[gmx-users] FW: Gromacs version 3.3

David van der Spoel spoel at xray.bmc.uu.se
Wed Nov 30 21:00:30 CET 2005

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?

>>  ./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?

>>Is there any way to run mdrun_mpi to produce further information about the problem?
>>Richard Wong
>>Atlas Centre
>>Rutherford Appleton Laboratory
>>United Kingdom
>>OX11 0QX
>>Telephone: 01235-446075
>>Email:  r.y.m.wong at rl.ac.uk
>>The contents of this email are sent in confidence for the use of the intended recipient only. If you are not one of the intended recipients do not take action on it or show it to anyone else, but return this email to the sender and delete your copy of it.
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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://xray.bmc.uu.se/~spoel

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