从 MPICH 切换到 OpenMPI [英] Switch from MPICH to OpenMPI

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本文介绍了从 MPICH 切换到 OpenMPI的处理方法,对大家解决问题具有一定的参考价值,需要的朋友们下面随着小编来一起学习吧!

问题描述

我的 Ubuntu 20.04 中有 mpich 和 openmpi.

I have both mpich and openmpi in my Ubuntu 20.04.

$ 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(可能是因为后来安装)似乎是 mpich.

The default (probably because it was installed later) appears to be mpich.

我将如何更改为 openmpi?

我想确保所有需要更改的内容都是真实的.到目前为止,我正在考虑头文件、可执行文件、库.我不知道哪些目录、链接等都必须更改.

I want to make sure that everything that needs to be changed actually is. So far, I am thinking about headers, executable, libraries. I do not know which are all directories, links, etc., that have to change.

例如,这里建议 cmake -DMPI_CC_COMPILER=/.../mpicc.并且在评论中提到它有效.但是:

For instance, here it is suggested cmake -DMPI_CC_COMPILER=/.../mpicc. And it was mentioned in comments that it worked. But:

  1. 我不确定它是否真的修复了所有标题等

  1. I am not sure it actually fixes all headers, etc.

我需要一种方法:

2.1.适用于系统中的所有用户

2.1. Works for all users in the system

2.2.不需要那些宏

2.3.也适用于 cmake

至于2.3,我现在尝试配置petsc

As for 2.3, I tried now to configure 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

<小时>

这个问题可以用 update-alternatives 解决吗?


Can this be fixed with update-alternatives?

我发现了这个,这让我觉得它可以,但在我的系统中它没有正确配置:

I found this, which makes me think it can, but in my system it is not correctly configured:

$ 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

<小时>

相关

  1. 用 OpenMPI 替换 MPICH 安装
  2. CMake:通过 openmpi 选择 mpich
  3. https://unix.stackexchange.com/questions/413099/flip-between-openmpi-and-mpich-as-default-using-linux-terminal
  4. mpi 和 mpich2 文件夹的区别?
  5. CMake:通过 openmpi 选择 mpich
  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

推荐答案

似乎都替代方案,除了一个(链接组 mpi),已经为openmpi设置了

It seems all alternatives, except for one (link group mpi), were already set for openmpi

$ 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)

To set link group mpi properly (and avoiding error-prone individual link operations)

sudo apt-get install --reinstall openmpi-bin

(拥有 mpicc.openmpi 的包).这显然解决了所有问题.到目前为止,它运行良好.

(the package owning mpicc.openmpi). This apparently fixed everything. So far it is working fine.

历史"注意:我发现(奇怪的是)mpicc.openmpi 不在 update-alternatives 中,而不是其他 3 个链接组

"Historical" note: I had found that (strangely) mpicc.openmpi was not in update-alternatives, as opposed to the other 3 link groups

$ 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中

even if it was installed in my system

$ 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

为什么不是一开始呢?我还是不知道.

Why would it not be in the first place? I still don't know.

我决定使用 reinstall,因为手动处理链接组可能很麻烦

I decided to go with the reinstall, since handling the link group manually might have been a mess

$ 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

这篇关于从 MPICH 切换到 OpenMPI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IT屋!

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