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
>
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Received on Thu Apr 29 2021 - 20:00:02 PDT
