Hi Olivia,
the first thing to try is to run this with the non-MPI version of pmemd on
one CPU, or using the sander program instead.
The error message sounds like a problem with your input file (terminal
newline missing maybe?) but you dont say if it occurs right on job
submission or after some runtime. Is the .in file downloaded or from some
other source?
Kind Regards,
Thomas
On Tue, Oct 3, 2023 at 7:59 PM Meyer, Olivia (meyerok) via AMBER <
amber.ambermd.org> wrote:
> **Warning** The sender address ("Meyer, Olivia \(meyerok\) via AMBER" )
> can not be verified, sender email address could be spoofed. Please take
> care to proceed.
> Hello,
>
> I am having trouble locating the source of this Fortran runtime error, and
> determining how to solve it. I am completing the Computing Binding Enthalpy
> Tutorial and am on Section 2, attempting to minimize the water box…Here is
> the following error after my command:
>
> mpirun -np 2 pmemd.MPI -O -i all_min.in -p water.prmtop -c water_iso.rst7
> -o water_min.out
> At line 975 of file
> /mnt/c/Users/LivMeyer/Desktop/amber22_src/src/pmemd/src/mdin_ctrl_dat.F90
> (unit = 5, file = 'all_min.in')
> Fortran runtime error: End of file
>
> Error termination. Backtrace:
> #0 0x7f5f9d67a960 in ???
> #1 0x7f5f9d67b4d9 in ???
> #2 0x7f5f9d67c10f in ???
> #3 0x7f5f9d8cf17b in ???
> #4 0x7f5f9d8d03c4 in ???
> #5 0x7f5f9d8d2e41 in ???
> #6 0x7f5f9d8d30e3 in ???
> #7 0x55dbf14d7816 in ???
> #8 0x55dbf1657c50 in ???
> #9 0x55dbf1638d06 in ???
> #10 0x55dbf14c020e in ???
> #11 0x7f5f9d20cd8f in ???
> #12 0x7f5f9d20ce3f in ???
> #13 0x55dbf14c0244 in ???
> #14 0xffffffffffffffff in ???
> --------------------------------------------------------------------------
> 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: [[40616,1],0]
> Exit code: 2
>
>
> Also, my input file script is as follows:
> All atoms minimization
> &cntrl
> imin = 1,
> maxcyc = 10000,
> ncyc = 500,
> ntb = 1,
> ntr = 0,
> cut = 10.0
> /
>
> Thanks!
>
>
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>
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>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Tue Oct 03 2023 - 23:30:02 PDT
