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/python3.10
-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 Thu Jul 13 2023 - 01:00:02 PDT
