Re: [AMBER-Developers] MPICH Failures for REMD - PMEMD

From: Charles Lin <clin92.ucsd.edu>
Date: Mon, 21 Mar 2016 22:02:13 +0000

gcc version 4.8.5 20150623 (Red Hat 4.8.5-4) (GCC)

Yea mpich is the only one I'm having errors with. I might have to recompile it later and test it again. If I'm the only one seeing these errors (which only occur for the REMD tests).
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Monday, March 21, 2016 2:47 PM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] MPICH Failures for REMD - PMEMD

Hi,

pmemd.MPI passes all REMD tests for me with the following config:

Fedora 22 (4.4.4-200.fc22.x86_64)
Compilers: Intel v 14.0
MPI: mpich 3.0.3
./configure -nomtkpp -norism -nofftw3 -noemil --no-updates -mpi intel

In $AMBERHOME/test
make clean && DO_PARALLEL="mpiexec -n 8" make test.pmemd.REM

Only 1 diff in the constant pH explicit REMD test:

possible FAILURE: check 1AKI.solv10.md1.mdout.0.dif
109,110c109,110
< NSTEP = 30 TIME(PS) = 4400.060 TEMP(K) = 271.67 PRESS = 0.
< Etot = -52395.6420 EKtot = 11051.9552 EPtot =
-63447.5972 
---
>  NSTEP =       30   TIME(PS) =    4400.060  TEMP(K) =   298.07  PRESS =     0.
>  Etot   =    -51321.7523  EKtot   =     12125.8449  EPtot      =    -63447.5972
Are you using gnu compilers? What version?
-Dan
On Sat, Mar 19, 2016 at 3:57 PM, Charles Lin <clin92.ucsd.edu> wrote:
> Hi all,
>
> I was wondering if anyone was seeing any REMD test case failures on master (segfaults) for PMEMD when using an older version of mpich such as v2.1.4 and v3.0.4.  It has also failed for the yum install version of mpich.  However these test cases pass with openmpi and mpich 3.2.  I am currently using CentOS 7.
>
> -Charlie
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> AMBER-Developers.ambermd.org
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Mar 21 2016 - 15:30:03 PDT
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