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Fix to allow Gaudi slc6 jobs to run inside apptainer #2333

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Fix to allow Gaudi slc6 jobs to run inside apptainer #2333

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144d276
Modified template such that Local jobs runs in
egede Apr 24, 2024
9596281
Fix typo
egede Apr 24, 2024
829aaa6
Proposed solution for running slc6 jobs
egede Apr 24, 2024
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13 changes: 10 additions & 3 deletions ganga/GangaCore/Lib/Localhost/LocalHostExec.py.template
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Original file line number Diff line number Diff line change
Expand Up @@ -69,9 +69,16 @@ gangadir = ###GANGADIR###
sys.path.insert(0, gangadir)
sys.path.insert(0,os.path.join(os.getcwd(),PYTHON_DIR))

runenv = os.environ.copy()
for key,value in environment.items():
runenv[key] = value
runenv = dict()
result = subprocess.run(["bash", "-lc", "printenv"], capture_output=True, encoding='utf-8')
for line in result.stdout.split('\\n'):
varval = line.strip().split('=')
if len(varval) < 2:
pass
else:
content = ''.join(varval[1:])
if not str(content).startswith('() {'):
runenv[varval[0]] = content

outfile=open('stdout','w')
errorfile=open('stderr','w')
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19 changes: 17 additions & 2 deletions ganga/GangaLHCb/Lib/RTHandlers/GaudiExecRTHandlers.py
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Expand Up @@ -191,7 +191,9 @@ def prepareCommand(app):
for _arg in app.run_args:
run_args += ' %s ' % _arg

run_cmd = ' export ganga_jobid=%s && ./run %s ' % (app.getJobObject().fqid, run_args)
run_cmd = f' export ganga_jobid={app.getJobObject().fqid} && ./run {run_args} '
if 'slc6' in app.platform:
run_cmd = f'sed -i "s/lb-run /lb-run --container apptainer /g" ./run && {run_cmd}'

if not app.useGaudiRun:
full_cmd = sourceEnv + run_cmd + 'python %s' % app.getWrapperScriptName()
Expand Down Expand Up @@ -792,13 +794,26 @@ def flush_streams(pipe):
# Extract any/_all_ (b/g)zip files on the WN
extractAllTarFiles('.')

runenv = dict()
result = subprocess.run(["bash", "-lc",
"source /cvmfs/lhcb.cern.ch/lib/LbEnv && printenv"],
capture_output=True, encoding='utf-8')
for line in result.stdout.split('\\n'):
varval = line.strip().split('=')
if len(varval) < 2:
pass
else:
content = ''.join(varval[1:])
if not str(content).startswith('() {'):
runenv[varval[0]] = content

print("Executing: %s" % '###COMMAND###'+' '+' '.join(sys.argv[1:]))

# Execute the actual command on the WN
# NB os.system caused the entire stream to be captured before being streamed in some cases
pipe = subprocess.Popen('###COMMAND###'+' '+' '.join(sys.argv[1:]), shell=True,
stdin=subprocess.PIPE, stdout=subprocess.PIPE,
universal_newlines=True, errors="replace")
universal_newlines=True, errors="replace", env=runenv)

# Flush the stdout/stderr as the process is running correctly
flush_streams(pipe)
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