[gmx-users] GROMACS with MPICH on Sun Cluster

[David van der Spoel]

Alok wrote:
> Hi,
> 
>  I am trying to run GROMACS in parallel on a SUN Cluster with MPICH. I 
> had installed FFTW 2.1.5 and Gromacs 3.2.1 without any error massage, 
> but when i tried to use mdrun_mpi (or even mdrun_mpi -h) I got the 
> following error message.
how about

mpirun mdrun -h

> 
> 
> ######################################################################################## 
> 
> 
> [0] MPI Abort by user Aborting program !
> 
> [0] Aborting program!
> 
> p0_1870:  p4_error: : 0
> 
> ######################################################################################## 
> 
> 
> I followed the follwing procedure for installing FFTW 2.1.5 and GROMACS 
> 3.2.1.
> 
> First of all I set the PATH for MPICH  files in my .profile file.
> PATH=/opt/mpichdefault-1.2.6/bin:$PATH
> PATH=/opt/mpichdefault-1.2.6/lib:$PATH
> PATH=/opt/mpichdefault-1.2.6/include:$PATH
> 
> ########################################### FFTW 2.1.5 
> #########################################
> export MPICC=mpicc
> 
> export LIBS="-lmpich -lfmpich -lpmpich"
> 
> export MPILIBS="-L/opt/mpichdefault-1.2.6/lib"
> 
> export CPPFLAGS="-I/opt/mpichdefault-1.2.6/include"
> 
> export LDFLAGS="-L/opt/mpichdefault-1.2.6/lib"
> 
> ./configure --enable-float 
> --prefix=/users/bsbe/phd/alokjain/install/fftw --enable-mpi
> make
> make install
> 
> ################################################################################################# 
> 
> 
> 
> 
> 
> ########################################## GROMACS 3.2.1 
> ########################################
> 
> export LDFLAGS="-L/opt/mpichdefault-1.2.6/lib 
> -L/users/bsbe/phd/alokjain/install/fftw/lib"
> 
> export CPPFLAGS="-I/opt/mpichdefault-1.2.6/include 
> -I/users/bsbe/phd/alokjain/install/fftw/include"
> 
> ./configure --enable-mpi 
> --prefix=/users/bsbe/phd/alokjain/install/gromacs --program-suffix=_mpi
> make
> 
> make install
> 
> ################################################################################################# 
> 
> 
> 
> 
> Any ideas regarding what is going wrong?
> 
> Please let me know if you need more information...
> 
> Thank you very much in advance,
> 
> regards,
> Alok jain
> 
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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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