From 4cecda39f36a8aae8a77bcb0e1fd9afc59364187 Mon Sep 17 00:00:00 2001
From: Adrian Schmitz <adrian.schmitz@rwth-aachen.de>
Date: Thu, 5 Oct 2023 09:26:23 +0200
Subject: [PATCH] Bug fixes
---
.gitlab-ci.yml | 2 +-
core/job.py | 7 +++----
core/modes/slurm/batch.py | 6 ++++--
core/modes/slurm/singularity.py | 2 +-
core/utility/defines.py | 2 +-
core/utility/executor.py | 2 +-
utility/runtime/scripts/batchWrapper.sh | 4 +++-
utility/runtime/scripts/chmodPath.sh | 2 +-
8 files changed, 15 insertions(+), 12 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 2df517d..223bbf4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -26,7 +26,7 @@ variables:
.local-template:
variables:
- RUNNER_TAG: "ja664344-dev"
+ RUNNER_TAG: "custom2"
.run-template:
stage: run
diff --git a/core/job.py b/core/job.py
index 9f784bf..4f9aa0a 100644
--- a/core/job.py
+++ b/core/job.py
@@ -90,11 +90,11 @@ class Job:
self.rt_utility_path = rep(settings["Runtime Utility Path"])
self.scripts_path = f'{self.rt_utility_path}/scripts'
if self.down_scoping:
- try:
+ if (get_cenv('HPC_CI_TOKEN') != None):
uid, pid = jwt.get_UID_PID_ID_TOKEN(get_cenv('HPC_CI_TOKEN'),
f"{get_cenv('CI_SERVER_URL')}/-/jwks")
- except:
- logging.warn("id token HPC_CI_TOKEN, with aud: aixCIlence not defined.")
+ else:
+ print("WARNING:id token HPC_CI_TOKEN, with aud: aixCIlence not defined.", file=sys.stderr)
try:
uid, pid = jwt.get_UID_PID_CI_JOB_JWT(get_cenv('CI_JOB_JWT'),
f"{get_cenv('CI_SERVER_URL')}/-/jwks")
@@ -112,7 +112,6 @@ class Job:
else:
self.user_path = rep(settings['User Path'])
-
def __setup(self):
self.__get_config()
if not self.down_scoping:
diff --git a/core/modes/slurm/batch.py b/core/modes/slurm/batch.py
index df3d64a..2c21dae 100644
--- a/core/modes/slurm/batch.py
+++ b/core/modes/slurm/batch.py
@@ -74,7 +74,8 @@ class Sbatch(Slurm, ABC):
tmp = os.getenv("TMP")
with open(f'{self.job.scripts_path}/batchWrapper.sh', 'r') as file:
filedata = file.read()
- filedata = filedata.replace('replaceme', f'{self.job.clone_path}/{get_cenv("BATCH_SCRIPT")}')
+ filedata = filedata.replace('replacesource', f'{self.job.shell_config}')
+ filedata = filedata.replace('replacescript', f'{self.job.clone_path}/{get_cenv("BATCH_SCRIPT")}')
with open(f'{tmp}/wrapper{self.job.jobid}', 'w') as file:
file.write(filedata)
return f'{tmp}/wrapper{self.job.jobid}'
@@ -126,7 +127,8 @@ class Default(Sbatch, ABC):
tmp = os.getenv("TMP")
with open(f'{self.job.scripts_path}/batchWrapper.sh', 'r') as file:
filedata = file.read()
- filedata = filedata.replace('replaceme', f'{self.job.clone_path}/script.')
+ filedata = filedata.replace('replacescript', f'{self.job.clone_path}/script.')
+ filedata = filedata.replace('replacesource', f'{self.job.shell_config}')
with open(f'{tmp}/wrapper{self.job.jobid}', 'w') as file:
file.write(filedata)
return f'{tmp}/wrapper{self.job.jobid}'
diff --git a/core/modes/slurm/singularity.py b/core/modes/slurm/singularity.py
index 5d20c20..cba750e 100644
--- a/core/modes/slurm/singularity.py
+++ b/core/modes/slurm/singularity.py
@@ -81,7 +81,7 @@ class Singularity_Batch(Default, ABC):
tmp = os.getenv("TMP")
with open(f'{self.job.runner_path}/utility/runtime/scripts/batchWrapper.sh', 'r') as file:
filedata = file.read()
- filedata = filedata.replace('replaceme',
+ filedata = filedata.replace('replacescript',
f'{self.job.clone_path}/singularity{self.job.jobid}.sh < '
f'{self.job.clone_path}/script{self.job.jobid}.sh')
with open(f'{tmp}/wrapper{self.job.jobid}', 'w') as file:
diff --git a/core/utility/defines.py b/core/utility/defines.py
index f916efe..2a17164 100644
--- a/core/utility/defines.py
+++ b/core/utility/defines.py
@@ -1,6 +1,6 @@
import logging
name = 'AixCIlenz CI Driver'
-version = '0.5.2'
+version = '0.5.3'
debug = False
stdout_logging = False
diff --git a/core/utility/executor.py b/core/utility/executor.py
index 370ec84..3657950 100644
--- a/core/utility/executor.py
+++ b/core/utility/executor.py
@@ -163,7 +163,7 @@ class Slurm_Executor(Executor, ABC):
allocator=self.get_srun_cmd(),
params=f'--jobid={self.simple_job_id} {self.get_default_params()} {params}',
wrapper_add=wrapper_add,
- pre_exec_scripts=[self.job.shell_config],
+ #pre_exec_scripts=[self.job.shell_config],
target_script=script, install_env=install_env,
text=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT).stdout
logging.debug(management_out)
diff --git a/utility/runtime/scripts/batchWrapper.sh b/utility/runtime/scripts/batchWrapper.sh
index 735e714..e00fb88 100644
--- a/utility/runtime/scripts/batchWrapper.sh
+++ b/utility/runtime/scripts/batchWrapper.sh
@@ -1,3 +1,5 @@
#!/usr/bin/zsh
-zsh -l replaceme
\ No newline at end of file
+source replacesource
+
+zsh -l replacescript
diff --git a/utility/runtime/scripts/chmodPath.sh b/utility/runtime/scripts/chmodPath.sh
index cb98165..d59bcac 100755
--- a/utility/runtime/scripts/chmodPath.sh
+++ b/utility/runtime/scripts/chmodPath.sh
@@ -2,7 +2,7 @@
_path=$1
set -e
while test "$_path" != "/work"; do
- chmod o+x "$_path"
+ chmod o+rx "$_path"
_path=$(dirname "$_path")
done
--
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