Hi,
Compilation of mpi4py fails in AmberTools23 installation.
My environment is CentOS7, with GCC 11.3.0, CMake 3.25.2 and OpenMPI 4.1.5.
Similar error happens in AmberTools22 installation.
[ 18%] Building mpi4py
running build
running build_src
running build_py
running build_clib
MPI configuration: [cmake-mpi] from
'/home/x09527a/src/ambertools23cpu_src/build/AmberTools/src/mpi4py-3.1.3/mpi.cfg'
MPI C compiler: /home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc
MPI C++ compiler: /home/center/opt/x86_64/cores/gcc/11.3.0/bin/g++
running build_ext
MPI configuration: [cmake-mpi] from
'/home/x09527a/src/ambertools23cpu_src/build/AmberTools/src/mpi4py-3.1.3/mpi.cfg'
MPI C compiler: /home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc
MPI C++ compiler: /home/center/opt/x86_64/cores/gcc/11.3.0/bin/g++
checking for MPI compile and link ...
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -DNDEBUG -fwrapv -O2
-Wall -fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -pthread
-I/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include/python3.11
-I/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include -c
_configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -DNDEBUG -fwrapv -O2
-Wall -fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -pthread
-I/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include/python3.11
-I/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include -c
_configtest.c -o _configtest.o
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -Wl,-rpath
-Wl,/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib
-Wl,--enable-new-dtags -pthread _configtest.o
-L/home/x09527a/src/ambertools23cpu_src/build/AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-cpython-311
-L/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib -lmpi -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for missing MPI functions/symbols ...
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -DNDEBUG -fwrapv -O2
-Wall -fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -pthread
-I/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include/python3.11
-I/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include -c
_configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
checking for function 'MPI_Type_create_f90_integer' ...
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -DNDEBUG -fwrapv -O2
-Wall -fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -pthread
-I/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include/python3.11
-I/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include -c
_configtest.c -o _configtest.o
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -Wl,-rpath
-Wl,/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib
-Wl,--enable-new-dtags -pthread _configtest.o
-L/home/x09527a/src/ambertools23cpu_src/build/AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-cpython-311
-L/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib -lmpi -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Type_create_f90_real' ...
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -DNDEBUG -fwrapv -O2
-Wall -fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -pthread
-I/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include/python3.11
-I/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include -c
_configtest.c -o _configtest.o
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -Wl,-rpath
-Wl,/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib
-Wl,--enable-new-dtags -pthread _configtest.o
-L/home/x09527a/src/ambertools23cpu_src/build/AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-cpython-311
-L/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib -lmpi -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Type_create_f90_complex' ...
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -DNDEBUG -fwrapv -O2
-Wall -fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -pthread
-I/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include/python3.11
-I/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include -c
_configtest.c -o _configtest.o
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -Wl,-rpath
-Wl,/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib
-Wl,--enable-new-dtags -pthread _configtest.o
-L/home/x09527a/src/ambertools23cpu_src/build/AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-cpython-311
-L/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib -lmpi -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Status_c2f' ...
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -DNDEBUG -fwrapv -O2
-Wall -fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -pthread
-I/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include/python3.11
-I/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include -c
_configtest.c -o _configtest.o
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -Wl,-rpath
-Wl,/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib
-Wl,--enable-new-dtags -pthread _configtest.o
-L/home/x09527a/src/ambertools23cpu_src/build/AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-cpython-311
-L/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib -lmpi -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Status_f2c' ...
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -DNDEBUG -fwrapv -O2
-Wall -fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -pthread
-I/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include/python3.11
-I/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include -c
_configtest.c -o _configtest.o
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -Wl,-rpath
-Wl,/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib
-Wl,--enable-new-dtags -pthread _configtest.o
-L/home/x09527a/src/ambertools23cpu_src/build/AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-cpython-311
-L/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib -lmpi -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for symbol 'MPI_LB' ...
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -DNDEBUG -fwrapv -O2
-Wall -fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -pthread
-I/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include/python3.11
-I/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include -c
_configtest.c -o _configtest.o
In file included from _configtest.c:2:
_configtest.c: In function ‘main’:
/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include/mpi.h:326:65:
error: static assertion failed: "MPI_LB was removed in MPI-3.0. Use
MPI_Type_create_resized instead."
326 | #define THIS_SYMBOL_WAS_REMOVED_IN_MPI30(symbol, new_symbol) 0;
_Static_assert(0, #symbol " was removed in MPI-3.0. Use " #new_symbol "
instead.")
| ^~~~~~~~~~~~~~
/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include/mpi.h:1152:24:
note: in expansion of macro ‘THIS_SYMBOL_WAS_REMOVED_IN_MPI30’
1152 | # define MPI_LB THIS_SYMBOL_WAS_REMOVED_IN_MPI30(MPI_LB,
MPI_Type_create_resized);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_configtest.c:5:23: note: in expansion of macro ‘MPI_LB’
5 | MPI_Datatype s; s = MPI_LB; (void)s;
| ^~~~~~
failure.
removing: _configtest.c _configtest.o
checking for symbol 'MPI_UB' ...
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -DNDEBUG -fwrapv -O2
-Wall -fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -pthread
-I/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include/python3.11
-I/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include -c
_configtest.c -o _configtest.o
In file included from _configtest.c:2:
_configtest.c: In function ‘main’:
/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include/mpi.h:326:65:
error: static assertion failed: "MPI_UB was removed in MPI-3.0. Use
MPI_Type_create_resized instead."
326 | #define THIS_SYMBOL_WAS_REMOVED_IN_MPI30(symbol, new_symbol) 0;
_Static_assert(0, #symbol " was removed in MPI-3.0. Use " #new_symbol "
instead.")
| ^~~~~~~~~~~~~~
/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include/mpi.h:1151:24:
note: in expansion of macro ‘THIS_SYMBOL_WAS_REMOVED_IN_MPI30’
1151 | # define MPI_UB THIS_SYMBOL_WAS_REMOVED_IN_MPI30(MPI_UB,
MPI_Type_create_resized);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_configtest.c:5:23: note: in expansion of macro ‘MPI_UB’
5 | MPI_Datatype s; s = MPI_UB; (void)s;
| ^~~~~~
failure.
removing: _configtest.c _configtest.o
checking for dlopen() availability ...
checking for header 'dlfcn.h' ...
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -DNDEBUG -fwrapv -O2
-Wall -fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -pthread
-I/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include/python3.11
-I/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include -c
_configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
success!
checking for library 'dl' ...
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -DNDEBUG -fwrapv -O2
-Wall -fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -pthread
-I/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include/python3.11
-I/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include -c
_configtest.c -o _configtest.o
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -Wl,-rpath
-Wl,/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib
-Wl,--enable-new-dtags -pthread _configtest.o
-L/home/x09527a/src/ambertools23cpu_src/build/AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-cpython-311
-L/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib -ldl -lmpi -o
_configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'dlopen' ...
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -DNDEBUG -fwrapv -O2
-Wall -fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -pthread
-I/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include/python3.11
-I/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include -c
_configtest.c -o _configtest.o
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -Wl,-rpath
-Wl,/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib
-Wl,--enable-new-dtags -pthread _configtest.o
-L/home/x09527a/src/ambertools23cpu_src/build/AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-cpython-311
-L/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/lib -ldl -lmpi -o
_configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.MPI' extension
/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc -DNDEBUG -fwrapv -O2
-Wall -fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include
-fPIC -O2 -isystem
/home/x09527a/src/ambertools23cpu_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/home/x09527a/src/ambertools23cpu_src/build/CMakeFiles/miniconda/install/include/python3.11
-I/home/center/opt/x86_64/apps/gcc/11/openmpi/4.1.5/include -c src/MPI.c
-o
/home/x09527a/src/ambertools23cpu_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 '/home/center/opt/x86_64/cores/gcc/11.3.0/bin/gcc' failed
with exit code 1
make[2]: ***
[AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/mpi4py-build.stamp]
Error 1
make[1]: *** [AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py.dir/all] Error 2
make: *** [all] Error 2
Best regards,
Kotaro Tanaka
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 27 2023 - 05:00:02 PDT
