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

[Bernhard Knapp]

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

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





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?

thx
bernhard