With earlier versions of Amber 12 (14) we have experienced this type of
error when the memory of the node was not enough to accommodate all MPI
threads requested ... Usually, we solved by reserving the node memory
and asking for less MPI threads than the node can accommodate ...
But I am not sure if this is the same with the new MMPBSA in Amber 16.
To test, you could easily check the memory consumption for 1 frame (its
in MMPBSA output) and see how many such calculations your node memory
can accommodate simultaneously ... In this way, you will know if this
is likely to be your problem and how many threads you can accommodate.
Having said this, the error is pretty generic (like a seg fault) and
there are different reasons for it .....
Best
Vlad
On 01/31/2017 10:12 AM, Elvis Martis wrote:
> Try this command before running your mmpbsa.py
> Source $AMBERHOME/amber.sh
> or
> Source $AMBERHOME/amber.csh
>
> Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in
> Skype. adrian_elvis12
>
>
>
>
> -----Original Message-----
> From: Albert [mailto:mailmd2011.gmail.com]
> Sent: Tuesday, January 31, 2017 1:31 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] MMPBSA failed
>
> here is my settings:
>
> &general
> endframe=100, verbose=1,
> /
> &gb
> igb=2, saltcon=0.150
> /
> &pb
> istrng=0.150, fillratio=4.0
> /
>
>
>
>
> On 01/31/2017 08:28 AM, Albert wrote:
>> Hello, I am trying to perform MM/PBSA with following command:
>>
>>
>> mpirun -np 12 MMPBSA.py.MPI -O -i ../../infile/06-mmpbsa.in -o
>> FINAL_RESULTS_MMPBSA.dat -sp sol.prmtop -cp com.prmtop -rp rec.prmtop
>> -lp lig.prmtop -y prod*.mdcrd
>>
>>
>> But it constantly failed with the following messages:
>>
>>
>> Loading and checking parameter files for compatibility...
>> mmpbsa_py_energy found! Using /soft/amber/16/bin/mmpbsa_py_energy
>> cpptraj found! Using /soft/amber/16/bin/cpptraj Preparing trajectories
>> for simulation...
>> 100 frames were processed by cpptraj for use in calculation.
>>
>> Running calculations on normal system...
>>
>> Beginning GB calculations with /soft/amber/16/bin/mmpbsa_py_energy
>> calculating complex contribution...
>> File "/soft/amber/16/bin/MMPBSA.py.MPI", line 100, in <module>
>> app.run_mmpbsa()
>> File
>> "/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
>> 218, in run_mmpbsa
>> self.calc_list.run(rank, self.stdout)
>> File
>> "/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py
>> ",
>> line 82, in run
>> calc.run(rank, stdout=stdout, stderr=stderr)
>> File
>> "/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py
>> ",
>> line 476, in run
>> self.prmtop))
>> CalcError: /soft/amber/16/bin/cpptraj failed with prmtop com.prmtop!
>> Error occured on rank 8.
>> Exiting. All files have been retained.
>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 8
>> File "/soft/amber/16/bin/MMPBSA.py.MPI", line 100, in <module>
>> app.run_mmpbsa()
>> File
>> "/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
>> 218, in run_mmpbsa
>> self.calc_list.run(rank, self.stdout)
>> File
>> "/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py
>> ",
>> line 82, in run
>> calc.run(rank, stdout=stdout, stderr=stderr)
>> File
>> "/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py
>> ",
>> line 476, in run
>> self.prmtop))
>> CalcError: /soft/amber/16/bin/cpptraj failed with prmtop com.prmtop!
>> Error occured on rank 9.
>> Exiting. All files have been retained.
>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 9
>>
>>
>>
>> I am just wondering where is the problem?
>>
>> Thank you very much.
>>
>> Albert
>
>
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--
Vlad Cojocaru, Ph.D., Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Tue Jan 31 2017 - 01:30:04 PST
