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Commit b7bd1539 authored by Nicolas Richart's avatar Nicolas Richart
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Adapting paths

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...@@ -3,8 +3,8 @@ ...@@ -3,8 +3,8 @@
"worker_bin_path" : "cryosparcw", "worker_bin_path" : "cryosparcw",
"cache_path" : "/scratch/${USER}/cryosparc/", "cache_path" : "/scratch/${USER}/cryosparc/",
"send_cmd_tpl" : "{{ command }}", "send_cmd_tpl" : "{{ command }}",
"qsub_cmd_tpl" : "/opt/slurm/current/bin/sbatch --chdir /scratch {{ script_path_abs }}", "qsub_cmd_tpl" : "/usr/bin/sbatch {{ script_path_abs }}",
"qstat_cmd_tpl" : "/opt/slurm/current/bin/squeue -j {{ cluster_job_id }}", "qstat_cmd_tpl" : "/usr/bin/squeue -j {{ cluster_job_id }}",
"qdel_cmd_tpl" : "/opt/slurm/current/bin/scancel {{ cluster_job_id }}", "qdel_cmd_tpl" : "/usr/bin/scancel {{ cluster_job_id }}",
"qinfo_cmd_tpl" : "/opt/slurm/current/bin/sinfo" "qinfo_cmd_tpl" : "/usr/bin/sinfo"
} }
...@@ -4,10 +4,10 @@ ...@@ -4,10 +4,10 @@
## {{ job_creator }} - name of the user that created the job (may contain spaces) ## {{ job_creator }} - name of the user that created the job (may contain spaces)
## {{ cryosparc_username }} - cryosparc username of the user that created the job (usually an email) ## {{ cryosparc_username }} - cryosparc username of the user that created the job (usually an email)
#SBATCH -A ACCOUNT
#SBATCH -p h100 #SBATCH -p h100
#SBATCH -n {{ num_cpu }} #SBATCH -n {{ num_cpu }}
#SBATCH -N 1 #SBATCH -N 1
#SBATCH --time 3:0:0
#SBATCH --gpus {{ num_gpu }} #SBATCH --gpus {{ num_gpu }}
#SBATCH --mem={{ (ram_gb*1000)|int }}MB #SBATCH --mem={{ (ram_gb*1000)|int }}MB
#SBATCH --job-name cryosparc_{{ project_uid }}_{{ job_uid }} #SBATCH --job-name cryosparc_{{ project_uid }}_{{ job_uid }}
...@@ -27,7 +27,7 @@ echo "TMPDIR="$TMPDIR ...@@ -27,7 +27,7 @@ echo "TMPDIR="$TMPDIR
mkdir -p ${TMPDIR} mkdir -p ${TMPDIR}
# load cryosarc # load cryosarc
source ${HOME}/cryosparc/cryosparc_worker.sh source ${HOME}/cryosparc/worker-config.sh
# {{ run_cmd }} # {{ run_cmd }}
export RUN_ARGS="{{ run_args }}" export RUN_ARGS="{{ run_args }}"
......
...@@ -3,8 +3,8 @@ ...@@ -3,8 +3,8 @@
"worker_bin_path" : "cryosparcw", "worker_bin_path" : "cryosparcw",
"cache_path" : "/scratch/${USER}/cryosparc/", "cache_path" : "/scratch/${USER}/cryosparc/",
"send_cmd_tpl" : "{{ command }}", "send_cmd_tpl" : "{{ command }}",
"qsub_cmd_tpl" : "/opt/slurm/current/bin/sbatch --chdir /scratch {{ script_path_abs }}", "qsub_cmd_tpl" : "/usr/bin/sbatch {{ script_path_abs }}",
"qstat_cmd_tpl" : "/opt/slurm/current/bin/squeue -j {{ cluster_job_id }}", "qstat_cmd_tpl" : "/usr/bin/squeue -j {{ cluster_job_id }}",
"qdel_cmd_tpl" : "/opt/slurm/current/bin/scancel {{ cluster_job_id }}", "qdel_cmd_tpl" : "/usr/bin/scancel {{ cluster_job_id }}",
"qinfo_cmd_tpl" : "/opt/slurm/current/bin/sinfo" "qinfo_cmd_tpl" : "/usr/bin/sinfo"
} }
...@@ -4,10 +4,10 @@ ...@@ -4,10 +4,10 @@
## {{ job_creator }} - name of the user that created the job (may contain spaces) ## {{ job_creator }} - name of the user that created the job (may contain spaces)
## {{ cryosparc_username }} - cryosparc username of the user that created the job (usually an email) ## {{ cryosparc_username }} - cryosparc username of the user that created the job (usually an email)
#SBATCH -A ACCOUNT
#SBATCH -p l40s #SBATCH -p l40s
#SBATCH -n {{ num_cpu }} #SBATCH -n {{ num_cpu }}
#SBATCH -N 1 #SBATCH -N 1
#SBATCH --time 3:0:0
#SBATCH --gpus {{ num_gpu }} #SBATCH --gpus {{ num_gpu }}
#SBATCH --mem={{ (ram_gb*1000)|int }}MB #SBATCH --mem={{ (ram_gb*1000)|int }}MB
#SBATCH --job-name cryosparc_{{ project_uid }}_{{ job_uid }} #SBATCH --job-name cryosparc_{{ project_uid }}_{{ job_uid }}
...@@ -27,7 +27,7 @@ echo "TMPDIR="$TMPDIR ...@@ -27,7 +27,7 @@ echo "TMPDIR="$TMPDIR
mkdir -p ${TMPDIR} mkdir -p ${TMPDIR}
# load cryosarc # load cryosarc
source ${HOME}/cryosparc/cryosparc_worker.sh source ${HOME}/cryosparc/worker-config.sh
# {{ run_cmd }} # {{ run_cmd }}
export RUN_ARGS="{{ run_args }}" export RUN_ARGS="{{ run_args }}"
......
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