Dear Elvis,
There is specific error message, every time it is giving
different error.
This is one of the error, I see everytime:
warnings.warn('ligand_mask overwritten with default\n')
> File "/home/deva/softwares/test/amber20_src/bin/MMPBSA.py.MPI", line
> 100, in <module>
> app.run_mmpbsa()
> File
> "/home/deva/softwares/test/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/home/deva/softwares/test/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/home/deva/softwares/test/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
> line 428, in run
> error_list = [s.strip() for s in out.split('\n')
> TypeError: a bytes-like object is required, not 'str'
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
> :
> system msg for write_line failure : Bad file descriptor
>
most of the times it is not creating mdout files for receptor,
ligand and complex thus job is getting terminated.
Thanks,
Divya.
On Thu, 17 Dec 2020, 07:02 Elvis Martis, <elvis_bcp.elvismartis.in> wrote:
> Could you post the error message here?
>
> On Wednesday, December 16, 2020, divyabharathi korlepara <
> divyabharathik938.gmail.com> wrote:
>
> > Dear Amber Experts,
> > I installed the Ambertools20 using openmpi-4.0.1 version using
> > the following steps.
> > cd amber_20src
> > module load openmpi/4.0.1
> > serial:
> > ./configure -noX11 gnu
> > make -j 4 install
> > source ~/amber_20src/amber.sh
> > amber.conda install mpi4py
> > ./configure -noX11 -mpi gnu
> > make -j4 install.
> >
> > I followed the above steps to install ambertools, I got serial and
> parallel
> > version executables of MMPBSA.
> >
> > serial version is working fine.
> >
> > The parallel version is giving me errors sometimes.
> >
> > Can someone tell me the problem with my installation.
> >
> > Thanks,
> > Divya.
> >
> >
> > Dr. Divya Bharathi,
> > Post Doctoral Fellow,
> > IIIT
> > Hyderabad-500032.
> > INDIA.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Best Regards
> Elvis
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>
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Received on Fri Dec 18 2020 - 05:00:03 PST
