[AMBER] Compiling pmemd (Amber 10) with OpenMPI, pathscale, etc.

From: Paul S. Nerenberg <psn.berkeley.edu>
Date: Thu, 22 Apr 2010 15:58:07 -0700

Hello AMBER community,

Over the last couple of weeks, I've tried (very unsuccessfully!) to
get pmemd compiled on our group's Linux cluster, which consists of a
mixed set of Opteron- and Xeon-based nodes. Looking through the list
archive I've found numerous posts related to pmemd and OpenMPI, and
implementing the knowledge gained from these posts, I've managed to
get pmemd to compile without displaying any errors (see [1]). But
when I run test.pmemd -- or short jobs that I know run fine with
sander -- immediately get MPI errors (see [2]). (N.B. I have "make
install" generate a binary called pmemd-test and have updated the
Makefile in the /test directory to reflect that change...just in case
anyone thought that was the problem.)

I have successfully compiled, tested, and run an MPI version of sander
to my heart's content (see [3] for my config_amber.h), so I don't
think there are any problems with our pathscale or OpenMPI
installations. I've also tried using the pubfft option when compiling
pmemd (instead of fftw), but get the same MPI errors from the compiled
binary either way. I've posted my config.h file for pmemd (see [4])
so that folks can take a look at that and make suggestions. (I should
note that I've also tried leaving the MPI_LIBS field blank and that
did not remedy things.) Hopefully it's something obvious that I'm
just missing...

Many thanks in advance,


[1] http://www.ocf.berkeley.edu/~psn/make_results.txt
[2] http://www.ocf.berkeley.edu/~psn/test.pmemd.txt
[3] http://www.ocf.berkeley.edu/~psn/config_amber.openmpi
[4] http://www.ocf.berkeley.edu/~psn/config.h

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Received on Thu Apr 22 2010 - 16:00:13 PDT
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