I had the same experience. There are two main problems with the OpenMPI
version included in CentOS 7 and 8:
- The version is positively ancient, and long out of support.
- The version is compiled without support for most of the usual schedulers.
In most environments, that makes the OpenMPI from the distribution useless.
To resolve that, you will need to download a supported version (currently,
3.1, 4.0 or 4.1) of OpenMPI as source tarball. Then install the correct dev
RPMs for the resource manager you are using (such as slurm, torque or the
like).
Current versions of OpenMPI include a spec file to build RPMs. You will
need to apply some tweaks to compile in the appropriate scheduler support.
Hint: I found that building a virtual machine as a compile environment with
the exactly right libraries etc. installed works wonders. I use vagrant for
that purpose.
Once this process is finished, you will have an RPM that you can distribute
to the HPC.
Hint 2: if you can, don't try to get several OpenMPI versions to coexist.
It is possible, but not quite trivial to do.
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On Thu, Apr 29, 2021 at 7:59 PM Gerald Monard <gerald.monard.gmail.com>
wrote:
> Hi,
>
> The MPI implementation of openmpi or mpich provided in CentOS is a pain.
> CentOS 8 is even worse. The best is to install your own version. You can
> use the configure_openmpi.sh script available in AmberTools/src if you
> want some automatic configuration and build.
>
> I have also experienced that these official implementations can hang
> forever. Not always on the same test scripts though ...
>
> Gerald.
>
> Le ven. 30 avr. 2021 à 01:00, Azurmendi, Hugo <Hugo.Azurmendi.fda.hhs.gov>
> a écrit :
>
> > Hello there.
> > I just finished installing AMBER 20 on a new Linux and found a few
> > problems that I think developers should be aware of. I did a fresh
> install
> > of Centos 7 installing the recommended packages for centos with yum. The
> > problems were:
> >
> > 1. For parallel I followed the instructions for Fedora to install
> > openmpi as follows (not sure all these are required, but it worked):
> > · yum install dnf
> > · dnf install openmpi openmpi-devel environment-modules
> > · source /etc/profile.d/modules.sh (to load modules)
> > · Add line 'module load mpi/openmpi-x86_64' to .bashrc/.cshrc.
> > At this point I could start ‘make test.parallel’, however it would stall
> > (without messages) after a few tests. I finally could get it to go all
> the
> > way through by taking out (renaming the corresponding
> > $AMBERHOME/test/testname) the tests for dhfr and rism3d. I haven’t
> > investigated further this issue.
> >
> >
> > 1. The initial installation and test I did it in bash, deciding to
> > switch to csh later. I sourced to amber.csh (located in the amber20
> folder)
> > in my .cshrc but didn’t work:
> > * It warned that the shell was not csh, which it was. I fixed
> > replacing ( "$0" != '-tcsh' && "$0" != '-csh' ) for ( "$0" !~ '*csh' ) in
> > the ‘if’ line of amber.csh.
> > * AMBERHOME was set to the path of the .cshrc instead of the path
> > to amber.csh. I commented the setenv line in amber.csh and set AMBERHOME
> in
> > my .cshrc in the old fashion.
> >
> > Hope that helps to improve future releases. Looking forward to comments
> if
> > I did something wrong.
> > Hugo
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
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Received on Thu Apr 29 2021 - 20:30:02 PDT
