Mpirun gmx_mpi command not working

User discussions
1

GROMACS version: 2021.4-plumed-2.7.3
GROMACS modification: Yes(plumed patch)

I am following the tutorial above and having problems at 2.6.2.

mpirun -np 5 gmx_mpi mdrun -v -deffnm rest2_ -plumed plumed.dat -multi 5 -replex 100 -hrex

The result first said that there is no “-multi” option, so I executed the command again without it.

mpirun -np 5 gmx_mpi mdrun -v -deffnm rest2_ -plumed plumed.dat -replex 100 -hrex

The result:

             :-) GROMACS - gmx mdrun, 2021.4-plumed-2.7.3 (-:

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GROMACS: gmx mdrun, version 2021.4-plumed-2.7.3
Executable: /opt/gromacs/2021.4/bin/gmx_mpi
Data prefix: /opt/gromacs/2021.4
Working dir: /home/users/eyg/gmx/REST2
Command line:
gmx_mpi mdrun -v -deffnm topol_ -plumed plumed.dat -replex 100 -hrex

Program: gmx mdrun, version 2021.4-plumed-2.7.3
Source file: src/gromacs/options/options.cpp (line 179)
Function: void gmx::internal::OptionSectionImpl::finish()
MPI rank: 4 (out of 5)

Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file ‘topol’ does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr

For more information and tips for troubleshooting, please check the GROMACS
website at

Program: gmx mdrun, version 2021.4-plumed-2.7.3
Source file: src/gromacs/options/options.cpp (line 179)
Function: void gmx::internal::OptionSectionImpl::finish()
MPI rank: 1 (out of 5)

Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file ‘topol’ does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr

For more information and tips for troubleshooting, please check the GROMACS
website at

Program: gmx mdrun, version 2021.4-plumed-2.7.3
Source file: src/gromacs/options/options.cpp (line 179)
Function: void gmx::internal::OptionSectionImpl::finish()
MPI rank: 2 (out of 5)

Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file ‘topol’ does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr

For more information and tips for troubleshooting, please check the GROMACS

Program: gmx mdrun, version 2021.4-plumed-2.7.3
Source file: src/gromacs/options/options.cpp (line 179)
Function: void gmx::internal::OptionSectionImpl::finish()
MPI rank: 3 (out of 5)

Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file ‘topol’ does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr

For more information and tips for troubleshooting, please check the GROMACS
website at

Program: gmx mdrun, version 2021.4-plumed-2.7.3
Source file: src/gromacs/options/options.cpp (line 179)
Function: void gmx::internal::OptionSectionImpl::finish()
MPI rank: 0 (out of 5)

Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file ‘topol’ does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr

For more information and tips for troubleshooting, please check the GROMACS
website at

MPI_ABORT was invoked on rank 1 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.

[bnode1:1696133] 4 more processes have sent help message help-mpi-api.txt / mpi-abort
[bnode1:1696133] Set MCA parameter “orte_base_help_aggregate” to 0 to see all help / error messages

This is my working directory below.

image
image622×685 12 KB

As the result said that it needs “.tpr” files, I have rest2_0.tpr ~ rest2_4.tpr, but it doesn’t seem gromacs reconizes them. I wonder if there’s any other option I have to add.

Any help would be appreciated.

2

Hi,
I guess the problem is that mdrun does not know tha your tpr file is called rest2_0.tpr. You have used the option -deffnm (Set the default filename for all file options ) thus mdrun is looking for a tpr file called rest2_ -plumed.tpr. If you want a different name for tpr file (the one defined in -deffnm), you can try to use the option -s file_name.tpr
\Alessandra

3

Hii alevilla,
Could you please help me to solve this problem/error.

error
error988×736 146 KB