Hi Elvis,
This was the error I saw,
cpptraj found! Using /home/deva/softwares/test/amber20_src/bin/cpptraj
> mmpbsa_py_energy found! Using
> /home/deva/softwares/test/amber20_src/bin/mmpbsa_py_energy
> Preparing trajectories for simulation...
> File "/home/deva/softwares/test/amber20_src/bin/MMPBSA.py.MPI", line 99,
> in <module>
> app.file_setup()
> File
> "/home/deva/softwares/test/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/main.py",
> line 130, in file_setup
> self.remove(0)
> File
> "/home/deva/softwares/test/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/main.py",
> line 871, in remove
> utils.remove(flag, mpi_size=self.mpi_size, fnpre=self.pre)
> File
> "/home/deva/softwares/test/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/utils.py",
> line 112, in remove
> for fil in tempfiles: os.remove(fil)
> FileNotFoundError: [Errno 2] No such file or directory:
> '_MMPBSA_dummycomplex.inpcrd'
> 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
>
>
Sometimes the MMPBSA.py.MPI is not giving me the error with the same set of
input files. I donot know the exact reason.
But the file it is looking for i created and is on the location.
Awaiting you reply,
Thanks,
Divya.
Dr. Divya Bharathi,
Post Doctoral Fellow,
IIIT
Hyderabad-500032.
INDIA.
On Thu, Dec 17, 2020 at 7:02 AM 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 18 2020 - 05:00:02 PST
