Dear Dave,
I finally installed AmberTools21 using both the tradition method and cmake, but it was not easy. Here are what I have seen:
1. In the cmake version, I had to first do "clean_build" in order to properly install the parallel version. 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.
2. I had to install the latest version of pnetcdf. I could not compile the one in $AMBERHOME/Ambertools/src/pnetcdf.
3. In the traditional version, before parallel installation, amber.pip needs to be utilized to install mpi4py. Interestingly, amber.pip is not available in the cmake version.
4. Even though MMPBSA.py and MMPBSA.py.MPI are the same files, it seems that the codes use the file name to decide if it is a parallel or serial run.
5. Also in both methods, in order to install the code in the cluster, I had to install the latest version of openmpi (openmpi-4.0.2) using configure_openmpi.
6. Also, the versions of gcc, gfortran, and g++ need to be same. I had some issues before.
I have tried so many things that it is possible that I might have missed some other observations, but hopefully this info might be helpful to some other people. I think both the traditional method and cmake version should not need users to install some programs/libs manually.
Best regards,
Ilyas Yildirim, Ph.D.
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________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Monday, February 7, 2022 1:28 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] mpi4py Problem
EXTERNAL EMAIL : Exercise caution when responding, opening links, or opening attachments.
On Mon, Feb 07, 2022, Ilyas Yildirim wrote:
>Specifically, the discussion in
>http://archive.ambermd.org/202102/0060.html
>is exactly the same problems I am having. Any suggestions are appreciated.
Ilyas: this is not all that clear: the archive message reports two problems,
one with "ModuleNotFoundError: No module named 'mpi4py' ", and a second
where the user installed mpi4py by hand, and then encountered subsequent
issues.
Which issue is happening to you? Can you run $AMBERHOME/bin/amber.python
and type "import mpi4py"? What happens? Did you search for "mpi4py" in your
cmake.log file?
....dac
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Received on Mon Feb 07 2022 - 21:00:02 PST
