AMBER Archive (2008)

Subject: Re: AMBER: AMBER-8 parallel installation - test run failure

From: Ming Lei (leiming72_at_gmail.com)
Date: Thu Jan 03 2008 - 08:08:46 CST

Are you sure if your mpich works well? I guess something was wrong with your
MPICH.

Best,
Jack

On Jan 3, 2008 6:10 PM, <brmeher_at_iitg.ernet.in> wrote:

> Dear AMBER Masterminds,
> I am installing the parallel version of AMBER-8 on Dual-Core AMD
> Opteron(tm) Processor 8218 with RHEL 4 as the OS with PGI Compilers.
>
> While installing for parallel run the compilations are successful ,but for
> testing of sander,it is giving segmentation fault and/or program error.
>
> These are the commands I gave and the outputs are given below.
> -----------------------------------------------------------
> $./configure -mpich -opteron pgf90
> $make parallel (no error)
> $cd $AMBERHOME/test
> $ make test.sander
>
> cd dmp; ./Run.dmp
> This test not set up for parallel
> cannot run in parallel with #residues < #pes
> cd adenine; ./Run.adenine
> This test not set up for parallel
> cannot run in parallel with #residues < #pes
> ==============================================================
> cd cytosine; ./Run.cytosine
> /usr/bin/mpich-1.2.7/bin/mpirun.ch_shmem: line 91: 27950 Segmentation
> fault /home/tools/amber8/test/cytosine/../../exe/sander "-O" "-i" "
> in.md" "-c" "crd.md.23" "-o" "cytosine.out"
> ./Run.cytosine: Program error
> make: *** [test.sander.no_lmod] Error 1
> -------------------------------------------
>
> Can anyone please suggest the possible solutions for the error I am
> facing.
>
> regards
> B R Meher
>
>
> ------------------------------
> This email was sent from IIT Guwahati Webmail.If you are not .
> "the intended recipient, please contact the sender by email and delete all
> copies; your cooperation in this regard is appreciated. "
> http://www.iitg.ernet.in/
> -----------------------------------------------------------------------
> The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To
> unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu