Hi dear gmx-usersI want to simulate gold surface - proteininteraction by
GOLP-CHARMM forcefield. In md step, after 7 ps , without anyreason mdrun
failed. md.mdp contains:
title = gold
cpp = cpp
include =
; RUN CONTROL PARAMETERS
Hello:
I try to submit Gromacs job with command:
mpirun -np 2 mdrun_mpi -s md.tpr -g -v
but it failed with messages:
--
It looks like opal_init failed for some reason; your parallel process is
likely to abort. There are
First, check your install of MPI works on a simple test program. Then,
check that GROMACS cmake picked up the MPI you expected, and that that's
really the one you're using at run time.
Mark
On Thu, May 15, 2014 at 3:28 PM, Albert mailmd2...@gmail.com wrote:
Hello:
I try to submit Gromacs
Hello Mark:
thanks a lot for reply.
The MPI works fine in my machine when I run another problem.
How can I check whether gromacs cmake picked up the MPI that I expected?
I've already specified with options:
CMAKE_PREFIX_PATH=/soft/intel/mkl/include/fftw:/soft/openmpi-1.7.5
thx a lot
Try mdrun -version and have a look at the flags and stuff. Do a make
VERBOSE=1 and check the compile line doesn't refer to some other MPI.
Inspect the CMakeCache.txt in the cmake build directory.
Mark
On Thu, May 15, 2014 at 5:39 PM, Albert mailmd2...@gmail.com wrote:
Hello Mark:
thanks a
