Re: amber-developers: problems with parallel installation of Amber 9

From: Ruzhu Chen <ruzhuchen.us.ibm.com>
Date: Thu, 2 Mar 2006 11:18:43 -0700

Hi Lachele,

I think I can answer your question about the MPICH linking problem:
1) If your mpich-1.1.6 having libpmpich.a, you can add it
(-Lyour-path-to-mpich-lib -lmpich -lpmpich) to solve this linking problem.

2). Actually you can use mpif90 or mpif77 to link, then you don't need to
specify any mpich libs in your config.h.
3). If you can't find libpmpich.a in your mpich lib path, there is likely
something wrong when you built your MPICH. You may need to rebuild it.

Hope it help!

Ruzhu Chen, PhD
IBM Life Sciences Solutions Enablement
KQ8S/P925, 2455 South Road, Poughkeepsie, NY 12601
Phone:845-433-8426 T/L:293-8426
Email: ruzhuchen.us.ibm.com



"David A. Case" <case.scripps.edu>
Sent by: owner-amber-developers.scripps.edu


2006-03-02 12:51


Please respond to
amber-developers.scripps.edu


To
"B. Lachele Foley" <lfoley.uga.edu>

cc
amber-developers.scripps.edu

Subject
amber-developers: problems with parallel installation of Amber 9







On Thu, Mar 02, 2006, B. Lachele Foley wrote:

> Someone asked me to compile sander for parallel on another
> machine. It got through a lot of the compile, but finally
> didn't work.

Please send these messages to amber-developers.scripps.edu (first
subscribe
by sending email to majordomo.scripps.edu with "subscribe
amber-developers"
in the body of the message). And/or post to the wiki:

   http://amber.scripps.edu/pmwiki/pmwiki.php/Main/Amber9pf

I'll cc this to the developers list in case someone can help.

>
> The main complaint seems to be that certain variables are not
> defined in the parallel libraries.
>
> I set MPICH_HOME to /usr/local/programs/mpich-1.2.6.

(Just a note, to everyone: the latest configure scripts follow the pmemd
model, and just use a single environment variable (MPI_HOME) for all forms
of MPI.)

>
> For example, here is a complaint:
>
>
/usr/local/programs/mpich-1.2.6/lib/libmpich.a(comm_split.o)(.text+0xf7):
> In function `MPI_Comm_split':
> : undefined reference to `PMPI_Allreduce'

It looks like you need to add -lpmpich to the LOADLIB string in config.h.
I'm guessing that some versions of mpich need this (earlier ones?
different
architectures?, different communicators?) and others don't.

I see that Bob Duke just includes "-lmpich -lpmpich" for mpich, whereas
sander is asking for "-lfmpich -lmpich". Does anyone know if there is a
universal correct answer to this, or a way (as with lam and openmpi) to
tell from the installation itself what is required?

[Aside: Bob's libraries for MPICH2 are also different than sander's. Yet
both seem to work for me on the same machine.... A significant number of
posts on the reflector have to do with parallel installation, so it would
be great to see if we can clean this up somehow.]

...thx...dac
Received on Wed Apr 05 2006 - 23:49:42 PDT
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