fix for slurm + singularity (wrong check-alive shell script)

ENCODE-DCC · Jun 11, 2019 · 6123bf7 · 6123bf7
1 parent 7dd1782
commit 6123bf7
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/caper/caper_backend.py b/caper/caper_backend.py
@@ -299,7 +299,9 @@ class CaperBackendSLURM(dict):
             ${if defined(gpu) then '--nv' else ''} \
             ${singularity} /bin/bash ${script}"
     """
-    CHECK_ALIVE = "squeue -j ${job_id}"
+    CHECK_ALIVE = """CHK_ALIVE=$(squeue --noheader -j ${job_id} --format=%i | grep ${job_id}); if [ -z "$CHK_ALIVE" ]; \
+then /bin/bash -c 'exit 1'; else echo $CHK_ALIVE; fi"""
+
     TEMPLATE = {
         "backend": {
             "providers": {

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name='caper',
-    version='v0.2.6',
+    version='v0.2.7',
     python_requires='>3.4.1',
     scripts=['bin/caper', 'mysql/run_mysql_server_docker.sh',
              'mysql/run_mysql_server_singularity.sh'],