Thank you for your suggestion but unfortunately this didn’t help. After
running “sudo ./run_cmake” with applied correction:
# Assume this is Linux:
cmake $AMBER_PREFIX/amber20_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20 \
-DCOMPILER=GNU \
-DMPI=TRUE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE \
-DDISABLE_TOOLS="mmpbsa_py" \
2>&1 | tee cmake.log
and “sudo make install” the same errors were reported:
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
error: Cannot link MPI programs. Check your configuration!!!
make[2]: ***
[AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py.dir/build.make:276:
AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/mpi4py-build.stamp]
Error 1
make[1]: *** [CMakeFiles/Makefile2:3734:
AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py.dir/all] Error 2
make: *** [Makefile:152: all] Error 2
In addition I observed the behavior already mentioned on the mailing
list (
http://archive.ambermd.org/202012/0083.html) where the cmake
reports at one stage that mpi4py "not found", but later, in the Build
Report, it indicates that it will be used. However, there seems to be no
solution offered.
All best,
Antonija
Dana 11.03.2022 14:02, David A Case je napisao(la):
> On Fri, Mar 11, 2022, Antonija Tomić wrote:
>>
>> After modifying “-DMPI=TRUE” and performing “sudo ./run_cmake” I
>> initialized “sudo make install” and got the following error (the whole
>> output is given in attached file):
>>
>> collect2: error: ld returned 1 exit status
>> failure.
>> removing: _configtest.c _configtest.o
>> error: Cannot link MPI programs. Check your configuration!!!
>
> Try adding the following line to your run_cmake file:
>
> -DDISABLE_TOOLS="mmpbsa_py"
>
> Updates to mpi4py (which get downloaded when you re-install miniconda)
> seem
> to have broken the parallel version of mmpbsa_py. This *should* all
> everything else to build, but I've not tested this myself.
>
> ...hope this helps....dac
>
>
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Received on Fri Mar 11 2022 - 06:00:02 PST
