[gmx-users] XT3 porting

[David van der Spoel]

Tom Joseph wrote:
> Providing a backtrace or two would really help.  Given the exact same 
> input files and run conditions, does it sometimes segfault and sometimes 
> not? Does this happen on a login node (full glibc and such) or just the 
> compute nodes (POSIX subset)?
> 
> Separately, is it a better idea to use fftw2 since it supports MPI?
No, gromacs now does the parallel FFT itself, and fftw3 is slightly faster.
> 
> (Hopefully soon my Teragrid access will extend to bigben, so I'm 
> especially interested in this...)
> 
> --Tom
> 
> On Apr 17, 2006, at 10:06 PM, Shawn T. Brown wrote:
> 
>> Hello, I am trying to port GROMACS 3.3.1 to the CRAY XT3, which is 
>> essentially an Opteron machine with the PGI compilers.  I can get 
>> everything to compile, but when I run mdrun, I am “randomly” getting 
>> segmentation faults.  This seems to happen no matter what input file I 
>> use.  It happens in init_forcerec (line 1001), in add_gbond, and in 
>> solvent_check.  Some times it runs fine.  I am configuring with the 
>> following command:
>>
>>  
>>
>> ./configure --with-fft=fftw3 --disable-nice --enable-mpi 
>> --program-suffix="_xt3" --enable-float --with-external-blas 
>> --with-external-lapack --disable-threads 
>> --prefix=/usr/local/packages/gromacs-3.3.1
>>
>>  
>>
>> I am wondering if anyone else has seen these types of problems and 
>> knows how to fix them.  I have tried compiling the code without 
>> optimization, to no avail.
>>
>>  
>>
>> Thanks in advance,
>>
>> Shawn
>>
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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