Failed building wheel for mpi4py

[pachequin1]

Hi everyone,

I'm trying to install gmx_MMPBSA on a centos machine using:

amber.python -m pip install gmx_MMPBSA

unfortunately, i got the following error:

###################################
/home/cmp/software/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: _configtest.c:(.text.startup+0x1a): undefined reference to `MPI_Finalize'
collect2: error: ld devolvi? el estado de salida 1
failure.
removing: _configtest.c _configtest.o
error: Cannot link MPI programs. Check your configuration!!!

ERROR: Failed building wheel for mpi4py
Failed to build mpi4py
ERROR: Could not build wheels for mpi4py which use PEP 517 and cannot be installed directly
###################################

Does anyone know how to fix this error?

I really appreciated.

Cesar

[Valdes-Tresanco-MS]

Did you install ambertools and compilers as indicated in amber documentation?

The installation of mpi4py must be done before compilers because this package modifies the mpi4py compilation environment.

[pachequin1]

Yes. I tried to install gmx_mmpbsa after ambertools 21 installation as indicated. Cesar

On Sat 20 Nov 2021 at 21:44 Mario Sergio Valdés Tresanco < ***@***.***> wrote: Did you install ambertools and compilers as indicated in amber documentation? The installation of mpi4py must be done before compilers because this package modifies the mpi4py compilation environment. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#93 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AWTBV5PGUSKSJL2B7FHHVQLUNBTKJANCNFSM5IOVOOHA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- ############################ César Millán Pacheco Facultad de Farmacia Universidad Autonoma del Estado de Morelos Tel: 777 3297020 Fax: 777 3207040 email: ***@***.*** ***@***.***

[Valdes-Tresanco-MS]

Follow these steps and tell me if it was resolved:

• Uninstall the compilers package (conda remove compilers)
• Install mpi4py (conda install -c conda-forge mpi4py)
• install compilers (conda install -c conda-forge compilers)
• install gmx_MMPBSA (python -m pip install gmx_MMPBSA)

Make sure you have the correct conda environment active

Cheers!
Mario S

[pachequin1]

Thank you, that does the trick. Best, Cesar ############################ César Millán Pacheco Facultad de Farmacia Universidad Autonoma del Estado de Morelos Tel: 777 3297020 Fax: 777 3207040 email: ***@***.*** ***@***.***

…

On Sat, Nov 20, 2021 at 10:16 PM Mario Sergio Valdés Tresanco < ***@***.***> wrote: Follow these steps and tell me if it was resolved: - Uninstall the compilers package (conda remove compilers) - Install mpi4py (conda install -c conda-forge mpi4py) - install compilers (conda install -c conda-forge compilers) - install gmx_MMPBSA (python -m pip install gmx_MMPBSA) Make sure you have the correct conda environment active Cheers! Mario S — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#93 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AWTBV5NJSFAM3LIOW44APRLUNBXB3ANCNFSM5IOVOOHA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.