File input/output error: > remd.log

User discussions
1

i’m using gromaces 2020.4 and trying to get replica-exchange using this code for 36 temepratures

for i in 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

do

gmx grompp -f nvt_$i.mdp -c em.gro -p topol.top -o remd_$i.tpr

done

mpirun -np 37 gmx_mpi mdrun -v -deffnm remd -multidir sim1 sim2 … sim36 -replex 500 >> replex.log

but got

Program: gmx mdrun, version 2021.3
Source file: src/gromacs/utility/futil.cpp (line 431)
MPI rank: 3 (out of 37)

File input/output error:
remd.log

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

i got in replex.log

MPI_ABORT was invoked on rank 5 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

MPI_ABORT was invoked on rank 4 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

2

can someone help please ?

3

is there any help, please ? i’m stuck in this problem and couldn’t find a solution

4

i am also having this problem

5

Are you doing exactly as in the original post? In that case try:

for i in {0..35}
do
    mkdir sim_$i
    gmx grompp -f nvt_$i.mdp -c em.gro -p topol.top -o sim_$i/topol.tpr
done
mpirun -np 36 gmx_mpi mdrun -v -multidir sim_{0..35} -replex 500 >> replex.log

Otherwise, my example might give you a clue how to make it work in your case.