从MPICH切换到OpenMPI

Question

我的Ubuntu20.04中有mpich和openmpi。

$ dpkg -l | grep mpi | grep lib
...
ii  libmpich-dev:amd64                            3.3.2-2build1                         amd64        Development files for MPICH
ii  libmpich12:amd64                              3.3.2-2build1                         amd64        Shared libraries for MPICH
...
ii  libopenmpi-dev:amd64                          4.0.3-0ubuntu1                        amd64        high performance message passing library -- header files
ii  libopenmpi3:amd64                             4.0.3-0ubuntu1                        amd64        high performance message passing library -- shared library
...
ii  openmpi-bin                                   4.0.3-0ubuntu1                        amd64        high performance message passing library -- binaries
ii  openmpi-common                                4.0.3-0ubuntu1                        all          high performance message passing library -- common files
..
$ dpkg -l | grep mpich
...
ii  mpich                                         3.3.2-2build1                         amd64        Implementation of the MPI Message Passing Interface standard

默认值(可能是因为后来安装的)似乎是mpich。

我怎么换到openmpi?

我想确保所有需要改变的东西实际上都是。到目前为止，我正在考虑标题、可执行文件、库。我不知道哪些是所有的目录，链接等，必须改变。

例如，这里 --建议使用cmake -DMPI_CC_COMPILER=/.../mpicc。有人在评论中提到它起了作用。但是：

1. 我不确定它是否真的修复了所有的标题，等等。
2. 我需要一种方法： 2.1。适用于系统中的所有用户。 2.2。不需要那些宏 2.3。也适用于cmake以外的其他编译方法。

至于2.3，我现在尝试配置petsc

$ ./configure --with-cc=mpicc --with-fc=mpif90 -with-cxx=mpicxx --with- make-np=10 --with-shared-libraries --download-f2cblaslapack --download-mumps --download-scalapack --with-debugging=0 COPTFLAGS="-O -O3 -march=native -mtune=native" FOPTF LAGS="-O -O3 -march=native -mtune=native" CXXOPTFLAGS="-O -O3 -march=native -mtune=native"

我得到了

Your libraries are from MPICH but it appears your mpiexec is from OpenMPI

可以用update-alternatives**?** 修复

我发现了这一点，这让我认为它可以，但在我的系统中，它没有正确地配置：

$ type mpiexec
mpiexec is hashed (/usr/bin/mpiexec)
$ ll /usr/bin/mpiexec
lrwxrwxrwx 1 root root 25 Jan 21 11:11 /usr/bin/mpiexec -> /etc/alternatives/mpiexec
$ ll /etc/alternatives/mpiexec
lrwxrwxrwx 1 root root 24 Jan 21 11:11 /etc/alternatives/mpiexec -> /usr/bin/mpiexec.openmpi
$ ll /usr/bin/mpiexec.openmpi
lrwxrwxrwx 1 root root 7 Apr 15  2020 /usr/bin/mpiexec.openmpi -> orterun

$ type mpirun
mpirun is /usr/bin/mpirun
$ ll /usr/bin/mpirun
lrwxrwxrwx 1 root root 24 Jan 21 11:11 /usr/bin/mpirun -> /etc/alternatives/mpirun
$ ll /etc/alternatives/mpirun
lrwxrwxrwx 1 root root 23 Jan 21 11:11 /etc/alternatives/mpirun -> /usr/bin/mpirun.openmpi
$ ll /usr/bin/mpirun.openmpi
lrwxrwxrwx 1 root root 7 Apr 15  2020 /usr/bin/mpirun.openmpi -> orterun

$ type mpicc
mpicc is hashed (/usr/bin/mpicc)
$ ll /usr/bin/mpicc
lrwxrwxrwx 1 root root 21 Feb 25 18:54 /usr/bin/mpicc -> /etc/alternatives/mpi
$ ll /etc/alternatives/mpi
lrwxrwxrwx 1 root root 20 Feb 25 18:54 /etc/alternatives/mpi -> /usr/bin/mpicc.mpich

相关

1. 用OpenMPI替换MPICH安装
2. CMake :选择mpich而不是openmpi
3. https://unix.stackexchange.com/questions/413099/flip-between-openmpi-and-mpich-as-default-using-linux-terminal
4. 不同的mpi和mpich2文件夹？
5. CMake :选择mpich而不是openmpi
6. 从MPICH切换到OpenMPI
7. 这个？https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=896189
8. 这个？https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=912437
9. https://unix.stackexchange.com/questions/81992/better-way-to-add-alternative-using-update-alternatives
10. https://askubuntu.com/questions/964600/how-to-add-slave-to-existing-update-alternatives-link-group

Answer 1

似乎所有的替代方案，除了一个(链接组mpi)，都已经设置为openmpi了。

$ update-alternatives --get-selections | grep mpi
h5pcc                          auto     /usr/bin/h5pcc.openmpi
mpi                            auto     /usr/bin/mpicc.mpich
mpi-x86_64-linux-gnu           auto     /usr/lib/x86_64-linux-gnu/openmpi/include
mpirun                         auto     /usr/bin/mpirun.openmpi

正确设置链接组mpi (并避免容易出错的单个链接操作)

sudo apt-get install --reinstall openmpi-bin

(拥有mpicc.openmpi的包)。这显然解决了所有的问题。到目前为止，一切都很顺利。

“历史”注释：我发现(奇怪的是，mpicc.openmpi不在update-alternatives中，而不是其他三个链接组)

$ update-alternatives --list mpirun
/usr/bin/mpirun.mpich
/usr/bin/mpirun.openmpi
$ update-alternatives --list h5pcc
/usr/bin/h5pcc.mpich
/usr/bin/h5pcc.openmpi
$ update-alternatives --list mpi-x86_64-linux-gnu
/usr/include/x86_64-linux-gnu/mpich
/usr/lib/x86_64-linux-gnu/openmpi/include
$ update-alternatives --list mpi
/usr/bin/mpicc.mpich

即使它安装在我的系统里

$ ll /usr/bin/mpicc*
lrwxrwxrwx 1 root root  21 Feb 25 18:54 /usr/bin/mpicc -> /etc/alternatives/mpi
-rwxr-xr-x 1 root root 11K Mar 22  2020 /usr/bin/mpicc.mpich
lrwxrwxrwx 1 root root  12 Apr 15  2020 /usr/bin/mpicc.openmpi -> opal_wrapper

为什么一开始就没有呢？我还是不知道。

我决定使用reinstall，因为手动处理链接组可能会很混乱。

$ update-alternatives --query mpi
Name: mpi
Link: /usr/bin/mpicc
Slaves:
 mpiCC /usr/bin/mpiCC
 mpiCC.1.gz /usr/share/man/man1/mpiCC.1.gz
 mpic++ /usr/bin/mpic++
 mpic++.1.gz /usr/share/man/man1/mpic++.1.gz
 mpicc.1.gz /usr/share/man/man1/mpicc.1.gz
 mpicxx /usr/bin/mpicxx
 mpicxx.1.gz /usr/share/man/man1/mpicxx.1.gz
 mpif77 /usr/bin/mpif77
 mpif77.1.gz /usr/share/man/man1/mpif77.1.gz
 mpif90 /usr/bin/mpif90
 mpif90.1.gz /usr/share/man/man1/mpif90.1.gz
 mpifort /usr/bin/mpifort
 mpifort.1.gz /usr/share/man/man1/mpifort.1.gz
Status: auto
Best: /usr/bin/mpicc.mpich
Value: /usr/bin/mpicc.mpich

Alternative: /usr/bin/mpicc.mpich
Priority: 40
Slaves:
 mpiCC /usr/bin/mpicxx.mpich
 mpiCC.1.gz /usr/share/man/man1/mpicxx.mpich.1.gz
 mpic++ /usr/bin/mpicxx.mpich
 mpic++.1.gz /usr/share/man/man1/mpicxx.mpich.1.gz
 mpicc.1.gz /usr/share/man/man1/mpicc.mpich.1.gz
 mpicxx /usr/bin/mpicxx.mpich
 mpicxx.1.gz /usr/share/man/man1/mpicxx.mpich.1.gz
 mpif77 /usr/bin/mpifort.mpich
 mpif77.1.gz /usr/share/man/man1/mpif77.mpich.1.gz
 mpif90 /usr/bin/mpifort.mpich
 mpif90.1.gz /usr/share/man/man1/mpif90.mpich.1.gz
 mpifort /usr/bin/mpifort.mpich
 mpifort.1.gz /usr/share/man/man1/mpifort.mpich.1.gz