUTPUT/XXXX__T1a_ADOS.mp4/json/keypoints_coco.json --write_video /srv/beegfs/scratch/shares/schaer2/saranew/2023/OUTPUT/XXXX_T1a_ADOS.mp4/Black_Video.avi

admin edit: code formating

2

Please share the sbatch.

3 
#!/bin/bash

#SBATCH --output=%J-test_adf.log
#SBATCH --error=%J-test_adf.err
#SBATCH --partition=shared-gpu
#SBATCH --cpus-per-task=4
#SBATCH --time=12:00:00
#SBATCH --gres=gpu:2


### <https://hpc-community.unige.ch/t/tutorial-launch-openpose-with-gpu-support-through-singularity/593>
# module load GCCcore/8.2.0 Singularity/3.4.0-Go-1.12
echo "Starting Processing at `date`   "
cd /srv/beegfs/scratch/shares/schaer2/saranew/2023/LOGS



FILENAME="DDDD_T1a_ADOS.mp4"
INPUT_DIR="/srv/beegfs/scratch/shares/schaer2/saranew/2023"
OUTPUT_DIR="/srv/beegfs/scratch/shares/schaer2/saranew/2023/OUTPUT"
OUTPUT_FOLDER=$OUTPUT_DIR/$FILENAME

echo $INPUT_DIR
echo $FILENAME

echo "Creating output folder ${OUTPUT_FOLDER}..."
rm -rf $OUTPUT_FOLDER
mkdir $OUTPUT_FOLDER
mkdir $OUTPUT_FOLDER/json

### ATTENTION, the original Docker image is available at
### <https://hub.docker.com/r/garyfeng/docker-openpose/>
###   NB, the "--pwd /openpose-master" option is mandatory since the
###       build/examples/openpose/openpose.bin is compiled with
###       relative-path dymanic libraries...
DOCKER_OPENPOSE_IMG_PATH="${HOME}/openpose_orchestrator/openpose.simg"
DOCKER_OPENPOSE_IMG_WORKING_DIRECTORY='/openpose-master'
DOCKER_OPENPOSE_IMG_OPENPOSE_BIN='build/examples/openpose/openpose.bin'
CMD="\
apptainer run --nv --pwd ${DOCKER_OPENPOSE_IMG_WORKING_DIRECTORY} ${DOCKER_OPENPOSE_IMG_PATH} ${DOCKER_OPENPOSE_IMG_OPENPOSE_BIN} \
--no_display \
--net_resolution '-1x368' \
--scale_number 4 \
--scale_gap 0.25 \
--video $INPUT_DIR/$FILENAME \
--disable_blending \
--write_coco_json $OUTPUT_FOLDER/json/keypoints_coco.json \
--write_video $OUTPUT_FOLDER/Black_Video.avi"


echo "Running the following command:"
echo "$CMD"
echo
time \
 eval ${CMD}

echo "JOB Complete at `date`   "

# Convert result.avi to result.mp4
#ffmpeg -i $OUTPUT_FOLDER/result.avi  -strict 2 $OUTPUT_FOLDER/result.mp4
#rm -rf $OUTPUT_FOLDER/result.avi


exit
5

Hi,

Kind reminder (the same apply for all the users requesting help): in order to get efficient support from us, always share your sbatch in your initial post and format your code.

Regarding your issue with scratch, you have the same problem as this user: File not found with Singularity - #2 by Yann.Sagon

Best