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
>
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Received on Thu Aug 04 2022 - 13:35:27 PDT
