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| #!/bin/bash | |
| #SBATCH | |
| if [[ "$SLURM_PROCID" = "0" ]]; then | |
| ssh -R 0.0.0.0:9999:localhost:8888 -f -N login-0-1 | |
| jupyter notebook | |
| elif [[ "$SLURM_PROCID" = "1" ]]; then | |
| ipcontroller --ip='*' | |
| elif [[ "$SLURM_PROCID" = "2" ]]; then | |
| mpirun --bind-to=none -n "$((SLURM_NTASKS-2))" ipengine | |
| fi |
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| #!/usr/bin/env python | |
| """ | |
| Usage: python launchable.py | |
| """ | |
| from __future__ import print_function | |
| tpls = {'setup': ''' | |
| mkdir -p $HOME/launchable | |
| tempdir=$(mktemp -d --tmpdir="$HOME/launchable") | |
| TUNNEL_PORT={tunnel_port} | |
| NB_PORT={nb_port} | |
| LOGIN_NODE=$(hostname) | |
| ''', | |
| 'scripts': ''' | |
| batch="$tempdir/batch.sh" | |
| run="$tempdir/run.sh" | |
| cat >"$batch" <<EOL | |
| #!/bin/bash | |
| #SBATCH --account=nn9279k | |
| #SBATCH --time=00:15:00 | |
| #SBATCH --mem-per-cpu=3900M | |
| #SBATCH --ntasks={n} | |
| rm -rf ~/.ipython/profile_default/security | |
| srun "$run" | |
| EOL | |
| cat >"$run" <<EOL | |
| #!/bin/bash | |
| source /etc/profile | |
| source /cluster/bin/jobsetup | |
| source /usit/abel/u1/oyvinev/fenics1.6_jupyter | |
| if [[ "\$SLURM_PROCID" = "0" ]]; then | |
| ssh -R $TUNNEL_PORT:localhost:$NB_PORT $LOGIN_NODE -f -N | |
| jupyter notebook --port $NB_PORT | |
| elif [[ "\$SLURM_PROCID" = "1" ]]; then | |
| ipcontroller --ip='*' | |
| elif [[ "\$SLURM_PROCID" = "2" ]]; then | |
| mpirun --bind-to none -n "\$((SLURM_NTASKS-2))" ipengine --timeout=60 | |
| fi | |
| EOL | |
| chmod +x $run $batch | |
| echo BATCH:$batch | |
| echo RUN:$run | |
| ''', | |
| 'run': ''' | |
| jobid=$(/cluster/bin/sbatch $batch | awk '{{print $4}}') | |
| echo "job id: $jobid" | |
| test -z "$jobid" && exit 1 | |
| state="wait" | |
| while [[ "$state" = "wait" ]]; do | |
| echo . | |
| # check squeue | |
| test -z "$(squeue -u `whoami` | grep $jobid)" && state='FAILED' | |
| curl -s http://localhost:$TUNNEL_PORT 2>&1 >/dev/null && state=AOK || sleep 1 | |
| done | |
| echo "$state" | |
| if [[ "$state" = "FAILED" ]]; then | |
| while [[ ! -f "$HOME/slurm-$jobid.out ]]; do | |
| sleep 1 | |
| end | |
| cat ~/slurm-$jobid.out | |
| exit 1 | |
| fi | |
| while true; do | |
| sleep 30 | |
| done | |
| '''} | |
| import argparse | |
| from random import randint | |
| import sys | |
| import webbrowser | |
| import pexpect | |
| def expect_echo(p): | |
| p.sendline('###END###') | |
| p.expect('###END###') | |
| def run_job(options): | |
| ns = options.__dict__ | |
| print("Tunneling {local_port} to {host}:{tunnel_port}".format(**ns)) | |
| p = pexpect.spawn('ssh', [ | |
| '-L', | |
| '%i:localhost:%i' % (options.local_port, options.tunnel_port), | |
| options.host, | |
| 'bash', | |
| ]) | |
| p.logfile = sys.stderr | |
| print('setup') | |
| p.send(tpls['setup'].format(**ns)) | |
| expect_echo(p) | |
| print('scripts') | |
| p.send(tpls['scripts'].format(**ns)) | |
| expect_echo(p) | |
| print('run') | |
| p.send(tpls['run'].format(**ns)) | |
| expect_echo(p) | |
| p.expect('job id:') | |
| p.expect('\r\n') | |
| jobid = int(p.before) | |
| try: | |
| p.expect(['AOK', 'FAILED'], timeout=600) | |
| except pexpect.EOF: | |
| print("Failed") | |
| print(p.before, file=sys.stderr) | |
| sys.exit(1) | |
| if p.after == 'FAILED': | |
| print("Failed") | |
| # got failed message, wait for EOF and show output | |
| p.expect(pexpect.EOF) | |
| print(p.before, file=sys.stderr) | |
| sys.exit(1) | |
| return p | |
| def main(): | |
| parser = argparse.ArgumentParser() | |
| parser.add_argument('--n', type=int, default=4) | |
| parser.add_argument('--port', dest='local_port', type=int, default=9999) | |
| parser.add_argument('--tunnel-port', type=int, default=randint(49152, 65535)) | |
| parser.add_argument('--nb-port', type=int, default=randint(49152, 65535)) | |
| parser.add_argument('--host', type=str, default='abel.uio.no') | |
| options = parser.parse_args() | |
| p = run_job(options) | |
| print("Opening browser") | |
| webbrowser.open('http://localhost:9999') | |
| # wait for exit | |
| p.expect(pexpect.EOF, timeout=None) | |
| if __name__ == '__main__': | |
| main() |
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| #SBATCH | |
| env | |
| if [[ "$SLURM_PROCID" = "0" ]]; then | |
| echo "hi" | |
| else | |
| mpirun python -c "import os; print(os.getpid())" | |
| fi |
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