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Default to add '-wdir' arguments #351

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merged 4 commits into from
Aug 2, 2023
Merged

Default to add '-wdir' arguments #351

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9f15fd0
default to add -wdir
Jul 28, 2023
adba4bd
remove mvapich run option as its no longer used
Jul 30, 2023
279fedb
run ldd to obtain the required binaries when submodels is initialised
Jul 31, 2023
f044039
change comment for slurm -wdir option
jo-basevi Aug 2, 2023
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -8,3 +8,4 @@ MANIFEST
/docs/_build
.coverage
.ipynb_checkpoints
.vscode
9 changes: 3 additions & 6 deletions payu/envmod.py
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Expand Up @@ -104,15 +104,12 @@ def lib_update(bin_path, lib_name):
slibs = ldd_output.split('\n')

for lib_entry in slibs:
if lib_name in lib_entry:
if lib_name in lib_entry and 'spack' not in lib_entry:
# Only load enviroment modules available - assuming spack built libs includes 'spack' in full path of library
lib_path = lib_entry.split()[2]

# pylint: disable=unbalanced-tuple-unpacking
mod_name, mod_version = fsops.splitpath(lib_path)[2:4]

module('unload', mod_name)
module('load', os.path.join(mod_name, mod_version))
return '{0}/{1}'.format(mod_name, mod_version)

# If there are no libraries, return an empty string
return ''
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module('load', os.path.join(mod_name, mod_version))
22 changes: 5 additions & 17 deletions payu/experiment.py
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Expand Up @@ -514,19 +514,18 @@ def run(self, *user_flags):
# Update MPI library module (if not explicitly set)
# TODO: Check for MPI library mismatch across multiple binaries
if mpi_module is None:
mpi_module = envmod.lib_update(
envmod.lib_update(
model.exec_path_local,
'libmpi.so'
)

model_prog = []

if mpi_module.startswith('openmpi'):
# Our MPICH wrapper does not support a working directory flag
model_prog.append('-wdir {0}'.format(model.work_path))
elif self.config.get('scheduler') == 'slurm':
wdir_arg = '-wdir'
if self.config.get('scheduler') == 'slurm':
# Slurm's launcher controls the working directory
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model_prog.append('--chdir {0}'.format(model.work_path))
wdir_arg = '--chdir'
model_prog.append(f'{wdir_arg} {model.work_path}')

# Append any model-specific MPI flags
model_flags = model.config.get('mpiflags', [])
Expand Down Expand Up @@ -590,13 +589,6 @@ def run(self, *user_flags):
if self.config.get('coredump', False):
enable_core_dump()

# Our MVAPICH wrapper does not support working directories
if mpi_module.startswith('mvapich'):
curdir = os.getcwd()
os.chdir(self.work_path)
else:
curdir = None

Comment on lines -593 to -599
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Just wanted to leave a comment to say deleting this relates directly to #350.

This just can't work with submodels and there is no attempt to test for that, nor do we want to support something that is so limited, so it is being removed.

# Dump out environment
with open(self.env_fname, 'w') as file:
file.write(yaml.dump(dict(os.environ), default_flow_style=False))
Expand All @@ -617,10 +609,6 @@ def run(self, *user_flags):
else:
rc = sp.call(shlex.split(cmd), stdout=f_out, stderr=f_err)

# Return to control directory
if curdir:
os.chdir(curdir)

f_out.close()
f_err.close()

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