How can I change the miniconda python version used in the installation
process?
Now by default the installed version is 3.11, and I want to try an older
version.
Because in some other softwares similar errors (fatal error:
longintrepr.h: No such file or directory )
are reported and attributed to the python 3.11.
Best regards,
Kotaro Tanaka
On 2023/07/27 20:38, Kotaro TANAKA via AMBER wrote:
> 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
--
田中 康太郎
国立大学法人東海国立大学機構 名古屋大学
細胞生理学研究センター (CeSPI)
〒464-8601 愛知県名古屋市千種区不老町
名古屋大学 創薬科学研究館 208号室
TEL: 052-747-6838 (内線 6838)
_______________________________________________
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Received on Sun Jul 30 2023 - 20:30:02 PDT
