Skip to content

enable MPI & external BLAS/LAPACK for GROMACS, add ictce/5.5.0 easyconfig for GROMACS 4.6.5#606

Merged
boegel merged 13 commits intoeasybuilders:developfrom
boegel:GROMACS_fixes_update
Dec 21, 2013
Merged

enable MPI & external BLAS/LAPACK for GROMACS, add ictce/5.5.0 easyconfig for GROMACS 4.6.5#606
boegel merged 13 commits intoeasybuilders:developfrom
boegel:GROMACS_fixes_update

Conversation

@boegel
Copy link
Copy Markdown
Member

@boegel boegel commented Dec 10, 2013

I still need to verify whether the -DGMX_EXTERNAL_BLAS=ON -DGMX_EXTERNAL_LAPACK=ON works as expected.

@boegel
Copy link
Copy Markdown
Member Author

boegel commented Dec 10, 2013

I should also check how to specify to GROMACS which compiler (and MPI lib) to use, to avoid that it picks up icc/ifort that may be available on the system, and prefer it over GCC (when building with goolf)...
Behavior like this was reported by @ocaisa

@fgeorgatos
Copy link
Copy Markdown
Contributor

you are likely looking for help from this:
http://www.hpcadvisorycouncil.com/pdf/GROMACS_Best_Practices.pdf
It seems you need something of the style
./configure --enable-mpi --with-fft=mkl CC=icc F77=ifort CXX=icpc,
yet watch out because around/before 4.6 gromacs transitioned to cmake build, so you'll need to adjust it.

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

hm... I come to realize that the above tunings are also relevant for the existing GROMACS/4.6.5-goolfc-2.6.10,
which has already been merged in; if you agree it is good idea to keep them in sync,
I'd suggest to bump the priority of this one and fix them in here...

…tely disable OpenMPI and MPI support, and -mt, -mpi and -hybrid variants (that work)
@boegel
Copy link
Copy Markdown
Member Author

boegel commented Dec 20, 2013

It turns out that simple enabling MPI support in GROMACS goolf easyconfigs is not the way to go: the regression test hangs with goolf or goolfc when MPI is enabled, in the first test run, i.e. regressiontests-4.6.1/simple/angles1. The cause is unclear.

I cleaned up the GROMACS easyconfigs by introducing a custom easyblock for GROMACS, see easybuilders/easybuild-easyblocks#335. The easyconfigs are now explicit one of the following options:

  • -seq: no OpenMP, no MPI
  • -mt: OpenMP, no MPI
  • -mpi: no OpenMPI, MPI
  • -hybrid: both OpenMP and MPI

For goolf and goolfc, the -mpi and -hybrid easyconfigs are left out, since the regression test seems to be hanging there (and eventually leads to a broken build when the test times out.

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Generic observation, no need for action yet:
the fact that this configuration is a heisenparameter is not a good sign
(why should the existence of an easyblock dictate if this should be here or not? something to improve, IMHO)

@boegel
Copy link
Copy Markdown
Member Author

boegel commented Dec 21, 2013

well-tested on top of easybuilders/easybuild-easyblocks#335, going in...

boegel added a commit that referenced this pull request Dec 21, 2013
enable MPI & external BLAS/LAPACK for GROMACS, add ictce/5.5.0 easyconfig for GROMACS 4.6.5
@boegel boegel merged commit 84b69b6 into easybuilders:develop Dec 21, 2013
@boegel boegel deleted the GROMACS_fixes_update branch December 21, 2013 14:45
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants