Hi,
The issue is caused by `amber22_src/build/CMakeFiles/miniconda/install/compiler_compat`. There are two files here:
```
total 4
-rw-rw-r-- 2 z00000r gr0001 173 Apr 25 16:07 README
lrwxrwxrwx 1 z00000r gr0001 32 Aug 22 16:14 ld -> ../bin/x86_64-conda-linux-gnu-ld
```
Remove the symbolic `ld` and fix it to use system's one:
```
rm -f ld
ln -s /usr/bin/ld ld
```
and try to build mpi4py again using `amber.pip install mpi4py`.
after that, revoke that change:
```
ln -sf ../bin/x86_64-conda-linux-gnu-ld
```
then MMPBSA.py.MPI will work.
See also
https://stackoverflow.com/questions/72680287/not-able-to-install-mpi4py-using-pip
Best,
Yoshitaka Moriwaki
On 2022/09/20 2:55, Adrian Roitberg via AMBER wrote:
> Hi
>
> I am still working on this with hpc. I am 100% sure it has to do with their mpi installation. They are checking things now.
>
> adrian
>
>
> On 9/19/22 1:50 PM, amirhossein taghavi via AMBER wrote:
>> [External Email]
>>
>> Hello,
>>
>> I got the following responses from HPC admin and it seems a separate python
>> installation is not an option on HPC. That would be great if any of the
>> Amber team could help with HPC's questions.
>>
>> Thanks,
>> Amir
>>
>> 1) they should correct the cmake to work with python + miniconda, no
>> separate python installs which mess up our python for general users.
>>
>> 2) Which versions of compiler+openmpi and python are officially supported
>> by the Amber team? The help says the latest is intel17 which is quite old,
>> is that true?
>>
>>
>> On Sun, Sep 18, 2022 at 7:43 PM Hai Nguyen <nhai.qn.gmail.com> wrote:
>>
>>> Are you able to install mpi4py via
>>>
>>> conda install mpi4py -c conda-forge
>>>
>>> Hai
>>>
>>> On Sun, Sep 18, 2022 at 2:44 PM amirhossein taghavi via AMBER <
>>> amber.ambermd.org> wrote:
>>>
>>>> Hello Amber Developers,
>>>>
>>>> We have a problem with building the MMPBSA.py.MPI on HPC following the
>>>> recommended installation by Amber manual. We have also tested the
>>>> suggestion by Prof. Case on copying the .py to .py.MPI and it didn't work.
>>>> The summary of the problem is provided as follows and any suggestions to
>>>> solve this problem is very much appreciated.
>>>>
>>>> Best,
>>>> Amir
>>>>
>>>> Executive summary:
>>>> ==================
>>>>
>>>> In a "standard" cmake MPI install
>>>>
>>>> ll /apps/intel/2019.1.144/openmpi/4.0.1/amber/20/bin/MM*
>>>> ls: cannot access /apps/intel/2019.1.144/openmpi/4.0.1/amber/20/bin/MM*:
>>>> No
>>>> such file or directory
>>>>
>>>> using miniconda, which is supposed to do the python part, the resulting
>>>> /bin
>>>> has no
>>>>
>>>> MMPBSA.py and MMPBSA.py.MPI
>>>>
>>>> and is non-python-fuctional.
>>>>
>>>> In a cmake non-MPI install, e.g.
>>>>
>>>> ll /apps/gcc/7.3.0/amber/20/bin/MM*
>>>> -rwxrwxr-x 1 dimi amber 4129 Jun 4 2020
>>>> /apps/gcc/7.3.0/amber/20/bin/MMPBSA.py
>>>>
>>>> python is OK, MMPBSA.py is there and works, no hacking involved.
>>>>
>>>> The idea to just cp MMPBSA.py to MMPBSA.py.MPI fails, not surprisingly
>>>> for a
>>>> serial install, on the lines
>>>>
>>>> if sys.argv[0].endswith('MPI'):
>>>> try:
>>>> from mpi4py import MPI
>>>>
>>>> MMPBSA.py.MPI
>>>> Traceback (most recent call last):
>>>> File "./MMPBSA.py.MPI", line 53, in <module>
>>>> from mpi4py import MPI
>>>> ModuleNotFoundError: No module named 'mpi4py'
>>>>
>>>> During handling of the above exception, another exception occurred:
>>>>
>>>> Traceback (most recent call last):
>>>> File "./MMPBSA.py.MPI", line 55, in <module>
>>>> raise MMPBSA_Error('Could not import mpi4py package! Use serial
>>>> version
>>>> '
>>>> MMPBSA_mods.exceptions.MMPBSA_Error: Could not import mpi4py package! Use
>>>> serial version or install mpi4py.
>>>>
>>>>
>>>> Summary: cmake serial and OMP installs work for python, but not MPI
>>>> installs.
>>>> _______________________________________________
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Received on Tue Sep 20 2022 - 22:30:03 PDT
