From e9bdc8378c906572bbf69d29afaf0ba7614589ba Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Fri, 10 Sep 2021 15:05:51 +0100
Subject: [PATCH] Copy bash script to run notebook to working directory
---
bin/slurm_calibrate.sh | 2 ++
src/xfel_calibrate/calibrate.py | 13 +++++++++----
2 files changed, 11 insertions(+), 4 deletions(-)
diff --git a/bin/slurm_calibrate.sh b/bin/slurm_calibrate.sh
index a22f322e8..700f21c89 100755
--- a/bin/slurm_calibrate.sh
+++ b/bin/slurm_calibrate.sh
@@ -1,4 +1,6 @@
#!/bin/bash
+# This script is used to run a parameterised copy of a Jupyter notebook. It is
+# typically run through Slurm with the sbatch command.
set -euo pipefail
diff --git a/src/xfel_calibrate/calibrate.py b/src/xfel_calibrate/calibrate.py
index a6bf414b2..ee8bd63c4 100755
--- a/src/xfel_calibrate/calibrate.py
+++ b/src/xfel_calibrate/calibrate.py
@@ -8,6 +8,7 @@ import math
import os
import pprint
import re
+import shutil
import stat
import string
import sys
@@ -771,7 +772,7 @@ def prepare_job(
nbformat.write(new_nb, nbpath)
return JobArgs([
- "{pkg_dir}/bin/slurm_calibrate.sh",
+ "pycalib-run-nb.sh",
new_name,
"{python}",
cluster_profile,
@@ -793,9 +794,7 @@ class JobArgs:
return isinstance(other, JobArgs) and (self.args == other.args)
def format_cmd(self, python):
- return [a.format(
- python=python, pkg_dir=PKG_DIR
- ) for a in self.args]
+ return [a.format(python=python) for a in self.args]
def run_direct(self, work_dir, python) -> int:
return call(self.format_cmd(python), cwd=work_dir)
@@ -1014,6 +1013,12 @@ def run():
# And save the invocation of this script itself
save_executed_command(run_tmp_path, version)
+ # Copy the bash script which will be used to run notebooks
+ shutil.copy2(
+ os.path.join(PKG_DIR, "bin", "slurm_calibrate.sh"),
+ os.path.join(run_tmp_path, "pycalib-run-nb.sh")
+ )
+
# wait on all jobs to run and then finalize the run by creating a report from the notebooks
out_path = Path(default_report_path) / detector.upper() / caltype.upper() / datetime.now().isoformat()
if try_report_to_output:
--
GitLab