Re: [AMBER] mmpbsa amber error while running decomp

From: Sucharita Dey <>
Date: Tue, 2 Sep 2014 07:31:55 +0000

Thanks Jason. I am not running in parallel. It ran OK when I reduced the endframe to 200, but when I invoked the command:
/app1/common/Apps/gnu/amber12/AmberTools/bin/ -O -i -cp -rp -lp -y -eo energies -deo dec_energies

It started with the following:

WARNING: It appears that your OpenFabrics subsystem is configured to only
allow registering part of your physical memory. This can cause MPI jobs to
run with erratic performance, hang, and/or crash.

This may be caused by your OpenFabrics vendor limiting the amount of
physical memory that can be registered. You should investigate the
relevant Linux kernel module parameters that control how much physical
memory can be registered, and increase them to allow registering all
physical memory on your machine.

See this Open MPI FAQ item for more information on these Linux kernel module

  Local host: atlas7-c01
  Registerable memory: 65536 MiB
  Total memory: 258528 MiB

Your MPI job will continue, but may be behave poorly and/or hang.
Loading and checking parameter files for compatibility...
sander found! Using /app1/common/Apps/gnu/amber12/bin/sander
cpptraj found! Using /app1/common/Apps/gnu/amber12/bin/cpptraj
Preparing trajectories for simulation...
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: atlas7-c01 (PID 17146)
  MPI_COMM_WORLD rank: 0

If you are *absolutely sure* that your application will successfully
and correctly survive a call to fork(), you may disable this warning
by setting the mpi_warn_on_fork MCA parameter to 0.
4 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /app1/common/Apps/gnu/amber12/bin/sander
  calculating complex contribution...
  calculating receptor contribution...
  calculating ligand contribution...

Total setup time: 0.108 min.
Creating trajectories with cpptraj: 0.209 min.
Total calculation time: 5.476 min.

Total GB calculation time: 5.476 min.

Statistics calculation & output writing: 0.005 min.
Total time taken: 5.799 min.


Then where is the problem when I need to process the entire trajectory.
Please note all the above I did in cluster where Amber12 and AmberTools 12 are installed.

Of second mention, I was initially trying in my personal Desktop where I only have Ambertools12 (not Amber), it gave error as was asking for Sander. Then I upgraded my AmberTools12 to 14 and surprisingly I could successfully run for the entire traj. So, the problem I am facing in our cluster, is it because of the Ambertools version or something else?

Thanks again,

From: Jason Swails []
Sent: Monday, September 1, 2014 10:51 PM
Subject: Re: [AMBER] mmpbsa amber error while running decomp

On Mon, 2014-09-01 at 05:52 +0000, Sucharita Dey wrote:
> Hello All,
> I am getting this error while running gb and decomp using Amber12 SANDER.
> gb ran successfully in separate. But when try to run decomp with the same
> set of top files it is giving this error :
> mmpbsa amber error failed with prmtop!
> But I checked it prepared some files like _MMPBSA_gb_decomp_com.mdin,
> _MMPBSA_dummycomplex.inpcrd, _MMPBSA_complex.mdcrd.0, (the same for ligand
> and receptor)_MMPBSA_normal_traj_cpptraj.out, _MMPBSA_restrt.0,
> _MMPBSA_complex_gb.mdout.0
> I checked the file _MMPBSA_complex_gb.mdout.0 ,it started writing and
> stopped abruptly after "minimizing coord set # 60"
> Here is my
> input file for running GB in serial
> &general
> startframe=1, endframe=12500, interval=50,

Are you running this in parallel? If so, make sure you look at all of
the output files (i.e., not just the mdout files that end with .0).
Also, try a small number of frames. Does it work if you change endframe
to 200, for instance?

What you have reported contains no error message, so it's impossible to
say what happened. Given the information you provided, it's just as
likely to be a problem outside Amber that killed your calculation as it
is to be a problem inside Amber itself...


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 02 2014 - 01:00:02 PDT
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