Hi,
It could be some other issue with your IB adapters. My next suggestion
is to compile a very simple MPI program and see if you can run that
with no issues. You may need to contact your local system admins for
further help.
-Dan
On Fri, Jul 22, 2022 at 1:18 PM Rybenkov, Valentin V. <valya.ou.edu> wrote:
>
> No, it did not help, still the same “WARNING: There was error initializing OpenFabrics device.”
>
>
>
> Valentin V. Rybenkov
> University of Oklahoma
> 101 Stephenson Parkway
> Norman, OK 73019
> Web: antibiotics.oucreate.com
>
>
>
> From: Daniel Roe
> Sent: Friday, July 22, 2022 9:37 AM
> To: Rybenkov, Valentin V.; AMBER Mailing List
> Subject: Re: [AMBER] error opening OpenFabrics device
>
>
>
> Hi,
>
> I've seen this happen due to system resource limits. Try adding
> 'ulimit -l unlimited' before running anything and see if that helps.
>
> -Dan
>
> On Fri, Jul 22, 2022 at 9:46 AM Rybenkov, Valentin V. via AMBER
> <amber.ambermd.org> wrote:
> >
> > Hi everybody,
> >
> > I am trying to install an MPI version of AmberTools22 on a CentOS 7 machine. I installed the serial version of AmberTools with a -DBUILD_PERL=FALSE. I then followed instructions and installed openmpi-4.1.4 in amber22_src/AmberTools/src and configured it using ./configure_openmpi gnu
> > Then set -DMPI=TRUE, ./run_cmake and make install
> >
> > At the testing stage (mpirun -np=4), I am getting many errors:
> > WARNING: There was error initializing OpenFabrics device.
> >
> > The error then repeated when I ran a test job using sander.MPI. Only one task was running, and the job took 3x longer than the pmemd.MPI from Amber18, about the same time as the serial version.
> >
> > So it appears that the parallel version of AmberTools failed to install.
> >
> > Any suggestions what is failing in the installation?
> >
> > Thanks,
> > Valentin
> > Valentin V. Rybenkov
> > University of Oklahoma
> > 101 Stephenson Parkway
> > Norman, OK 73019
> > Web: antibiotics.oucreate.com
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Thu Aug 04 2022 - 13:35:31 PDT
