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Hi everyone, I found a bug while testing N10 LAMMPS in podman-hpc
Image: localhost:/n10-lammps:1.0
Run script:
podman-hpc run --gpu --mpi localhost/n10-lammps:1.0 /opt/lammps/install/bin/lmp -k on g 4 -sf kk -pk kokkos newton on neigh half -in /opt/exaalt/benchmarks/common/in.snap.test -var snapdir /opt/exaalt/benchmarks/common/2J8_W.SNAP -var nx 256 -var ny 256 -var nz 256 -var nsteps 1
Error:
Traceback (most recent call last):
File "./podman-hpc", line 11, in <module>
load_entry_point('podman-hpc==1.1.0', 'console_scripts', 'podman-hpc')()
File "/global/homes/s/shubhp/work/exaalt/container/podman-build/usr/lib/python3.6/site-packages/podman_hpc/podman_hpc.py", line 445, in main
podhpc(prog_name="podman-hpc")
File "/usr/lib/python3.6/site-packages/click/core.py", line 764, in __call__
return self.main(*args, **kwargs)
File "/usr/lib/python3.6/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/usr/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/lib/python3.6/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/lib/python3.6/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/usr/lib/python3.6/site-packages/click/decorators.py", line 64, in new_func
return ctx.invoke(f, obj, *args, **kwargs)
File "/usr/lib/python3.6/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/usr/lib/python3.6/site-packages/click/decorators.py", line 17, in new_func
return f(get_current_context(), *args, **kwargs)
File "/global/homes/s/shubhp/work/exaalt/container/podman-build/usr/lib/python3.6/site-packages/podman_hpc/podman_hpc.py", line 398, in call_podman
_shared_run(siteconf, podman_args, **site_opts)
File "/global/homes/s/shubhp/work/exaalt/container/podman-build/usr/lib/python3.6/site-packages/podman_hpc/podman_hpc.py", line 263, in _shared_run
valid_params = cpt.filterValidOptions(list(run_args), cmd)
File "/global/homes/s/shubhp/work/exaalt/container/podman-build/usr/lib/python3.6/site-packages/podman_hpc/click_passthrough.py", line 215, in filterValidOptions
unknowns = p.parse_known_args(valid_options)[1]
TypeError: 'NoneType' object is not subscriptable
Reason for this error: When container arguments are parsed, podman options are filtered out but we never take overlapping into account i.e -i podman is a boolean flag but for lammps means input file so it expects a value, thus the error.
Solution: Disable filtering of container arguments with podman options
Create a simple script named test_input_arg_value.sh;
Run podman-hpc run --rm -v $PWD:/test ubuntu:latest /test/test_input_arg_value.sh -i "this is my input_file"
> cat test_input_arg_value.sh
#!/bin/bash
input_arg_value=$2
echo $input_arg_value
> podman-hpc run --rm -v $PWD:/test ubuntu:latest /test/test_input_arg_value.sh -i "this is my input_file"
this is my input_file
Hi everyone, I found a bug while testing N10 LAMMPS in podman-hpc
Image: localhost:/n10-lammps:1.0
Run script:
Error:
Reason for this error: When container arguments are parsed, podman options are filtered out but we never take overlapping into account i.e
-i
podman is a boolean flag but for lammps means input file so it expects a value, thus the error.Solution: Disable filtering of container arguments with podman options
Test program to replicate this error:
Regards,
Shubh
PEM intern, NERSC
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