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

From: Paul S. Nerenberg <>
Date: Thu, 22 Apr 2010 16:50:57 -0700

Hi Ross,

That patch did the trick! pmemd seems to work perfectly now -- it
passed all of test.pmemd and ran my short test jobs fine. Thanks so
much! (In the very near future I'll see how many of the old flags I
can toss out and post updated config files to my website for those who
are interested.)



On Apr 22, 2010, at 4:23 PM, Ross Walker wrote:

> Hi Paul,
> A fix is coming for this in a few minutes. It is related to issues
> with
> bugfix.31. Try the attached patch file and let me know if it works.
> cd $AMBERHOME/src/pmemd/src/
> cp /path_to_patch/patch ./
> patch -p0 < patch
> cd ../
> make
> With regards to building for openMPI etc. The problem is the PMEMD
> 10 build
> scripts all try to guess at the MPI libraries rather than using
> mpif90 and
> mpicc which can leave one in a world of trouble. This has been
> addressed in
> AMBER 11 and it should be much simpler to build things.
> For the time being what you did in the config.h file is correct.
> Basically
> empty the MPI_LIBS line and replace all occurrences of the C or
> Fortran
> compilers with mpicc and mpif90 respectively. Note the optimization
> flags
> are hopelessly out of date for PGF90 since I don't think any of the
> developers have access to newer versions of the Portland group
> compilers,
> preferring to stick with Intel and/or Gnu. What you have though
> looks good
> to me.
> I wouldn't bother too much with FFTW. It makes a marginal difference
> at best
> and tends to just complicate the build process.
> All the best
> Ross
>> -----Original Message-----
>> From: [] On
>> Behalf Of Paul S. Nerenberg
>> Sent: Thursday, April 22, 2010 3:58 PM
>> To:
>> Subject: [AMBER] Compiling pmemd (Amber 10) with OpenMPI, pathscale,
>> etc.
>> 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,
>> Paul
>> [1]
>> [2]
>> [3]
>> [4]
>> _______________________________________________
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Received on Thu Apr 22 2010 - 17:00:03 PDT
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