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

[Rajib Biswas]

That makes sense. Thanks, a lot.

On Sun, Sep 15, 2019 at 4:53 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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*
> > > >>>> --
> > > >>>> Gromacs Users mailing list
> > > >>>>
> > > >>>> * Please search the archive at
> > > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> before
> > > >>>> posting!
> > > >>>>
> > > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >>>>
> > > >>>> * For (un)subscribe requests visit
> > > >>>>
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > >>>> send a mail to gmx-users-request at gromacs.org.
> > > >>>>
> > > >>> --
> > > >>> Gromacs Users mailing list
> > > >>>
> > > >>> * Please search the archive at
> > > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > >>> posting!
> > > >>>
> > > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >>>
> > > >>> * For (un)subscribe requests visit
> > > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > >>> send a mail to gmx-users-request at gromacs.org.
> > > >>>
> > > >>
> > >
> > >
> > > --
> > > David van der Spoel, Ph.D., Professor of Biology
> > > Head of Department, Cell & Molecular Biology, Uppsala University.
> > > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> > > http://www.icm.uu.se
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>