[gmx-users] problems to get gromacs running on cluster

[Florian Haberl]

Hi,

On Friday, 30. May 2008 09:17, Bernhard Knapp wrote:
> hi,
>
> i have some problems to get gromacs running on a cluster
>
>
> configured Gromacs with following command:
>    ./configure --enable-mpi --prefix /home/agp110105/local/gromacs
> CPPFLAGS="-I/home/agp110105/local/fftw/include
> -I/opt/mpich/intel/include" LDFLAGS="-L/home/agp110105/local/fftw/lib
> -L/opt/mpich/intel/lib" LIBS=-lmpich MPICC=/opt/mpich/intel/bin/mpicc
>
> grompp is executed using "-np 2"!
>
>
> starting mdrun in parallel:
> mdrun -np 2 -s NAc1-11_Y.em.tpr -o NAc1-11_Y.em.trr -c NAc1-11_Y.em.pdb
> -g NAc1-11_Y.em.log -e NAc1-11_Y.em.edr -v
you don`t start mdrun in parallel, you only start the executable in serial 
mode. You need something like mpirun or mpiexec (depends on your installed 
cluster  software) to start it in parallel.

mpirun -n[p] 2 mdrun ...


Sometimes you have to expand the path to mdrun completly.

>
> results in:
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.3
> Source code file: init.c, line: 69
>
> Fatal error:
> run input file NAc1-11_Y.em.tpr was made for 2 nodes,
>             while mdrun expected it to be for 1 nodes.
> -------------------------------------------------------
>
> "The Poodle Bites" (F. Zappa)
>
> Halting program mdrun
>
> gcq#175: "The Poodle Bites" (F. Zappa)
>
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
> p0_1606:  p4_error: : -1
>    p4_error: latest msg from perror: No such file or directory
>
>
try the same with grompp without '-np 2' than it should work

>
>
>
> starting mdrun with mpirun in parallel:
>    /opt/mpich/intel/bin/mpirun -np 2
> /home/agp110105/local/gromacs/bin/mdrun -np 2 -s NAc1-11_Y.em.tpr -o
> NAc1-11_Y.em.trr -c NAc1-11_Y.em.pdb -g NAc1-11_Y.em.log -e
> NAc1-11_Y.em.edr -v
>
> results in:
> p0_1729:  p4_error: Program is not an executable or is not accessible
> while starting /home/agp110105/local/gromacs/bin/mdrun with ssh on
> blade.labs.fhv.at: -1
>    p4_error: latest msg from perror: Permission denied
> p0_1729: (2.003906) net_send: could not write to fd=4, errno = 32
> p0_1729: (2.003906) net_send: could not write to fd=4, errno = 32
>
> any ideas what is going wrong?

is this directory mounted everywhere on the cluster?

in the path there `s something like 'local' , try to run an interactive job to 
see if it works.




>
> thx
> bernhard
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greetings,

Florian
-- 
-------------------------------------------------------------------------------
 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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