[gmx-users] Batch mode error in GROMACS version 2019.2

[Mark Abraham]

Hi,

I can imagine some MPI setups would control whether and how the shell
streams used in such redirections are passed through, so the fact that gmx
works and gmx_mpi doesn't seems consistent. Use gmx if you need scripting.
You only need the MPI build for running mdrun, so you'll have a good time
if you build your workflows around that notion.

Mark

On Sat, 14 Sep 2019 at 10:16, Rajib Biswas <chemrajib at gmail.com> wrote:

> Hi David,
>
> As I said in my previous email, when I am using
>
> echo 18 0 | gmx_mpi energy -f traj.edr -o temperature
>
> getting the following error:
>
> Program:     gmx energy, version 2019.2
> Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296)
>
> Fatal error:
> No energy terms selected
>
>
> However, if I use
>
> echo 18 0 | gmx_d energy -f traj.edr -o temperature
>
> There is no error.
> Note that for both the cases (i.e. gmx_mpi and gmx_d) interactive mode is
> working fine.
>
>
> Thanks.
>
> With regards,
> Rajib
>
>
> On Sat, Sep 14, 2019 at 12:56 PM David van der Spoel <spoel at xray.bmc.uu.se
> >
> wrote:
>
> > Den 2019-09-14 kl. 08:36, skrev Rajib Biswas:
> > > I did some more experimentation about this and found that this error is
> > > coming only with the mpi enabled version.
> > please give the exact command line
> > >
> > > Rajib
> > >
> > > On Fri, Sep 13, 2019 at 10:58 PM Rajib Biswas <chemrajib at gmail.com>
> > wrote:
> > >
> > >> Hi Mark,
> > >>
> > >> Thanks!
> > >>
> > >> Interactively I could do it without any error. However, this error
> only
> > >> arises whenever I have tried to use batch mode.
> > >>
> > >> With regards,
> > >> *Rajib*
> > >>
> > >>
> > >> On Fri, Sep 13, 2019 at 6:06 PM Mark Abraham <
> mark.j.abraham at gmail.com>
> > >> wrote:
> > >>
> > >>> What happens when you do it interactively?
> > >>>
> > >>> Mark
> > >>>
> > >>> On Fri, 13 Sep 2019 at 14:21, Rajib Biswas <chemrajib at gmail.com>
> > wrote:
> > >>>
> > >>>> Dear All,
> > >>>>
> > >>>> I am trying to use the post-processing tools in batch mode. I am
> using
> > >>> the
> > >>>> following commands
> > >>>>
> > >>>> echo 18 0 | gmx_mpi energy -f traj.edr -o temperature
> > >>>>
> > >>>> Getting the following error:
> > >>>>
> > >>>> Program:     gmx energy, version 2019.2
> > >>>> Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296)
> > >>>>
> > >>>> Fatal error:
> > >>>> No energy terms selected
> > >>>>
> > >>>>
> > >>>> I have even tried all the options mentioned
> > >>>>
> > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
> > >>>> however, could not get it worked for version 2019.2.
> > >>>>
> > >>>> Any help will be appreciated.
> > >>>>
> > >>>> With regards,
> > >>>> *Rajib*
> > >>>> --
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> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Head of Department, Cell & Molecular Biology, Uppsala University.
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