如何在Linux羣集上安裝numpy？

我是一個共享linux（RHEL 4）羣集上的用戶（他對這個東西也相當陌生），我試圖安裝numpy。該集羣實際上安裝了它，但它使用了Python 2.3版本，幾乎所有的腳本都只適用於Python 2.7。所以我下載了numpy-1.6.1，解壓縮了它，運行了setup並得到了以下內容（見下文）。我也嘗試了「安裝」而不是構建參數，但這也不起作用。我一直在努力幾個小時才能使這個工作，所以我非常感謝幫助。有什麼想法嗎？如何在Linux羣集上安裝numpy？

$ Python-2.7.2/python setup.py build --fcompiler=gfortran

Running from numpy source directory.non-existing path in 'numpy/distutils': 'site.cfg' F2PY Version 2 blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /usr/local/lib64 libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib64 libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE

atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries ptf77blas,ptcblas,atlas not found in /usr/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/lib NOT AVAILABLE

atlas_blas_info: libraries f77blas,cblas,atlas not found in /usr/local/lib64 libraries f77blas,cblas,atlas not found in /usr/local/lib customize GnuFCompiler Found executable /usr/bin/g77 gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler using config compiling '_configtest.c':

/* This file is generated from numpy/distutils/system_info.py */ void ATL_buildinfo(void); int main(void) { ATL_buildinfo(); return 0; }

C compiler: /usr/bin/gcc4 -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

compile options: '-c' gcc4: _configtest.c /usr/bin/gcc4 _configtest.o -L/usr/lib64 -lf77blas -lcblas -latlas -o _configtest ATLAS version 3.7.11 built by root on Mon Jun 5 10:14:12 EDT 2006: UNAME : Linux intel1.lsf.platform.com 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux INSTFLG :
MMDEF : /export/madison/src/roll/hpc/BUILD/ATLAS/CONFIG/ARCHS/P4E64SSE3/gcc/gemm ARCHDEF : /export/madison/src/roll/hpc/BUILD/ATLAS/CONFIG/ARCHS/P4E64SSE3/gcc/misc F2CDEFS : -DAdd__ -DStringSunStyle CACHEEDGE: 393216 F77 : /usr/bin/g77, version GNU Fortran (GCC) 3.4.5 20051201 (Red Hat 3.4.5-2) F77FLAGS : -fomit-frame-pointer -O -m64 CC : /usr/bin/gcc, version gcc (GCC) 3.4.5 20051201 (Red Hat 3.4.5-2) CC FLAGS : -fomit-frame-pointer -O3 -funroll-all-loops -m64 MCC : /usr/bin/gcc, version gcc (GCC) 3.4.5 20051201 (Red Hat 3.4.5-2)
MCCFLAGS : -fomit-frame-pointer -O -m64 success! removing: _configtest.c _configtest.o _configtest FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib64'] language = c define_macros = [('ATLAS_INFO', '"\"3.7.11\""')]

FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib64'] language = c define_macros = [('ATLAS_INFO', '"\"3.7.11\""')]

lapack_opt_info: lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in /usr/local/lib64 libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib64
libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE

NOT AVAILABLE

atlas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64 libraries lapack_atlas not found in /usr/local/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries ptf77blas,ptcblas,atlas not found in /usr/lib64 libraries lapack_atlas not found in /usr/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2 libraries lapack_atlas not found in /usr/lib/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib numpy.distutils.system_info.atlas_threads_info
NOT AVAILABLE

atlas_info: libraries f77blas,cblas,atlas not found in /usr/local/lib64 libraries lapack_atlas not found in /usr/local/lib64 libraries f77blas,cblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib64 numpy.distutils.system_info.atlas_info FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib64'] language = f77 define_macros = [('ATLAS_INFO', '"\"3.7.11\""')]

FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib64'] language = f77 define_macros = [('ATLAS_INFO', '"\"3.7.11\""')]

running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building py_modules sources building library "npymath" sources customize Gnu95FCompiler Found executable /usr/bin/gfortran customize Gnu95FCompiler using config C compiler: /usr/bin/gcc4 -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/scratch/groups/crabtree/Python-2.7.2/Include -I/scratch/groups/crabtree/Python-2.7.2 -c' gcc4: _configtest.c /usr/bin/gcc4 _configtest.o -o _configtest success! removing: _configtest.c _configtest.o _configtest C compiler: /usr/bin/gcc4 -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/scratch/groups/crabtree/Python-2.7.2/Include -I/scratch/groups/crabtree/Python-2.7.2 -c' gcc4: _configtest.c _configtest.c:1: warning: conflicting types for built-in function 'exp' /usr/bin/gcc4 _configtest.o -o _configtest _configtest.o(.text+0x5): In function main': /scratch/groups/crabtree/numpy-1.6.1/_configtest.c:6: undefined reference to exp' collect2: ld returned 1 exit status _configtest.o(.text+0x5): In function main': /scratch/groups/crabtree/numpy-1.6.1/_configtest.c:6: undefined reference to exp' collect2: ld returned 1 exit status failure. removing: _configtest.c _configtest.o C compiler: /usr/bin/gcc4 -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/scratch/groups/crabtree/Python-2.7.2/Include -I/scratch/groups/crabtree/Python-2.7.2 -c' gcc4: _configtest.c _configtest.c:1: warning: conflicting types for built-in function 'exp' /usr/bin/gcc4 _configtest.o -lm -o _configtest success! removing: _configtest.c _configtest.o _configtest building extension "numpy.core._sort" sources adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources. adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources. executing numpy/core/code_generators/generate_numpy_api.py adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h' to sources. numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h'] building extension "numpy.core.multiarray" sources adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources. adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources. executing numpy/core/code_generators/generate_numpy_api.py adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h' to sources. numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h'] building extension "numpy.core.umath" sources adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources. adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources. executing numpy/core/code_generators/generate_ufunc_api.py adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h' to sources. adding 'build/src.linux-x86_64-2.7/numpy/core/src/umath' to include_dirs. numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/src/umath/funcs.inc', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h'] building extension "numpy.core.scalarmath" sources adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources. adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources. executing numpy/core/code_generators/generate_numpy_api.py adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h' to sources. executing numpy/core/code_generators/generate_ufunc_api.py adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h' to sources. numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h'] building extension "numpy.core._dotblas" sources adding 'numpy/core/blasdot/_dotblas.c' to sources. building extension "numpy.core.umath_tests" sources building extension "numpy.core.multiarray_tests" sources building extension "numpy.lib._compiled_base" sources building extension "numpy.numarray._capi" sources building extension "numpy.fft.fftpack_lite" sources building extension "numpy.linalg.lapack_lite" sources adding 'numpy/linalg/lapack_litemodule.c' to sources. adding 'numpy/linalg/python_xerbla.c' to sources. building extension "numpy.random.mtrand" sources C compiler: /usr/bin/gcc4 -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/scratch/groups/crabtree/Python-2.7.2/Include -I/scratch/groups/crabtree/Python-2.7.2 -c' gcc4: _configtest.c /usr/bin/gcc4 _configtest.o -o _configtest _configtest failure. removing: _configtest.c _configtest.o _configtest building data_files sources build_src: building npy-pkg config files running build_py copying numpy/version.py -> build/lib.linux-x86_64-2.7/numpy copying numpy/config.py -> build/lib.linux-x86_64-2.7/numpy copying build/src.linux-x86_64-2.7/numpy/config.py -> build/lib.linux-x86_64-2.7/numpy copying numpy/distutils/config.py -> build/lib.linux-x86_64-2.7/numpy/distutils copying build/src.linux-x86_64-2.7/numpy/distutils/config.py -> build/lib.linux-x86_64-2.7/numpy/distutils running build_clib customize UnixCCompiler customize UnixCCompiler using build_clib running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize Gnu95FCompiler customize Gnu95FCompiler using build_ext building 'numpy.core._dotblas' extension compiling C sources C compiler: /usr/bin/gcc4 -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

compile options: '-DATLAS_INFO="\"3.7.11\"" -Inumpy/core/blasdot -Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/scratch/groups/crabtree/Python-2.7.2/Include -I/scratch/groups/crabtree/Python-2.7.2 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c' gcc4: numpy/core/blasdot/_dotblas.c numpy/core/blasdot/_dotblas.c: In function 'dotblas_matrixproduct': numpy/core/blasdot/_dotblas.c:239: warning: comparison of distinct pointer types lacks a cast numpy/core/blasdot/_dotblas.c:257: warning: passing argument 3 of '*(PyArray_API + 2240u)' from incompatible pointer type numpy/core/blasdot/_dotblas.c:292: warning: passing argument 3 of '*(PyArray_API + 2240u)' from incompatible pointer type gcc -pthread -shared build/temp.linux-x86_64-2.7/numpy/core/blasdot/_dotblas.o -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.7 -lf77blas -lcblas -latlas -o build/lib.linux-x86_64-2.7/numpy/core/_dotblas.so /usr/bin/ld: /usr/lib64/libcblas.a(cblas_dgemm.o): relocation R_X86_64_32 against a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/libcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status /usr/bin/ld: /usr/lib64/libcblas.a(cblas_dgemm.o): relocation R_X86_64_32 against a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/libcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status error: Command "gcc -pthread -shared build/temp.linux-x86_64-2.7/numpy/core/blasdot/_dotblas.o -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.7 -lf77blas -lcblas -latlas -o build/lib.linux-x86_64-2.7/numpy/core/_dotblas.so" failed with exit status 1

來源

2011-10-21 user1006351

我的蟒蛇2.7和numpy的，SciPy的各個版本之間了兼容性問題的地段，matplotlib ......我不得不安裝。最後，最好的選擇是使用apt-get工具（在ubuntu下），確保所有軟件包之間的版本兼容。

現在，在閱讀您的日誌時，我發現您沒有安裝LAPACK。首先看到BLAS和/或ATLAS包。您還需要以前安裝Fortran編譯器。還有包含所需頭文件和靜態文件的python2.7-dev軟件包。所以，我會按照你的情況的過程如下：

什麼是海灣合作委員會的版本你有嗎？

[email protected]:~$ gcc -v 
Using built-in specs. 
Target: i686-linux-gnu 
Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.4.4-14ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.4 --enable-shared --enable-multiarch --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc --enable-targets=all --disable-werror --with-arch-32=i686 --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu 
Thread model: posix 
gcc version 4.4.5 (Ubuntu/Linaro 4.4.4-14ubuntu5)

檢查你有gcc版本4至少（能夠處理64位浮點作爲numpy的需要他們）或更新您的O.S.小心！更新GCC不是一個無辜的軟件包調優...

安裝Fortran編譯器。
最終安裝LAPACK庫。它會通過預編譯大部分例程併爲CPU調整它們來嚴重加速numpy。
安裝python-dev的

，那麼你可能python setup build。

希望這有幫助！

來源

2011-10-21 08:03:38 Louis

如何在Linux羣集上安裝numpy？

回答

相關問題