[gmx-users] question about mpi run

孔韧 kongren at emails.bjut.edu.cn
Fri Jan 14 02:45:08 CET 2005

Hello everyone, I have got some problems when I try to run a job on a mechine with
two cpus.

This is my mdp file:
 cpp                      = /lib/cpp
constraints            =none
define                  = -DFLEXIBLE
integrator             = cg
dt                        = 0.002
nsteps                  = 100000
nslist                    = 10
ns_type               = grid
rlist                      = 1.0
coulombtype        = PME
rcoulomb              = 1.0
rvdw                     = 1.0

nstcgsteep            = 100
emtol                    = 1000.0
emstep                  = 0.001

These are the comand I used :
gromppmpi -v -f cg.mdp -c confout.gro -o topol_cg.tpr -p ../topol.top -shuffle
-sort -np 2
nohup mpirun -c 2 -c2c mdrunmpi -v -s topol_cg.tpr -o traj.trr -e ener.edr -c
confout.gro -g pr.log -nice 0 -np 2&

This is the output error information:
One of the processes started by mpirun has exited with a nonzero exit
code.  This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.

PID 5368 failed on node n0 with exit status 1.

However, I have run a job with a system of one protein in water successfully.
When I try this job with a system of two proteins in water, it stopped.

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