f2py:在fortran中使用openMP并行失败

问题描述

我正在尝试使用f2py编译将openMP用于python的fortran例程.

I am trying to compile a fortran routine that uses openMP for python using f2py.

这是文件bsp.f90:

module OTmod
  !$ use omp_lib
  implicit none

  public :: get_threads

contains

  function get_threads() result(nt)
    integer :: nt

    nt = 0
    !$ nt = omp_get_max_threads()

    !$omp parallel num_threads(nt)
        write( *, * ) 'hello world!'
    !$omp end parallel

  end function get_threads

end module OTmod

如果我用它编译

f2py -m testmod --fcompiler=gfortran --f90flags='-fopenmp' -lgomp -c bsp.f90

编译有效，但是将其导入python失败并显示错误

compilation works, but importing it to python fails with the error

ImportError: dlopen(/Users/USER/omp_py/testmod/testmod.cpython-36m-darwin.so, 2): Symbol not found: _GOMP_parallel
  Referenced from: /Users/USER/omp_py/testmod/testmod.cpython-36m-darwin.so
  Expected in: flat namespace
 in /Users/USER/omp_py/testmod/testmod.cpython-36m-darwin.so

但是，如果我只删除构成并行循环的两行

However if I remove only the two lines that make the parallel loop

!$omp parallel num_threads(nt)

和

!$omp end parallel

然后导入到python并执行它可以工作，因此omp_get_max_threads()可以工作，但是并行循环导致它失败.这是Anaconda和我的brew install gcc之间的不匹配吗?我该如何解决?

then importing to python and executing it works, so omp_get_max_threads() works, but the parallel loop causes it to fail. Is this some mismatch between Anaconda and my brew install gcc? How can I fix this?

下面的系统设置信息

macOS 10.13

macOS 10.13

Python 3.6.2 |Anaconda custom (x86_64)| (default, Sep 21 2017, 18:29:43)
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin

gfortran -v

Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/7.2.0/libexec/gcc/x86_64-apple-darwin17.0.0/7.2.0/lto-wrapper
Target: x86_64-apple-darwin17.0.0
Configured with: ../configure --build=x86_64-apple-darwin17.0.0 --prefix=/usr/local/Cellar/gcc/7.2.0 --libdir=/usr/local/Cellar/gcc/7.2.0/lib/gcc/7 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-7 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --enable-checking=release --with-pkgversion='Homebrew GCC 7.2.0' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues --disable-nls
Thread model: posix
gcc version 7.2.0 (Homebrew GCC 7.2.0)

f2py -c --help-fcompiler

Gnu95FCompiler instance properties:
  archiver        = ['/usr/local/bin/gfortran', '-cr']
  compile_switch  = '-c'
  compiler_f77    = ['/usr/local/bin/gfortran', '-Wall', '-g', '-ffixed-
                    form', '-fno-second-underscore', '-m64', '-fPIC', '-O3', '
                    -funroll-loops']
  compiler_f90    = ['/usr/local/bin/gfortran', '-Wall', '-g', '-fno-second-
                    underscore', '-m64', '-fPIC', '-O3', '-funroll-loops']
  compiler_fix    = ['/usr/local/bin/gfortran', '-Wall', '-g', '-ffixed-
                    form', '-fno-second-underscore', '-Wall', '-g', '-fno-
                    second-underscore', '-m64', '-fPIC', '-O3', '-funroll-
                    loops']
  libraries       = ['gfortran']
  library_dirs    = ['/usr/local/Cellar/gcc/7.2.0/lib/gcc/7/gcc/x86_64-apple
                    -darwin17.0.0/7.2.0']
  linker_exe      = ['/usr/local/bin/gfortran', '-Wall', '-Wall']
  linker_so       = ['/usr/local/bin/gfortran', '-Wall', '-g', '-m64', '-
                    Wall', '-g', '-undefined', 'dynamic_lookup', '-bundle']
  object_switch   = '-o '
  ranlib          = ['/usr/local/bin/gfortran']
  version         = LooseVersion ('7.2.0')
  version_cmd     = ['/usr/local/bin/gfortran', '-dumpversion']
Fortran compilers found:
  --fcompiler=gnu95  GNU Fortran 95 compiler (7.2.0)

otool -L testmod.cpython-36m-darwin.so

/Users/USER/omp_py/testmod/testmod.cpython-36m-darwin.so:
    @rpath/libgomp.1.dylib (compatibility version 2.0.0, current version 2.0.0)
    @rpath/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.0.0)
    /usr/local/lib/gcc/7/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
    @rpath/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)

推荐答案

我不确定如何解决此问题以进行动态链接.它主要与与LD_LIBRARY_PATH相关的问题有关.

I am not sure how to solve this issue for dynamic linking. It mostly has to do with something related to LD_LIBRARY_PATH or something.

但是，作为解决方法，您可以static链接库

But as a workaround you can do static linking of the library

将-static选项添加到setup.py

extra_link_args=['-lgomp -static']

这将消除在运行时定位依赖项的需求

This will remove the need for locating the dependency at run-time

这篇关于f2py:在fortran中使用openMP并行失败的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持！