Re: [AMBER] sander QM/MM with terachem using MPI

From: Andreas Goetz <agoetz.sdsc.edu>
Date: Thu, 18 Sep 2014 23:52:20 -0600

Hi Dan,

I am sorry I had missed this message. Did you get the MPI interface between sander and terachem to work? OpenMPI can cause problems but I have tested this with MPICH which never made problems. Which version of terachem are you using?

All the best,
Andy

--
Dr. Andreas W. Goetz
Assistant Project Scientist
San Diego Supercomputer Center
Tel  : +1-858-822-4771
Email: agoetz.sdsc.edu
Web  : www.awgoetz.de
On May 31, 2014, at 9:21 AM, Daniel Hollas wrote:
> Dear amber users,
> 
> I am trying to run QM/MM simulations an Amber14 (sander module) using Terachem.
> Specifically, I want to use the MPI version as it is supposed to be
> faster and also I want to use it later for adaptive solvent QM/MM.
> 
> However, I am unable to make it work (I also tested in Amber12).
> First, I launch terachem as "terachem -UseMPI >out &
> 
> The output says, that it is waiting for Amber..
> 
> However, when I launch amber, it crashes with message:
> 
> [a30:11472] *** An error occurred in MPI_Lookup_name
> [a30:11472] *** on communicator MPI_COMM_WORLD
> [a30:11472] *** MPI_ERR_NAME: invalid name argument
> [a30:11472] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 0 with PID 11472 on
> node a30 exiting improperly. There are two reasons this could occur:
> 
> 1. this process did not call "init" before exiting, but others in
> the job did. This can cause a job to hang indefinitely while it waits
> for all processes to call "init". By rule, if one process calls "init",
> then ALL processes must call "init" prior to termination.
> 
> 2. this process called "init", but exited without calling "finalize".
> By rule, all processes that call "init" MUST call "finalize" prior to
> exiting or it will be considered an "abnormal termination"
> 
> This may have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> 
> The output fropm Amber seems fine.
> What am I doing wrong? By the way, I tested both OpenMPI and MPICH versions.
> 
> Thanks for help.
> 
> Dan Hollas
> 
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Received on Thu Sep 18 2014 - 23:00:02 PDT