On Tue, Feb 08, 2022, Ilyas Yildirim wrote:
>
>I finally installed AmberTools21 using both the tradition method and cmake,
>but it was not easy. Here are what I have seen:
Can you say what operating system and version you are using. The
"traditional" installation system is no longer maintained, is not documented
in the Reference Manual, and will be disabled in future releases.
I have installed the parallel version of AmberTools21 under Windows 10/WSL, Ubuntu 16.04, and Centos EL7 (Intel CPU). I think cmake will be a good option once the issues are fixed; I needed to run 3drism calculations for a project, which only works under Amber20, and thus wanted to install as soon as possible.
> Nevertheless, mpi4py needs to be
> installed. It is a little bit trickly; I think (but I am not sure as I
> have tried a lot of combinations) amber.conda works.
Volunteers, especially those who use mmpbsa.py are solicited here. Adrian:
is there anyone at your end who could look at this (and other problems with
mmpbsa.py? Do we have a test case for MMPBSA.py.MPI?
Developers: can you see if you can import mpi4py on your machines, assuming
that you downloaded at the build stage? The reason that amber.pip is
missing is because the miniconda download no longer provides the pip file
that amber.pip would be pointing to. Perhaps people are not getting mpi4py
because they are not getting pip.
I think in my case the main issue was with mpi4py not being installed properly. Once I installed using amber.pip, the rest was missing packages such as pnetcdf (the correct version). Again, they need to be included in the installation process. Maybe even a proper version of openmpi could be automatically installed and placed under $AMBERHOME. This is what I do in our cluster here as the modules available in the cluster for openmpi most of the time does not satisfy the requirements (such as specific versions of gfortran/gcc/g++).
Best regards,
Ilyas
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Received on Tue Feb 08 2022 - 08:30:02 PST
