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Chemshell integration proper #120

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jimboid opened this issue Feb 21, 2019 · 0 comments
Open
3 tasks

Chemshell integration proper #120

jimboid opened this issue Feb 21, 2019 · 0 comments
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jimboid commented Feb 21, 2019 •
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Previous integration of the new pychemshell was reliant on linking the underlying executable. This meant bypassing the wrapper script and thus not having the user friendly environment configuration it brings with it.

An attempt to address this has been made on the chemshell side, however this did not go well. A summary of what happened is here (taken from chemshell gitlab):

The modifications done here in the issue2 branch basically don't work. We have run into issues with the way Python works with the native environments. The environment is tweaked on a per machine basis by Chemshell to make things more user friendly, sadly this means that the environment is not persisted once the wrapper exits. Our planned route to using the wrapper to configure the environment as part of a Longbow submit script is not viable.
You Lu has commited code to fix the default behavior of between the interactive and submit modes internal to chemshell in commit f2234b0f.
Next step is to code something on the Longbow side to provide a "hook" into the the core code to allow a per app override to be prescribed for submitting. This will allow users in other domains using python wrapper based apps to use Longbow, so has some benefits for us too :).

The next approach to try is to code in hooks to allow generic python/anaconda wrapped apps to be launched by Longbow.

  • Code
  • Test
  • Document
@jimboid jimboid self-assigned this Feb 21, 2019
@jimboid jimboid added this to the v1.5.3 milestone Feb 21, 2019
jimboid added a commit that referenced this issue Feb 26, 2019
@jimboid
Chemshell integration issue #120
2a1f14f 
Added rest of code to make the basic functionality work. Longbow now has
overrides in the submission portion of its core such that the chemshell
wrapper can be used natively without going via qsub scripts.

The unit tests for the existing longbow core code required fixing,
however the chemshell plugin current does not have tests.
jimboid added a commit that referenced this issue Feb 28, 2019
@jimboid
More for issue #120
779c082 
Added some of the commandline flags to see if Longbow could pass them on
and run a job.
jimboid added a commit that referenced this issue Mar 7, 2019
@jimboid
Different approach to issue #120
18c6411 
This approach is based on modifications to the Chemshell code so that
during compilation an environment file is spat out. Longbow can then
load this into the environment and call the chemsh.x directly along with
qsub or whatever platform specific submitter is.
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