[gmx-users] FW: Gromacs version 3.3

Wong, RYM (Richard) R.Y.M.Wong at rl.ac.uk
Thu Dec 1 10:19:54 CET 2005

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org]On Behalf Of David van der Spoel
Sent: 30 November 2005 20:01
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] FW: Gromacs version 3.3

Wong, RYM (Richard) wrote:
>>I have installed Gromacs version 3.3 on a machine running Linux 2.4.21-37.ELsmp.
>The configuration command syntax I used to compile the MPI version of Gromacs-3.3:
What kind of machine?

The system contains 20 dual Intel Xeon processors.
The version of MPI is MPICH-1.2.5..10 associated with GNU (i.e. mpicc invokes gcc-3.2.3).
Multiprocessors are connected together via Myrinet GM version 2.0.8.
Do you need any other information?
>>  ./configure --prefix=/usr/local/applications/bioinformatics/gromacs-3.3 --exec-prefix=/usr/local/applications/bioinformatics/gromacs-3.3 --enable-mpi --enable-shared --with-fft=fftw2 --program-suffix="_mpi" 
>>CPPFLAGS=-I/usr/local/applications/libraries/numerical/fft/include LDFLAGS=-L/usr/local/applications/libraries/numerical/fft/lib CC=mpicc
>>Then executed "make"
>>Then executed "make install"
>>Then I used the command "grompp -np 2" to create the input data files in the sample "water" provided by the Gromacs development team.
>>When I run the command "mdrun_mpi" , I get 'segmentation fault' error.
>>  Warning: main: task 0 died with signal 11 (Segmentation fault)
>>  Warning: main: task 1 died with signal 11 (Segmentation fault)
Did you use mpirun?
Due to the security reason, we use mpiexec version 0.75 instead of using mpirun directly.
We are using MPICH-1.2.5..10 and Myrinet GM-2.0.8.
Do you need any other information?

Thank you

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