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 - 09:30:03 PDT
