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create_reserved_lanes.sh
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Created
Wed, Apr 24, 00:36
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text/x-shellscript
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Fri, Apr 26, 00:36 (1 d, 23 h)
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rSCCRYOSPARC scitas-cryosparc-scripts
create_reserved_lanes.sh
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#!/bin/bash
set
-euo pipefail
# Script made from the page
# https://docs.ycrc.yale.edu/clusters-at-yale/guides/cryosparc/
script_path
=
$(
dirname
"$0"
)
# relative
script_path
=
$(
cd
"${script_path}"
&&
pwd
)
# absolutized and normalized
install_path
=
"$HOME"
/cryosparc
# Usage
usage
()
{
echo
"Usage:"
echo
" -p install path : prefix for installation [${install_path}] "
echo
" -v : be verbose"
echo
" -h : print this notice"
echo
""
}
VERBOSE
=
false
read
-p
"Enter group account at SCITAS: "
hpc_account
read
-p
"Enter reservation name: "
reservation_name
# Parse options
while
getopts
":p:vh"
opt;
do
case
$opt
in
p
)
install_path
=
"${OPTARG}"
;;
v
)
VERBOSE
=
true
;;
h
)
usage
OPTIND
=
1
exit
0
;;
\?
)
echo
"Invalid option: -$OPTARG"
>&2
usage
OPTIND
=
1
exit
1
;;
:
)
echo
"Option -$OPTARG requires an argument."
>&2
usage
OPTIND
=
1
exit
1
;;
esac
done
# Reset OPTIND to allow the next invocation to work
OPTIND
=
1
message
()
{
if
$VERBOSE
then
echo
"${1}"
fi
}
echo
"[Info] Starting the master if needed"
if
[
$(${
script_path
}
/cryosparcm.sh status | grep -c
"CryoSPARC is not running"
)
-eq 1
]
;
then
${
script_path
}
/cryosparcm.sh start
fi
cd
${
install_path
}
/site_configs
for
_account in
$hpc_account
;
do
if
[
$(
sacctmgr show assoc where
account
=
${
_account
}
format
=
ParentName%100 -P | grep -v
"Par Name"
| grep -c courses
)
-eq 0
]
;
then
_worker_name
=
${
HOSTNAME
}
-
${
_account
}
-reserved
max_wall
=
$(
sacctmgr show assoc where
account
=
${
_account
}
format
=
MaxWall -P | grep -v MaxWall | head -1
)
for
mem in 90;
do
mkdir -p
${
install_path
}
/site_configs/
${
_worker_name
}
_
${
mem
}
gb
&&
cd
${
install_path
}
/site_configs/
${
_worker_name
}
_
${
mem
}
gb
cat
<< EOF > cluster_info.json
{
"name": "${_worker_name}_${mem}gb",
"worker_bin_path": "${install_path}/cryosparc_worker/bin/cryosparcw",
"cache_path": "/tmp/{{ cryosparc_username }}/cryosparc_cache",
"cache_reserve_mb": 10000,
"cache_quota_mb": 1000000,
"send_cmd_tpl": "{{ command }}",
"qsub_cmd_tpl": "sbatch {{ script_path_abs }}",
"qstat_cmd_tpl": "squeue -j {{ cluster_job_id }}",
"qdel_cmd_tpl": "scancel {{ cluster_job_id }}",
"qinfo_cmd_tpl": "sinfo"
}
EOF
cat
<< EOF > cluster_script.sh
#!/bin/bash -l
#SBATCH --job-name cryosparc_{{ project_uid }}_{{ job_uid }}
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task={{ num_cpu }}
#SBATCH --qos=gpu
#SBATCH --gres=gpu:{{ num_gpu }}
#SBATCH --mem ${mem}GB
#SBATCH --time 3-00:00:00
#SBATCH -o {{ job_dir_abs }}/slurm.out
#SBATCH -e {{ job_dir_abs }}/slurm.err
#SBATCH -A ${_account}
#SBATCH --reservation $reservation_name
module load gcc cuda python
mkdir -p /tmp/${USER}
ln -sf \${TMPDIR} /tmp/${USER}/cryosparc_cache
{{ run_cmd }}
EOF
${
script_path
}
/cryosparcm.sh cluster connect
done
fi
done
for
_account in
$hpc_account
;
do
if
[
$(
sacctmgr show assoc where
account
=
${
_account
}
format
=
ParentName%100 -P | grep -v
"Par Name"
| grep -c courses
)
-eq 0
]
;
then
_worker_name
=
${
HOSTNAME
}
-
${
_account
}
-reserved-CPUOnly-Max20
max_wall
=
$(
sacctmgr show assoc where
account
=
${
_account
}
format
=
MaxWall -P | grep -v MaxWall | head -1
)
for
mem in 90;
do
mkdir -p
${
install_path
}
/site_configs/
${
_worker_name
}
_
${
mem
}
gb
&&
cd
${
install_path
}
/site_configs/
${
_worker_name
}
_
${
mem
}
gb
cat
<< EOF > cluster_info.json
{
"name": "${_worker_name}_${mem}gb",
"worker_bin_path": "${install_path}/cryosparc_worker/bin/cryosparcw",
"cache_path": "/tmp/{{ cryosparc_username }}/cryosparc_cache",
"cache_reserve_mb": 10000,
"cache_quota_mb": 1000000,
"send_cmd_tpl": "{{ command }}",
"qsub_cmd_tpl": "sbatch {{ script_path_abs }}",
"qstat_cmd_tpl": "squeue -j {{ cluster_job_id }}",
"qdel_cmd_tpl": "scancel {{ cluster_job_id }}",
"qinfo_cmd_tpl": "sinfo"
}
EOF
cat
<< EOF > cluster_script.sh
#!/bin/bash -l
#SBATCH --job-name cryosparc_{{ project_uid }}_{{ job_uid }}
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task={{ num_cpu }}
#SBATCH --qos=gpu
#SBATCH --gres=gpu:1
#SBATCH --mem ${mem}GB
#SBATCH --time 3-00:00:00
#SBATCH -o {{ job_dir_abs }}/slurm.out
#SBATCH -e {{ job_dir_abs }}/slurm.err
#SBATCH -A ${_account}
#SBATCH --reservation $reservation_name
module load gcc cuda python
mkdir -p /tmp/${USER}
ln -sf \${TMPDIR} /tmp/${USER}/cryosparc_cache
{{ run_cmd }}
EOF
${
script_path
}
/cryosparcm.sh cluster connect
done
fi
done
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