Re: [AMBER] bad atom type o

From: Jason Swails <>
Date: Wed, 20 Aug 2014 13:41:31 -0400

On Wed, Aug 20, 2014 at 1:37 PM, Hallel Freedman <>

> It doesn't seem to be getting that far - there is no file with that name.
> Maybe I should mention that I am getting a warning:
> An MPI process has executed an operation involving a call to the
> "fork()" system call to create a child process. Open MPI is currently
> operating in a condition that could result in memory corruption or
> other system errors; your MPI job may hang, crash, or produce silent
> data corruption. The use of fork() (or system() or other calls that
> create child processes) is strongly discouraged.
> The process that invoked fork was:
> Local host: (PID 19790)
> MPI_COMM_WORLD rank: 0
> Could this be related to the problem?

‚ÄčIf you're having trouble in parallel, the first thing to do (if possible)
is to run in serial. It's a very simple way to help reduce the number of
places one has to look for the source of the problem.

I can't recall the exact name of the output file off the top of my head,
but the name should indicate it is the mdout file of rank 0 (.mdout.0) for
the complex. The output files often hide the true error messages.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 20 2014 - 11:00:03 PDT
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