Re-establish APBS remote invocation via Python #381

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keith923 opened this Issue Nov 18, 2015 · 3 comments

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keith923 commented Nov 18, 2015

There was some cruft in the ENABLE_PYTHON option of the main CMakeLists.txt file that I removed as part of issue #372. Apparently it was once useful! From @sobolevnrm:

It allowed users to run APBS on offsite servers from the command line --
everything was the same except for the command line options, so it could be
a drop-in replacement for APBS when used with visualization software like
VMD or PyMOL.

@sobolevnrm would like it back. Before just resurrecting the cruft that was there, I would like to understand why it needed to be part of the APBS build at all? Given what it does, why can't we just make a Python file available that points to the correct servers to allow users to submit jobs?

@keith923 keith923 added the apbs label Nov 18, 2015

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sobolevnrm Nov 18, 2015

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Yes, a Python file would be much cleaner. It doesn't need to be part of
the build except that there are some compiled dependencies related to
Opal that need to be built. So it will need to be built somewhere but
doesn't need to be part of the APBS build.

On Wed, Nov 18, 2015 at 7:22 AM Keith T. Star notifications@github.com
wrote:

There was some cruft in the ENABLE_PYTHON option of the main
CMakeLists.txt file that I removed as part of issue #372
#372. Apparently
it was once useful! From @sobolevnrm https://github.com/sobolevnrm:

It allowed users to run APBS on offsite servers from the command line --
everything was the same except for the command line options, so it could be
a drop-in replacement for APBS when used with visualization software like
VMD or PyMOL.

@sobolevnrm https://github.com/sobolevnrm would like it back. Before
just resurrecting the cruft that was there, I would like to understand why
it needed to be part of the APBS build at all? Given what it does, why
can't we just make a Python file available that points to the correct
servers to allow users to submit jobs?


Reply to this email directly or view it on GitHub
#381.

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sobolevnrm commented Nov 18, 2015

Yes, a Python file would be much cleaner. It doesn't need to be part of
the build except that there are some compiled dependencies related to
Opal that need to be built. So it will need to be built somewhere but
doesn't need to be part of the APBS build.

On Wed, Nov 18, 2015 at 7:22 AM Keith T. Star notifications@github.com
wrote:

There was some cruft in the ENABLE_PYTHON option of the main
CMakeLists.txt file that I removed as part of issue #372
#372. Apparently
it was once useful! From @sobolevnrm https://github.com/sobolevnrm:

It allowed users to run APBS on offsite servers from the command line --
everything was the same except for the command line options, so it could be
a drop-in replacement for APBS when used with visualization software like
VMD or PyMOL.

@sobolevnrm https://github.com/sobolevnrm would like it back. Before
just resurrecting the cruft that was there, I would like to understand why
it needed to be part of the APBS build at all? Given what it does, why
can't we just make a Python file available that points to the correct
servers to allow users to submit jobs?


Reply to this email directly or view it on GitHub
#381.

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keith923 Nov 18, 2015

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Huh. I didn't notice anything about Opal in the build script. @kmonson do you know anything about that? Perhaps we could get this sorted out together?

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keith923 commented Nov 18, 2015

Huh. I didn't notice anything about Opal in the build script. @kmonson do you know anything about that? Perhaps we could get this sorted out together?

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kmonson Nov 18, 2015

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Sure.

I'll have to look at the script to see what we need to do. We might move
this over to pdb2pqr or make it a separate build target in apbs.

On Wed, Nov 18, 2015 at 8:14 AM, Keith T. Star notifications@github.com
wrote:

Huh. I didn't notice anything about Opal in the build script. @kmonson
https://github.com/kmonson do you know anything about that? Perhaps we
could get this sorted out together?


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#381 (comment)
.

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kmonson commented Nov 18, 2015

Sure.

I'll have to look at the script to see what we need to do. We might move
this over to pdb2pqr or make it a separate build target in apbs.

On Wed, Nov 18, 2015 at 8:14 AM, Keith T. Star notifications@github.com
wrote:

Huh. I didn't notice anything about Opal in the build script. @kmonson
https://github.com/kmonson do you know anything about that? Perhaps we
could get this sorted out together?


Reply to this email directly or view it on GitHub
#381 (comment)
.

@lizutah lizutah added this to the APBS 1.5.x milestone Jan 12, 2016

@lizutah lizutah modified the milestones: Someday, APBS 1.5.x Aug 12, 2016

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