GROMACS version:2021.1
GROMACS modification: No
Dear collegues,
I want to run one protein in water simulation in cluster. I have generated the tpr files also. but when i am keeping it for md run the job is being aborted. my tpr file name is fine and it is also present is the directory. one more thing when the same file i am running in workstation its running without any error. i am not getting what is the problem behind that. i want to run in cluster because it will save my time. please help me with this.
for the reference i am attaching the error:
/var/spool/pbs/mom_priv/jobs/167170.master1.cmsd.uohyd.SC: line 7: cd: /home/nppsls/subhasree_2022/1yamb_in: No such file or directory
Number of nodes is 1
Number of processors is 20
Node list is node05.cmsd.uohyd
/var/spool/pbs/mom_priv/jobs/167170.master1.cmsd.uohyd.SC: line 16: cd: /home/nppsls/subhasree_2022/1yamb_in: No such file or directory
:-) GROMACS - gmx mdrun, 2021.1 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx mdrun, version 2021.1
Executable: /home/hpc/apps/gromacs-2021-openmpi-312-gcc820/bin/gmx_mpi
Data prefix: /home/hpc/apps/gromacs-2021-openmpi-312-gcc820
Working dir: /home/nppsls
Command line:
gmx_mpi mdrun -v -s npt.tpr -deffnm npt
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Program: gmx mdrun, version 2021.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 1 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 3 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 5 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 7 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 8 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 9 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 6 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 11 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 13 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 15 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 16 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 17 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 12 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 0 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 18 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 2 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 4 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 19 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 10 (out of 20)
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 14 (out of 20)
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
Error in user input:
Invalid command-line options
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In command-line option -s
File ‘npt.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
MPI_ABORT was invoked on rank 18 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 6 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.
MPI_ABORT was invoked on rank 14 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 16 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 13 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 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 19 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 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.
MPI_ABORT was invoked on rank 3 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 15 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 7 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 12 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 17 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 0 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 10 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 8 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 11 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 9 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 2 in communicator MPI_COMM_WORLD
with errorcode 1.