Re: [AMBER] Fwd: MPI Runtime Error

From: David A Case <>
Date: Sat, 30 May 2015 12:18:40 -0400

On Sat, May 30, 2015, Kusum Mehla wrote:

> I have been facing problems with MPI parallel run. It shows error
> student.student-ThinkCentre-M81:~/Desktop/CJE/M2-Cje$ ./

I don't think people on the list have any idea what "" is doing.

> Starting Heating
> Starting Density
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> Starting Equilibration
> Unit 30 Error on OPEN:
> density.rst

As a wild guess, this looks like you have a (parallel?) script that is
trying to do several jobs in succession. It looks like the "Heating" part
failed, and then all the subsequent parts also failed.

Please look at the mdout file for the first part, as it is likely have the
relevant error messages. (If you are new to Amber, run things in serial
first, and don't try complex scripts that have multiple parts to them: try
each step on its own, and examine the outputs.)

> For your reference, I am attaching complex PDB file. Please help

None of the Amber parallel programs take PDB files as input. You need to use
LEaP to process staring PDB files to create files for Amber minimizations or
dynamics. If you haven't done so, please work through the tutorials
(especially the first one).

...good luck....dac

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Received on Sat May 30 2015 - 09:30:02 PDT
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