Question

我有CentOS 7，我安装了mpicc（它可以在C中运行并编译openmpi）。我也有python 2.7.5并且刚刚安装了pip。我正在运行此命令并收到以下错误：

sudo pip install mpi4py

Collecting mpi4py   Using cached mpi4py-2.0.0.tar.gz Installing
> collected packages: mpi4py   Running setup.py install for mpi4py ...
> error
>     Complete output from command /usr/bin/python2 -u -c "import setuptools,
> tokenize;__file__='/tmp/pip-build-x5jD4O/mpi4py/setup.py';exec(compile(getattr(tokenize,
> 'open', open)(__file__).read().replace('\r\n', '\n'), __file__,
> 'exec'))" install --record /tmp/pip-mpMoZO-record/install-record.txt
> --single-version-externally-managed --compile:
>     running install
>     running build
>     running build_src
>     running build_py
>     creating build
>     creating build/lib.linux-x86_64-2.7
>     creating build/lib.linux-x86_64-2.7/mpi4py
>     copying src/__main__.py -> build/lib.linux-x86_64-2.7/mpi4py
>     copying src/__init__.py -> build/lib.linux-x86_64-2.7/mpi4py
>     creating build/lib.linux-x86_64-2.7/mpi4py/include
>     creating build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>     copying src/include/mpi4py/mpi4py.MPI.h -> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>     copying src/include/mpi4py/mpi4py.MPI_api.h -> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>     copying src/include/mpi4py/mpi4py.h -> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>     copying src/include/mpi4py/__init__.pxd -> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>     copying src/include/mpi4py/libmpi.pxd -> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>     copying src/include/mpi4py/MPI.pxd -> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>     copying src/include/mpi4py/__init__.pyx -> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>     copying src/include/mpi4py/mpi.pxi -> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>     copying src/include/mpi4py/mpi4py.i -> build/lib.linux-x86_64-2.7/mpi4py/include/mpi4py
>     copying src/MPI.pxd -> build/lib.linux-x86_64-2.7/mpi4py
>     copying src/libmpi.pxd -> build/lib.linux-x86_64-2.7/mpi4py
>     running build_clib
>     MPI configuration: [mpi] from 'mpi.cfg'
>     checking for library 'lmpe' ...
>     gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -c _configtest.c -o _configtest.o
>     gcc -pthread _configtest.o -llmpe -o _configtest
>     /bin/ld: cannot find -llmpe
>     collect2: error: ld returned 1 exit status
>     failure.
>     removing: _configtest.c _configtest.o
>     building 'mpe' dylib library
>     creating build/temp.linux-x86_64-2.7
>     creating build/temp.linux-x86_64-2.7/src
>     creating build/temp.linux-x86_64-2.7/src/lib-pmpi
>     gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -c src/lib-pmpi/mpe.c -o build/temp.linux-x86_64-2.7/src/lib-pmpi/mpe.o
>     creating build/lib.linux-x86_64-2.7/mpi4py/lib-pmpi
>     gcc -pthread -shared -Wl,-z,relro build/temp.linux-x86_64-2.7/src/lib-pmpi/mpe.o -o
> build/lib.linux-x86_64-2.7/mpi4py/lib-pmpi/libmpe.so
>     checking for library 'vt-mpi' ...
>     gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -c _configtest.c -o _configtest.o
>     gcc -pthread _configtest.o -lvt-mpi -o _configtest
>     /bin/ld: cannot find -lvt-mpi
>     collect2: error: ld returned 1 exit status
>     failure.
>     removing: _configtest.c _configtest.o
>     checking for library 'vt.mpi' ...
>     gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -c _configtest.c -o _configtest.o
>     gcc -pthread _configtest.o -lvt.mpi -o _configtest
>     /bin/ld: cannot find -lvt.mpi
>     collect2: error: ld returned 1 exit status
>     failure.
>     removing: _configtest.c _configtest.o
>     building 'vt' dylib library
>     gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -c src/lib-pmpi/vt.c -o build/temp.linux-x86_64-2.7/src/lib-pmpi/vt.o
>     gcc -pthread -shared -Wl,-z,relro build/temp.linux-x86_64-2.7/src/lib-pmpi/vt.o -o
> build/lib.linux-x86_64-2.7/mpi4py/lib-pmpi/libvt.so
>     checking for library 'vt-mpi' ...
>     gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -c _configtest.c -o _configtest.o
>     gcc -pthread _configtest.o -lvt-mpi -o _configtest
>     /bin/ld: cannot find -lvt-mpi
>     collect2: error: ld returned 1 exit status
>     failure.
>     removing: _configtest.c _configtest.o
>     checking for library 'vt.mpi' ...
>     gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -c _configtest.c -o _configtest.o
>     gcc -pthread _configtest.o -lvt.mpi -o _configtest
>     /bin/ld: cannot find -lvt.mpi
>     collect2: error: ld returned 1 exit status
>     failure.
>     removing: _configtest.c _configtest.o
>     building 'vt-mpi' dylib library
>     gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -c src/lib-pmpi/vt-mpi.c -o build/temp.linux-x86_64-2.7/src/lib-pmpi/vt-mpi.o
>     gcc -pthread -shared -Wl,-z,relro build/temp.linux-x86_64-2.7/src/lib-pmpi/vt-mpi.o -o
> build/lib.linux-x86_64-2.7/mpi4py/lib-pmpi/libvt-mpi.so
>     checking for library 'vt-hyb' ...
>     gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -c _configtest.c -o _configtest.o
>     gcc -pthread _configtest.o -lvt-hyb -o _configtest
>     /bin/ld: cannot find -lvt-hyb
>     collect2: error: ld returned 1 exit status
>     failure.
>     removing: _configtest.c _configtest.o
>     checking for library 'vt.ompi' ...
>     gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -c _configtest.c -o _configtest.o
>     gcc -pthread _configtest.o -lvt.ompi -o _configtest
>     /bin/ld: cannot find -lvt.ompi
>     collect2: error: ld returned 1 exit status
>     failure.
>     removing: _configtest.c _configtest.o
>     building 'vt-hyb' dylib library
>     gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -c src/lib-pmpi/vt-hyb.c -o build/temp.linux-x86_64-2.7/src/lib-pmpi/vt-hyb.o
>     gcc -pthread -shared -Wl,-z,relro build/temp.linux-x86_64-2.7/src/lib-pmpi/vt-hyb.o -o
> build/lib.linux-x86_64-2.7/mpi4py/lib-pmpi/libvt-hyb.so
>     running build_ext
>     MPI configuration: [mpi] from 'mpi.cfg'
>     checking for MPI compile and link ...
>     gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -c _configtest.c -o _configtest.o
>     _configtest.c:2:17: fatal error: mpi.h: No such file or directory
>      #include <mpi.h>
>                      ^
>     compilation terminated.
>     failure.
>     removing: _configtest.c _configtest.o
>     error: Cannot compile MPI programs. Check your configuration!!!

我尝试了迄今为止找到的所有解决方案，似乎没有任何解决方案，有人对这个问题有什么想法吗？谢谢

Answer 1

遇到相同的问题并通过以下方法解决：

yum install openmpi-devel
export CC=/usr/lib64/openmpi/bin/mpicc
pip install mpi4py

Answer 2

似乎你错过了在Centos上安装OpenMPI的development文件，这里的关键是：

_configtest.c:2:17: fatal error: mpi.h: No such file or directory
  #include <mpi.h>

您应该通过openmpi-devel安装yum（或同等版本），您应该重新安装mpi4py模块。

Answer 3

您也可以尝试：

CentOS

yum install python-mpi4py
yum install python3-mpi4py

Debian

apt install python-mpi4py
apt install python3-mpi4py

Answer 4

对于遇到此问题的其他任何人，我都会发布此答案，以防万一您遇到与我类似的问题。 @francis的答案是关键。在我的Centos7.7系统上，我能够使用@ iakov-nakhimovski建议的CC环境变量来安装mpi4py，但它无法正常工作，并且出现运行时错误。问题原来是系统上安装的其他软件在其路径上有其自己的python安装，这会干扰mpi4py的设置。解决方案是从路径中删除此其他安装，并加载openmpi-devel软件包随附的openmpi模块（我认为）。

module load mpi/openmpi-x86_64

然后使用pip安装mpi4py（请注意，由于环境模块将所有这些工具放入路径中，因此无需显式定义CC = mpicc）。当运行需要mpi4py的python脚本时，您还需要加载此模块。

无法在CentOS 7上安装mpi4py

4 个答案: