error running LammpsExample__TE

OpenKIM
1

I’m not sure how to debug this error. Before running I did run the 6 different kimitems install on the Examples page.

openkim@openkim-vm:~$ pipeline_runpair LammpsExample__TE_565333229701_001 Pair_Lennard_Jones_Shifted_Bernardes_MedCutoff_Ar__MO_126566794224_001
2014-08-12 17:51:28,443 - INFO - pipeline.development - Running combination <<Test(LammpsExample__TE_565333229701_001)>, <Model(Pair_Lennard_Jones_Shifted_Bernardes_MedCutoff_Ar__MO_126566794224_001)>
2014-08-12 17:51:36,172 - INFO - pipeline.compute - running <Test(LammpsExample__TE_565333229701_001)> with <Model(Pair_Lennard_Jones_Shifted_Bernardes_MedCutoff_Ar__MO_126566794224_001)>
2014-08-12 17:51:36,191 - INFO - pipeline.compute - launching run…
2014-08-12 17:51:36,368 - INFO - pipeline.compute - Run completed in 0.17686200141906738 seconds
2014-08-12 17:51:36,383 - ERROR - pipeline.compute - Runner returned error code 1, ‘Operation not permitted’
2014-08-12 17:51:36,396 - INFO - pipeline.compute - Copying the contents of /home/openkim/openkim-repository/te/LammpsExample_running4dd3b18f-2249-11e4-8cc7-c64c81573eec__TE_565333229701_001/output to /home/openkim/openkim-repository/er/4dd3b18f-2249-11e4-8cc7-c64c81573eec
2014-08-12 17:51:36,446 - ERROR - pipeline.compute - PipelineRuntimeError()
Traceback (most recent call last):
File “/home/openkim/openkim-pipeline/tools/pipeline_runpair”, line 33, in
Computation(runner, subject, d.get_result_code()).run()
File “/home/openkim/openkim-pipeline/compute.py”, line 345, in run
raise PipelineRuntimeError(e, outs)
config.PipelineRuntimeError: KIMRuntimeError: Executable <Test(LammpsExample__TE_565333229701_001)> returned error code 1

Traceback (most recent call last):
File “/home/openkim/openkim-pipeline/compute.py”, line 326, in run
self.execute_in_place()
File “/home/openkim/openkim-pipeline/compute.py”, line 191, in execute_in_place
raise KIMRuntimeError("Executable %r returned error code r" (self.runner_temp, self.retcode))
KIMRuntimeError: Executable <Test(LammpsExample__TE_565333229701_001)> returned error code 1

output/pipeline.stdout:

2

Sorry for the cryptic error message, I think the error is due the item not being compiled. If you run

kimitems build

then it should work fine.

3

I received an error running kimitems build. It looks like this is recalling the last command called, which wasn’t kimitem install – however, I’m unable to successfully rerun the install because the file already exists.

Before I delete and re-install, does kimitems build need to be ran after each kimitems install?

openkim@openkim-vm:~$ kimitems build
Building all packages…
Traceback (most recent call last):
File “/home/openkim/openkim-pipeline/tools/kimitems”, line 240, in
action_build()
File “/home/openkim/openkim-pipeline/tools/kimitems”, line 123, in action_build
kimapi.make_all()
File “/home/openkim/openkim-pipeline/kimapi.py”, line 49, in make_all
o.make()
File “/home/openkim/openkim-pipeline/kimobjects.py”, line 256, in make
if not version.Version(self.kim_api_version) in version.Specifier(kim_api_version_spec):
File “/usr/local/lib/python2.7/dist-packages/packaging/version.py”, line 120, in init
match = self._regex.search(version)
TypeError: expected string or buffer

4

There’s a bit of a tension between the pipeline and the API examples in that the pipeline tools expect fully compliant tests with extended KIM IDs, pipeline.stdin.tpl files, etc. kimitems is meant to be an interface to these fully compliant tests and models. We are working to make some of the tools a bit more flexible in this regard, but in the meantime I think you can get by running

bootcamputil --build

instead. It should build all of the objects, not just the examples.

5

That worked! Thanks for the quick help. I’m looking forward to playing around some more.

–Shawn