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Joined: Nov 2017
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Allen Offline OP
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Joined: Nov 2017
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Hi,
I just install charmm37b1 on my Linux system via "./install.com 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).
--------------------------------------------------------------------------
1
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
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This is a very old version. Upgrade! You can download the most recent version for free:
http://charmm.chemistry.harvard.edu/charmm_lite.php
(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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