Re: [AMBER] MPI install with openmpi

From: Makoto Chikira <chikira.kc.chuo-u.ac.jp>
Date: Sun, 6 Oct 2013 22:36:27 +0900

Dear dac,

After installation of AmberTools13MPI, I implemented export
DO_PARALLEL="mpirun -np 4" and make test.
I got lots of error message as in the attached log file. A part of the
messages are in Japanese, which you may not read, but I hope you can guess
the meaning, comparing with other English log files.

Anyway, my amber12 looks still not properly installed. I would appreciate if
I could get another advice again.

Sincerely,

Makoto

****************************************
I did as you suggested below and could succeed in the installation of
AmberTools13MPI.
Thank you again for your nice advice.

Best regards,

Makoto

-----Original Message-----
From: case [mailto:case.biomaps.rutgers.edu]
Sent: Sunday, October 06, 2013 1:50 AM
To: AMBER Mailing List
Subject: Re: [AMBER] MPI install with openmpi

On Sun, Oct 06, 2013, Makoto Chikira wrote:
>
> Attached is the config.h file and (2) worked nice to get a message
> "Installation of amber12 (parallel) is complete at 2013.10.6 Sunday
> 00:04:32 JST". I will check next how the compiled amber12 and AmberTools13
work.

Thanks for the update. What you are missing now are the parallel versions
for AmberTools. I will explore what might be happening there. If you want
to try another thing, do this:

edit $AMBERHOME/AmberTools/src/Makefile to comment out the line (in the
"parallel" section) that says

    (cd mdgx && $(MAKE) $(MDGX) )

I think this is about line 135. Then cd to $AMBERHOME/AmberTools/src and
type "make install". If the problem is only with mdgx, then you will have
parallel versions of everything else.

Of course, if the only parallel programs you need (as for most people) are
sander.MPI and pmemd.MPI, you are fine.

...regards...dac


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Received on Sun Oct 06 2013 - 07:00:03 PDT
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