I actually think I fixed the original build issue here:
https://gitlab.ambermd.org/amber/amber/-/merge_requests/1001, which will
allow mpi4py and MMPBSA.py.MPI to continue to build and test in CI. It
also updates mpi4py to the latest version.
Thanks,
Jason
On Fri, Feb 25, 2022 at 3:28 PM Jason Swails <jason.swails.gmail.com> wrote:
>
>
> On Fri, Feb 25, 2022 at 1:59 PM David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Fri, Feb 25, 2022, Jason Swails wrote:
>> >
>> >I'm trying to update the docker image used in the builds (it was using
>> >Ubuntu 18.04 as a base -- I'm trying 20.04 now). My operating hypothesis
>> >is that the mpich version bundled in Ubuntu 18.04 isn't including the
>> librt
>> >library that supplies some of the aio_* symbols that is causing the
>> mpi4py
>> >config/build failure. Hopefully Ubuntu 20.04 has a later version of
>> mpich
>> >that doesn't have the same problem.
>> >
>> >If this fixes the problem, I'll update the docker images in Docker Hub
>> and
>> >the builds should start working again. Otherwise we would have to skip
>> >building mpi4py (not just the MMPBSA.py MPI tests).
>>
>> I'm doubtful: I have Ubuntu 20.04, and see the same problem (again with
>> Ubunutu's version of mpich. Trying openMPI just gives a different set of
>> unsatisfied symbols....) But maybe the combination of updating mpi4py
>> to 3.1.3 and going to Ubuntu 20.04 might work....
>>
>> As a temporary workaround, we could add -DFORCE_DISABLE_LIBS="mpi4py" to
>> the
>> default run_cmake script. I think all the pending MR's are orthogonal to
>> the
>> mpi4py stuff, so people could be getting code checked in, giving us
>> (probably
>> you) time to ponder what's best here.
>>
>
> Done here: https://gitlab.ambermd.org/amber/amber/-/merge_requests/1004.
> Hopefully this passes and we can work on merging master into the branches
> that all failed.
>
> Thanks,
> Jason
>
> --
> Jason M. Swails
>
--
Jason M. Swails
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Received on Fri Feb 25 2022 - 16:00:02 PST
