Respected sir,
Have done that too. But still I cannot complete the job.
mpirun -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -i prod_md.in -c
water_npt2.rst7 -p water.prmtop -o water_prod1.out -r water_prod1.rst7 -x
water_prod1.nc
Unit 6 Error on OPEN: water_prod1.out
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
On Mon, Jan 27, 2020 at 6:01 PM Gerardo Zerbetto De Palma <
g.zerbetto.gmail.com> wrote:
> Try removing all output files (mdout, coordinates and trajectory) and run
> again.
>
> El lun., 27 de ene. de 2020 09:22, Sruthi Sudhakar <
> sruthisudhakarraji.gmail.com> escribió:
>
> > I have both read and write permission for the directory
> >
> > On Mon, Jan 27, 2020 at 6:19 PM Sruthi Sudhakar <
> > sruthisudhakarraji.gmail.com> wrote:
> >
> > > Thank you for the quick reply. I have run the command once gain using
> > > mpirun:
> > >
> > > mpirun -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -i prod_md.in -c
> > > water_npt2.rst7 -p water.prmtop -o water_prod1.out -r water_prod1.rst7
> -x
> > > water_prod1.nc
> > > At line 135 of file master_setup.F90 (unit = 6, file =
> 'water_prod1.out')
> > > Fortran runtime error: Cannot write to file opened for READ
> > >
> >
> --------------------------------------------------------------------------
> > > Primary job terminated normally, but 1 process returned
> > > a non-zero exit code. Per user-direction, the job has been aborted.
> > >
> >
> --------------------------------------------------------------------------
> > >
> >
> --------------------------------------------------------------------------
> > > mpirun detected that one or more processes exited with non-zero status,
> > > thus causing
> > > the job to be terminated. The first process to do so was:
> > >
> > > Process name: [[36132,1],0]
> > > Exit code: 2
> > >
> > > The error occurred gain. I would check for the read and write
> permission.
> > >
> > > On Mon, Jan 27, 2020 at 5:28 PM Elvis Martis <elvis_bcp.elvismartis.in
> >
> > > wrote:
> > >
> > >> Check if you have read and write permissions in your working directory
> > >> Best Regards
> > >>
> > >>
> > >>
> > >> On Mon, 27 Jan 2020 at 17:22, Sruthi Sudhakar <
> > >> sruthisudhakarraji.gmail.com>
> > >> wrote:
> > >>
> > >> > Dear group members,
> > >> >
> > >> > I have been trying to run a job using pmemd.cuda.MPI in our system.
> I
> > >> have
> > >> > encountered the following error:
> > >> >
> > >> > pmemd.cuda.MPI -O -i prod_md.in -c water_npt2.rst7 -p water.prmtop
> -o
> > >> > water_prod1.out -r water_prod1.rst7 -x water_prod1.nc
> > >> >
> > >> > At line 135 of file master_setup.F90 (unit = 6, file =
> > >> 'water_prod1.out')
> > >> > Fortran runtime error: Cannot write to file opened for READ
> > >> >
> > >> > Since I am using the parallel version for the first time I am unable
> > to
> > >> > understand the error here. Also attaching the input file.
> > >> >
> > >> > Thank you all in advance.
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> > >> >
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> > >
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Received on Mon Jan 27 2020 - 05:00:02 PST
