发布使用pip与Anaconda一起安装petsc4py，以指示外部PETSc目录

2）安装PETSc3.13

配置从{}中指示{}和{}，并使用-O2编译器优化下载blas/lapack、scalapack、腮腺炎、METIS、PARMETIS和PTSCOTCH（注意：我使用MKL进行blas/lapack和scalapack）。在./configure中还指示PETSC_DIR文件夹位置和PETSC_ARCH名称。我选择了没有C++编译器的选项。

然后make all和make check。我还做了一个make test，花了很长时间。没有失败，只有成功，跳过去做

export{}和PETSC_ARCH（对pets4py很重要）

四）错误

错误如下所示

（奖金元问题：有没有办法在堆栈溢出的代码围栏中设置自动换行？）

Collecting petsc4py Downloading petsc4py-3.12.0.tar.gz (1.8 MB) |████████████████████████████████| 1.8 MB 2.8 MB/s Requirement already satisfied: numpy in ./anaconda3/lib/python3.7/site-packages (from petsc4py) (1.18.1) Building wheels for collected packages: petsc4py Building wheel for petsc4py (setup.py) ... error ERROR: Command errored out with exit status 1: command: /home/breno/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-5qdqmoex/petsc4py/setup.py'"'"'; __file__='"'"'/tmp/pip-install-5qdqmoex/petsc4py/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-khk8pv9d cwd: /tmp/pip-install-5qdqmoex/petsc4py/ Complete output (97 lines): running bdist_wheel running build running build_src running build_py creating build creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/petsc4py copying src/PETSc.py -> build/lib.linux-x86_64-3.7/petsc4py copying src/__init__.py -> build/lib.linux-x86_64-3.7/petsc4py copying src/__main__.py -> build/lib.linux-x86_64-3.7/petsc4py creating build/lib.linux-x86_64-3.7/petsc4py/lib copying src/lib/__init__.py -> build/lib.linux-x86_64-3.7/petsc4py/lib creating build/lib.linux-x86_64-3.7/petsc4py/include creating build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.PETSc_api.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.PETSc.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/numpy.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.i -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/PETSc.pxd -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/__init__.pxd -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/__init__.pyx -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/PETSc.pxd -> build/lib.linux-x86_64-3.7/petsc4py copying src/lib/petsc.cfg -> build/lib.linux-x86_64-3.7/petsc4py/lib running build_ext PETSC_DIR: /home/breno/Documents/petsc PETSC_ARCH: MUMPS-mkl-real-opt version: 3.13.0 release integer-size: 32-bit scalar-type: real precision: double language: CONLY compiler: /home/breno/.openmpi/bin/mpicc linker: /home/breno/.openmpi/bin/mpicc building 'PETSc' extension creating build/temp.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/MUMPS-mkl-real-opt creating build/temp.linux-x86_64-3.7/MUMPS-mkl-real-opt/src /home/breno/.openmpi/bin/mpicc -pthread -B /home/breno/anaconda3/compiler_compat -Wl,--sysroot=/ -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -O2 -march=native -mtune=native -fPIC -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -I/home/breno/Documents/petsc/MUMPS-mkl-real-opt/include -I/home/breno/Documents/petsc/include -Isrc/include -I/home/breno/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/home/breno/anaconda3/include/python3.7m -c src/PETSc.c -o build/temp.linux-x86_64-3.7/MUMPS-mkl-real-opt/src/PETSc.o In file included from src/PETSc.c:4:0: src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_3Sys_28infoAllow’: src/petsc4py.PETSc.c:65427:47: error: too many arguments to function ‘PetscInfoAllow’ __pyx_t_2 = __pyx_f_8petsc4py_5PETSc_CHKERR(PetscInfoAllow(__pyx_v_tval, NULL)); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(27, 163, __pyx_L1_error) ^~~~~~~~~~~~~~ In file included from /home/breno/Documents/petsc/include/petscsys.h:1474:0, from /home/breno/Documents/petsc/include/petscbag.h:4, from /home/breno/Documents/petsc/include/petsc.h:5, from src/petsc4py.PETSc.c:596, from src/PETSc.c:4: /home/breno/Documents/petsc/include/petsclog.h:56:29: note: declared here PETSC_EXTERN PetscErrorCode PetscInfoAllow(PetscBool); ^~~~~~~~~~~~~~ In file included from src/PETSc.c:4:0: src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_3Mat_304matMultSymbolic’: src/petsc4py.PETSc.c:148044:47: warning: implicit declaration of function ‘MatMatMultSymbolic’; did you mean ‘MatProductSymbolic’? [-Wimplicit-function-declaration] __pyx_t_5 = __pyx_f_8petsc4py_5PETSc_CHKERR(MatMatMultSymbolic(__pyx_v_self->mat, __pyx_v_mat->mat, __pyx_v_rval, (&__pyx_v_result->mat))); if (unlikely(__pyx_t_5 == ((int)-1))) __PYX_ERR(36, 1309, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~ MatProductSymbolic src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_3Mat_306matMultNumeric’: src/petsc4py.PETSc.c:148235:47: warning: implicit declaration of function ‘MatMatMultNumeric’; did you mean ‘MatProductNumeric’? [-Wimplicit-function-declaration] __pyx_t_4 = __pyx_f_8petsc4py_5PETSc_CHKERR(MatMatMultNumeric(__pyx_v_self->mat, __pyx_v_mat->mat, __pyx_v_result->mat)); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(36, 1317, __pyx_L1_error) ^~~~~~~~~~~~~~~~~ MatProductNumeric src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_6DMStag_54get1DCoordinateLocationSlot’: src/petsc4py.PETSc.c:265960:3: warning: ‘DMStagGet1dCoordinateLocationSlot’ is deprecated [-Wdeprecated-declarations] __pyx_t_2 = __pyx_f_8petsc4py_5PETSc_CHKERR(DMStagGet1dCoordinateLocationSlot(__pyx_v_self->__pyx_base.dm, __pyx_v_sloc, (&__pyx_v_slot))); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(47, 274, __pyx_L1_error) ^~~~~~~~~ In file included from /home/breno/Documents/petsc/include/petsc.h:22:0, from src/petsc4py.PETSc.c:596, from src/PETSc.c:4: /home/breno/Documents/petsc/include/petscdmstag.h:127:130: note: declared here PETSC_DEPRECATED_FUNCTION("Use DMStagGetProductCoordinateLocationSlot() (since version 3.13") PETSC_STATIC_INLINE PetscErrorCode DMStagGet1dCoordinateLocationSlot(DM dm,DMStagStencilLocation loc,PetscInt *s) {return DMStagGetProductCoordinateLocationSlot(dm,loc,s);} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/PETSc.c:4:0: src/petsc4py.PETSc.c: In function ‘__pyx_pymod_exec_PETSc’: src/petsc4py.PETSc.c:309773:43: error: ‘MATLMVMBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBROYDEN’? __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 78, __pyx_L1_error) ^~~~~~~~~~~ MATLMVMBROYDEN src/petsc4py.PETSc.c:309773:43: note: each undeclared identifier is reported only once for each function it appears in src/petsc4py.PETSc.c:309785:43: error: ‘MATLMVMBADBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBRDN’? __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMBADBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 79, __pyx_L1_error) ^~~~~~~~~~~~~~ MATLMVMBRDN src/petsc4py.PETSc.c:309797:43: error: ‘MATLMVMSYMBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBADBRDN’? __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMSYMBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 80, __pyx_L1_error) ^~~~~~~~~~~~~~ MATLMVMBADBRDN src/petsc4py.PETSc.c:309809:43: error: ‘MATLMVMSYMBADBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMSYMBRDN’? __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMSYMBADBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 81, __pyx_L1_error) ^~~~~~~~~~~~~~~~~ MATLMVMSYMBRDN src/petsc4py.PETSc.c:309821:43: error: ‘MATLMVMDIAGBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBADBRDN’? __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMDIAGBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 82, __pyx_L1_error) ^~~~~~~~~~~~~~~ MATLMVMBADBRDN error: command '/home/breno/.openmpi/bin/mpicc' failed with exit status 1 ---------------------------------------- ERROR: Failed building wheel for petsc4py Running setup.py clean for petsc4py Failed to build petsc4py Installing collected packages: petsc4py Running setup.py install for petsc4py ... error ERROR: Command errored out with exit status 1: command: /home/breno/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-5qdqmoex/petsc4py/setup.py'"'"'; __file__='"'"'/tmp/pip-install-5qdqmoex/petsc4py/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-_npojm20/install-record.txt --single-version-externally-managed --compile --install-headers /home/breno/anaconda3/include/python3.7m/petsc4py cwd: /tmp/pip-install-5qdqmoex/petsc4py/ Complete output (97 lines): running install running build running build_src running build_py creating build creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/petsc4py copying src/PETSc.py -> build/lib.linux-x86_64-3.7/petsc4py copying src/__init__.py -> build/lib.linux-x86_64-3.7/petsc4py copying src/__main__.py -> build/lib.linux-x86_64-3.7/petsc4py creating build/lib.linux-x86_64-3.7/petsc4py/lib copying src/lib/__init__.py -> build/lib.linux-x86_64-3.7/petsc4py/lib creating build/lib.linux-x86_64-3.7/petsc4py/include creating build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.PETSc_api.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.PETSc.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/numpy.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.i -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/PETSc.pxd -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/__init__.pxd -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/include/petsc4py/__init__.pyx -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py copying src/PETSc.pxd -> build/lib.linux-x86_64-3.7/petsc4py copying src/lib/petsc.cfg -> build/lib.linux-x86_64-3.7/petsc4py/lib running build_ext PETSC_DIR: /home/breno/Documents/petsc PETSC_ARCH: MUMPS-mkl-real-opt version: 3.13.0 release integer-size: 32-bit scalar-type: real precision: double language: CONLY compiler: /home/breno/.openmpi/bin/mpicc linker: /home/breno/.openmpi/bin/mpicc building 'PETSc' extension creating build/temp.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/MUMPS-mkl-real-opt creating build/temp.linux-x86_64-3.7/MUMPS-mkl-real-opt/src /home/breno/.openmpi/bin/mpicc -pthread -B /home/breno/anaconda3/compiler_compat -Wl,--sysroot=/ -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -O2 -march=native -mtune=native -fPIC -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -I/home/breno/Documents/petsc/MUMPS-mkl-real-opt/include -I/home/breno/Documents/petsc/include -Isrc/include -I/home/breno/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/home/breno/anaconda3/include/python3.7m -c src/PETSc.c -o build/temp.linux-x86_64-3.7/MUMPS-mkl-real-opt/src/PETSc.o In file included from src/PETSc.c:4:0: src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_3Sys_28infoAllow’: src/petsc4py.PETSc.c:65427:47: error: too many arguments to function ‘PetscInfoAllow’ __pyx_t_2 = __pyx_f_8petsc4py_5PETSc_CHKERR(PetscInfoAllow(__pyx_v_tval, NULL)); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(27, 163, __pyx_L1_error) ^~~~~~~~~~~~~~ In file included from /home/breno/Documents/petsc/include/petscsys.h:1474:0, from /home/breno/Documents/petsc/include/petscbag.h:4, from /home/breno/Documents/petsc/include/petsc.h:5, from src/petsc4py.PETSc.c:596, from src/PETSc.c:4: /home/breno/Documents/petsc/include/petsclog.h:56:29: note: declared here PETSC_EXTERN PetscErrorCode PetscInfoAllow(PetscBool); ^~~~~~~~~~~~~~ In file included from src/PETSc.c:4:0: src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_3Mat_304matMultSymbolic’: src/petsc4py.PETSc.c:148044:47: warning: implicit declaration of function ‘MatMatMultSymbolic’; did you mean ‘MatProductSymbolic’? [-Wimplicit-function-declaration] __pyx_t_5 = __pyx_f_8petsc4py_5PETSc_CHKERR(MatMatMultSymbolic(__pyx_v_self->mat, __pyx_v_mat->mat, __pyx_v_rval, (&__pyx_v_result->mat))); if (unlikely(__pyx_t_5 == ((int)-1))) __PYX_ERR(36, 1309, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~ MatProductSymbolic src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_3Mat_306matMultNumeric’: src/petsc4py.PETSc.c:148235:47: warning: implicit declaration of function ‘MatMatMultNumeric’; did you mean ‘MatProductNumeric’? [-Wimplicit-function-declaration] __pyx_t_4 = __pyx_f_8petsc4py_5PETSc_CHKERR(MatMatMultNumeric(__pyx_v_self->mat, __pyx_v_mat->mat, __pyx_v_result->mat)); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(36, 1317, __pyx_L1_error) ^~~~~~~~~~~~~~~~~ MatProductNumeric src/petsc4py.PETSc.c: In function ‘__pyx_pf_8petsc4py_5PETSc_6DMStag_54get1DCoordinateLocationSlot’: src/petsc4py.PETSc.c:265960:3: warning: ‘DMStagGet1dCoordinateLocationSlot’ is deprecated [-Wdeprecated-declarations] __pyx_t_2 = __pyx_f_8petsc4py_5PETSc_CHKERR(DMStagGet1dCoordinateLocationSlot(__pyx_v_self->__pyx_base.dm, __pyx_v_sloc, (&__pyx_v_slot))); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(47, 274, __pyx_L1_error) ^~~~~~~~~ In file included from /home/breno/Documents/petsc/include/petsc.h:22:0, from src/petsc4py.PETSc.c:596, from src/PETSc.c:4: /home/breno/Documents/petsc/include/petscdmstag.h:127:130: note: declared here PETSC_DEPRECATED_FUNCTION("Use DMStagGetProductCoordinateLocationSlot() (since version 3.13") PETSC_STATIC_INLINE PetscErrorCode DMStagGet1dCoordinateLocationSlot(DM dm,DMStagStencilLocation loc,PetscInt *s) {return DMStagGetProductCoordinateLocationSlot(dm,loc,s);} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/PETSc.c:4:0: src/petsc4py.PETSc.c: In function ‘__pyx_pymod_exec_PETSc’: src/petsc4py.PETSc.c:309773:43: error: ‘MATLMVMBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBROYDEN’? __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 78, __pyx_L1_error) ^~~~~~~~~~~ MATLMVMBROYDEN src/petsc4py.PETSc.c:309773:43: note: each undeclared identifier is reported only once for each function it appears in src/petsc4py.PETSc.c:309785:43: error: ‘MATLMVMBADBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBRDN’? __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMBADBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 79, __pyx_L1_error) ^~~~~~~~~~~~~~ MATLMVMBRDN src/petsc4py.PETSc.c:309797:43: error: ‘MATLMVMSYMBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBADBRDN’? __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMSYMBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 80, __pyx_L1_error) ^~~~~~~~~~~~~~ MATLMVMBADBRDN src/petsc4py.PETSc.c:309809:43: error: ‘MATLMVMSYMBADBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMSYMBRDN’? __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMSYMBADBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 81, __pyx_L1_error) ^~~~~~~~~~~~~~~~~ MATLMVMSYMBRDN src/petsc4py.PETSc.c:309821:43: error: ‘MATLMVMDIAGBRDN’ undeclared (first use in this function); did you mean ‘MATLMVMBADBRDN’? __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVMDIAGBRDN); if (unlikely(!__pyx_t_7)) __PYX_ERR(36, 82, __pyx_L1_error) ^~~~~~~~~~~~~~~ MATLMVMBADBRDN error: command '/home/breno/.openmpi/bin/mpicc' failed with exit status 1 ---------------------------------------- ERROR: Command errored out with exit status 1: /home/breno/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-5qdqmoex/petsc4py/setup.py'"'"'; __file__='"'"'/tmp/pip-install-5qdqmoex/petsc4py/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-_npojm20/install-record.txt --single-version-externally-managed --compile --install-headers /home/breno/anaconda3/include/python3.7m/petsc4py Check the logs for full command output.

1条回答

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1楼 · 发布于 2024-09-27 22:34:14

我试图用当时最新发布的版本3.12.0安装petsc4py，同时安装并配置了PETSc版本3.13.0。这个现在似乎很明显是行不通的，但在documentation中没有明确提到这一点

您可以使用pip install https://bitbucket.org/petsc/petsc4py/issues/137/error-installing-in-anaconda-environment安装未发布的版本，也可以等待正式发布

重要结论

确保您的PETSc版本与petsc4py相同

一）问题

二）版本

三）复制问题

1）使用户安装OpenMPI4.0.3

2）安装PETSc3.13

3）使用`pip`安装`mpi4py`

4）尝试使用`pip`安装`petsc4py`

四）错误

重要结论

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