I recompiled with mpich 3.0.4 and GNU 4.4.7; all REMD tests pass (with
the exception of the test diff I previously mentioned).
On Mon, Mar 21, 2016 at 5:16 PM, Charles Lin <clin92.ucsd.edu> wrote:
> $ which mpirun
> ~/mpich-3.0.4/bin/mpifun
This seems weird ("mpirun" vs "mpifun"; I'm assuming you typed and
didn't paste the above?
Is is possible that your mpich 3.0.4 was compiled with an older
version of GCC? Maybe try recompiling a fresh copy of mpich 3.0.4?
-Dan
> $ mpif90 -show
> gfortran -I/server-home1/charlie/mpich-3.0.4/include -I/server-home1/charlie/mpich-3.0.4/include -L/server-home1/charlie/mpich-3.0.4/lib -lmpichf90 -lmpich -lopa -lmpl -lrt -lpthread
> $ which mpiexec
> ~/mpich-3.0.4/bin/mpiexec
> $ mpiexec --version
> Version: 3.0.4
> $ gcc -v
> gcc version 4.8.5 20150623 (Red Hat 4.8.5-4) (GCC)
> ________________________________________
> From: Ross Walker [ross.rosswalker.co.uk]
> Sent: Monday, March 21, 2016 3:05 PM
> To: AMBER Developers Mailing List
> Subject: Re: [AMBER-Developers] MPICH Failures for REMD - PMEMD
>
> Be sure the mpirun / mpiexec you use is the same one as the mpi environment you used to build AMBER with and that the compiler you used for AMBER is the same one (version etc) used to compile the MPI library. Such mismatches is a classic for causing weird segfaults in my experience.
>
>> On Mar 21, 2016, at 15:02, Charles Lin <clin92.ucsd.edu> wrote:
>>
>> 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
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>>
>>
>> --
>> -------------------------
>> 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)
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
--
-------------------------
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)
_______________________________________________
AMBER-Developers mailing list
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Received on Tue Mar 22 2016 - 09:00:03 PDT
