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Joined: Nov 2017
Posts: 4
Allen Offline OP
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Joined: Nov 2017
Posts: 4
I just install charmm37b1 on my Linux system via "./ gnu large M keepf keepo"
It looked like it compiled fine. So I sourced the environment variables and try to run md via
"mpirun -np 20 charmm < md.inp > &md.out&"
but it doesn't work. The outputfile md.out shows there:
[node9:63457] *** An error occurred in MPI_Irecv
[node9:63457] *** on communicator MPI_COMM_WORLD
[node9:63457] *** MPI_ERR_RANK: invalid rank
[node9:63457] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
mpirun has exited due to process rank 8 with PID 63457 on
node node9 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 37b1 September 30, 2012
Copyright(c) 1984-2001 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-2.6.32-431.el6.x86_64(x86_64)@node9[+ 9]
Created on 11/2/17 at 9:52:14 by user: wzlai

Maximum number of ATOMS: 60120, and RESidues: 20040

ps:I have tried run it via
"mpirun -np 20 charmm -input md.inp > md.out"
but I got the output file similar to output file I showed.

Joined: Sep 2003
Posts: 4,883
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This is a very old version. Upgrade! You can download the most recent version for free:
(this version does not support high-end parallelization using domain decomposition, but everything else, including GPU support, is identical to the full version)

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  lennart, rmv 

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