The current truth is that the software was installed by ITS staff. When I load half of a GPU node (has 14 cores) and use the following command to run it,
mpirun -n 14 charm -I step.inp > step.out;
I found duplications in the output file for 14 times such as:
1
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 41b2 February 15, 2017
Copyright(c) 1984-2014 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-3.10.0-693.11.6.el7.x86_64(x86_64)@nod
Created on 8/24/18 at 22:33:26 by user: lzhang
Maximum number of ATOMS: 360720, and RESidues: 120240
1
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 41b2 February 15, 2017
Copyright(c) 1984-2014 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-3.10.0-693.11.6.el7.x86_64(x86_64)@nod
Created on 8/24/18 at 22:33:26 by user: lzhang
1
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 41b2 February 15, 2017
Copyright(c) 1984-2014 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-3.10.0-693.11.6.el7.x86_64(x86_64)@nod
Created on 8/24/18 at 22:33:26 by user: lzhang
Maximum number of ATOMS: 360720, and RESidues: 120240
Maximum number of ATOMS: 360720, and RESidues: 120240
1
Chemistry at HARvard Macromolecular Mechanics
1
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 41b2 February 15, 2017
Copyright(c) 1984-2014 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-3.10.0-693.11.6.el7.x86_64(x86_64)@nod
1
....
On the other hand, if I loaded it without using mpirun command, it is not fast at all. I am wondering where is wrong and what I should do. Thank you.