Dear Amber users,
Adding 'set(MINICONDA_VERSION py310_23.5.2-0)' line 91,
i.e. forcing the use of python3.10 instead of python3.11, before:
set(MINICONDA_INSTALLER_FILENAME "Miniconda${PYTHON_MAJOR_RELEASE}-...
in amber22_src/cmake/UseMiniconda.cmake seems to solve the problem.
This may be an ugly workaround, but the compilation ends...
Best Francois
Quoting FyD via AMBER <amber.ambermd.org>:
> Dear Amber users,
>
> On Rocky Linux release 8.6 (Green Obsidian) with default gcc version 8.5.0
>
> Currently Loaded Modules:
> 1) compiler/gnu9/9.4.0 2) hwloc/2.7.0 3) ucx/1.11.2
> 4) libfabric/1.13.0 5) openmpi4/4.1.1 6) nvidia/nccl/2.18.1
>
> Here is the part of the 'amber22_src/build/run_cmake' script:
> cmake $AMBER_PREFIX/amber22_src \
>
> -DCMAKE_INSTALL_PREFIX=.../amber22_src-frontal-gnu9.4.0-openmpi4.1.1-nomkl
> \
> -DCOMPILER=GNU \
> -DMPI=TRUE -DOPENMP=FALSE \
> -DCUDA=FALSE -DNCCL=FALSE \
> -DINSTALL_TESTS=TRUE \
> -DDOWNLOAD_MINICONDA=TRUE \
> 2>&1 | tee cmake.log
>
> using (last week):
> -Python Interpreter: Internal Miniconda (version 3.10)
> -compilation options: -Wno-unused-result -Wsign-compare -DNDEBUG
> -fwrapv -O2 -Wall -fPIC -O2 -isystem
> -> the compilation goes fine - however without intel mkl :-(
> see below 1)
>
> using (yesterday):
> -Python Interpreter: Internal Miniconda (version 3.11)
> -compilation options: -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem
> -> the compilation does not end correctly
> see below 2)
>
> Same problems/differences for gnu9.4.0-openmpi4.1.1-nomkl or
> gnu12.2.0-openmpi4.1.4-nomkl
> - with/without (cuda 12.0 & nccl2.18.1)
> - compilations done on intel/amd cpus with/without gpu
>
> Any idea? what is the problem? what I do wrong?
>
> thank you, Francois
>
> 1)
> removing: _configtest.c _configtest.o _configtest
> building 'mpi4py.MPI' extension
> /opt/ohpc/pub/compiler/gcc/9.4.0/bin/gcc -Wno-unused-result
> -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem
> /users/fyd/bin/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC
> -O2 -isystem
> /users/fyd/bin/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC
> -pthread -DPyMPI_MISSING_MPI_LB=1 -DPyMPI_MISSING_MPI_UB=1
> -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1
> -I/users/fyd/bin/amber22_src/build/CMakeFiles/miniconda/install/include/
> -I/opt/ohpc/pub/mpi/openmpi4-gnu9/4.1.1/include -c src/MPI.c -o
> /users/fyd/bin/amber22_src/build/AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-cpython-310/src/MPI.o
>
> 2)
> removing: _configtest.c _configtest.o _configtest
> building 'mpi4py.MPI' extension
> /opt/ohpc/pub/compiler/gcc/9.4.0/bin/gcc -DNDEBUG -fwrapv -O2 -Wall
> -fPIC -O2 -isystem
> /users/fyd/bin/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC
> -O2 -isystem
> /users/fyd/bin/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC
> -pthread -DPyMPI_MISSING_MPI_LB=1 -DPyMPI_MISSING_MPI_UB=1
> -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1
> -I/users/fyd/bin/amber22_src/build/CMakeFiles/miniconda/install/include/python3.11
> -I/opt/ohpc/pub/mpi/openmpi4-gnu9/4.1.1/include -c src/MPI.c -o
> /users/fyd/bin/amber22_src/build/AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-cpython-311/src/MPI.o
> In file included from src/MPI.c:4:
> src/mpi4py.MPI.c:198:12: fatal error: longintrepr.h: No such file or
> directory
> 198 | #include "longintrepr.h"
> | ^~~~~~~~~~~~~~~
> compilation terminated.
> error: command '/opt/ohpc/pub/compiler/gcc/9.4.0/bin/gcc' failed with
> exit code 1
> make[2]: ***
> [AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py.dir/build.make:203:
> AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/mpi4py-build.stamp]
> Error 1
> make[1]: *** [CMakeFiles/Makefile2:5017:
> AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py.dir/all] Error 2
> make: *** [Makefile:156: all] Error 2
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Received on Fri Jul 14 2023 - 08:00:03 PDT
