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Bug #1754

tune_pme in gromacs 5 does not use "gmx mdrun" by default.

Added by Åke Sandgren over 4 years ago. Updated over 4 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
core library
Target version:
Affected version - extra info:
problem gets worse in 5.1-rc1
Affected version:
Difficulty:
uncategorized
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Description

When running gmx tune_pme without setting $MDRUN it tries to run mdrun instead of gmx mdrun.

gmx tune_pme -ntmpi 28 -s ion_channel.tpr ...
...
Fatal error:
Cannot execute mdrun. Please check benchtest.log for problems!

cat benchtest.log
sh: 1: mdrun: not found

Associated revisions

Revision 1cacfdf5 (diff)
Added by Mark Abraham over 4 years ago

Require tune_pme to take -mdrun parameter

The transition away from many binaries in 5.0, and the removal of
symlinks in 5.1 mean there is even less chance that a sensible default
command line for calling mdrun can be provided. In general, mdrun
might be in either precision, with or without MPI, with or without
some custom suffix, inside the wrapper binary or from an mdrun-only
build, or from a custom directory.

Thus, the user is now required to say what command to call to run the
simulation they want to optimize. The MDRUN environment variable
remains as an undocumented and deprecated convenience feature for 5.1.

Fixes #1754

Change-Id: Ia2c278732ef2a79d7304967b230149eca4597888

History

#1 Updated by Gerrit Code Review Bot over 4 years ago

Gerrit received a related patchset '1' for Issue #1754.
Uploader: Rossen Apostolov ()
Change-Id: I2567d63ce2415a1bedb2b4923577b2f2af02ebe9
Gerrit URL: https://gerrit.gromacs.org/4771

#2 Updated by Mark Abraham over 4 years ago

But by default there should be a symlink mdrun wherever gmx is installed. Frankly, I think the best behaviour is to require the user to specify which binary to run.

#3 Updated by Gerrit Code Review Bot over 4 years ago

Gerrit received a related patchset '2' for Issue #1754.
Uploader: Mark Abraham ()
Change-Id: Ia2c278732ef2a79d7304967b230149eca4597888
Gerrit URL: https://gerrit.gromacs.org/4963

#4 Updated by Mark Abraham over 4 years ago

  • Category set to core library
  • Status changed from New to Feedback wanted
  • Assignee set to Mark Abraham
  • Target version set to 5.1
  • Affected version - extra info set to problem gets worse in 5.1-rc1
  • Affected version changed from 5.x to 5.0.7

My fix is targeted at 5.1, because there are no longer symlinks available there.

In 5.0.x, I think Ake's use case should be solved by setting MDRUN if somehow there is not a symlink to mdrun available.

#5 Updated by Mark Abraham over 4 years ago

  • Status changed from Feedback wanted to Resolved
  • % Done changed from 0 to 100

#6 Updated by Mark Abraham over 4 years ago

  • Status changed from Resolved to Closed

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