Join Log in
Score:2
sfwalter avatar Ubuntu

How Do I change the Environmental Variables for OpenMPI?

cn flag
sfwalter

I have Ubuntu 20.04 installed and need to install OpenMPI 3.1.6 with gcc 8.4.0.

I downloaded the tar ball from OpenMPI and installed it with the following command

tar-xzf openmpi-3.1.6.tar.gz && cd openmpi-3.1.6
PARGS="env CC=/usr/bin/gcc FC=/usr/bin/gfortran CXX=/usr/bin/g++"
ARGS=" --enable-shared --enable-mpi-fortran=usempi"
ARGS+=" --enable-mpi-thread-multiple"
ARGS+=" --prefix=/openmpi/3.1.6/gcc/8.4.0"
mkdir -p build && cd build
$PARGS ../configure $ARGS
$PARGS make -j8 && make install

It installed just fine, no problems. But when I try

mpirun --version

I get the following error

Command 'mpirun' not found, but can be installed with:

and then gives various options using sudo apt-get (which is how I installed it originally, but it doesn't support 3.1.6).

I assumed it had to do with the environmental variables, that Linux just can't find the software. So I went looking and found that in the OpenMPI FAQ, it mentions the following:

"assuming that you have already adjusted your PATH and/or LD_LIBRARY_PATH environment variables to the new location where Open MPI now resides"

...but then it doesn't say how to do that. I tried searching but it talks about all kinds of different ~/.FILE (where file is bash or lib64 or lib32 or other files).

What do I actually have to change in the environment variables and in which file? I use the Ubuntu terminal for pretty much everything.

============================================ Thank you, ubfan1! I had to add the following to /.profile:

# set the OpenMPI path
export OMPI=/openmpi/3.1.6/gcc/8.4.0
export PATH=$PATH:$OMPI/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$OMPI/lib

And now it works! My system can find mpirun and the version is 3.1.6!

223
1 + 2
N0rbert avatar
zw flag
N0rbert
What was wrong with OpenMPI 4.0.3 from [official repositories](https://packages.ubuntu.com/focal/libopenmpi-dev)? What is your final idea?
0
Reply
sfwalter avatar
cn flag
sfwalter
The software I am using doesn't run with OpenMPI that is newer than 3.1.6. It's research code so it doesn't get updated when other packages update.
0
Reply
Score:1
avatar Ubuntu
cc flag
ubfan1

Look in your home directory's .profile to see how to add things to your PATH.
Where you installed the openmpi probably has subdirectories named bin, lib64, etc. For example, $HOME/openMPI is where you selected to install it, so add $HOME/openMPI/bin to your PATH at the end of your .profile: export PATH="$HOME/openMPI/bin:$PATH" Then add the line:" export LD_LIBRARY_PATH=$HOME/openMPI/lib64 (assuming you have no existing LD_LIBRARY_PATH.) Now that you have a location ...openMPI/bin early in your PATH, you can override the standard system commands by putting new ones there, like a link named gcc to the gcc-8.4 version (which is available in 20.04). If you needed a version of gcc not available in the standard packages, you could simply put the entire executable (from wherever you get it) in place of the link. Maybe you prefer not to override gcc every time you login. In that case, just set up a script to run instead of putting the changes into your .profile.

The usual gotchas:

  1. Your login does not really create a login shell, so .profile is not executed (Usually not an Ubuntu problem, but all the suggestions for putting PATH mods into .bashrc stem from this issue.
  2. You made a .bash_profile which overrides the .profile -- well you should know if you did that, and modify .bash_profile instead.
  3. Suggestions to modify /etc/alternatives to change system default gcc will basically cranch your system the next time you update and need the standard, released, tested compiler.

Your path addition probably should start with a /, so /home/openmpi/... rather than just openmpi/... However, look in the openmpi directory, and see if there is a bin directory, that is the one I expect if there are actually openmpi executables to run. Into that one you can add the gcc link to the lower level gcc...bin just to keep all the openmpi programs together. Note that the gcc 8.4 is available as a standard package in Ubuntu 20.04, but if your openmpi install has one, it's OK to use it, it just won't get any updates, if any.

0 + 3
sfwalter avatar
cn flag
sfwalter
Thank you so much for this. What I am not sure about...my .profile has things like the following: # set PATH so it includes user's private bin if it exists if [ -d "$HOME/bin" ] ; then PATH="$HOME/bin:$PATH" fi So would I add # set PATH for OpenMPI (note that it's not in $HOME/openmpi, rather one directory above...is that a problem? if [ -d "openmpi/3.1.6/gcc/8.4.0/bin" ] ; then PATH="openmpi/3.1.6/gcc/8.4.0/bin:$PATH" fi Does that look right?
0
Reply
sfwalter avatar
cn flag
sfwalter
It worked! # set the OpenMPI path export OMPI=/openmpi/3.1.6/gcc/8.4.0 export PATH=$PATH:$OMPI/bin export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$OMPI/lib
0
Reply
cc flag
ubfan1
Easier for you to add to your original posting, and you get to format it as code.
0
Reply
ธงชาติไทย
Elon Musk
I sit in a Tesla and translated this thread with Ai:

mangohost

Post an answer

Most people don’t grasp that asking a lot of questions unlocks learning and improves interpersonal bonding. In Alison’s studies, for example, though people could accurately recall how many questions had been asked in their conversations, they didn’t intuit the link between questions and liking. Across four studies, in which participants were engaged in conversations themselves or read transcripts of others’ conversations, people tended not to realize that question asking would influence—or had influenced—the level of amity between the conversationalists.