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I would like to install openmpi from repository and need to use it with GCC. The problem is I have installed intel libraries too and it causes problems like this: 

mpicc.openmpi --version
mpicc.openmpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory

Version of my GCC is:

gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 20160609

I'm trying to install openmpi with following command:

sudo aptitude install  openmpi-bin libopenmpi-dev

So, how can I install OpenMPI from repositories in the way which would ignore intel libraries and use only GCC?

EDIT

which mpicc.openmpi
/usr/bin/mpicc.openmpi

ldd $(which mpicc.openmpi)
linux-vdso.so.1 =>  (0x00007fffd6fc0000)
libopen-pal.so.13 => /usr/local/lib/libopen-pal.so.13 (0x00007f9b0c8d0000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f9b0c6b3000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f9b0c2e9000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f9b0bfe0000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f9b0bddc000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f9b0bbd3000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f9b0b9d0000)
libimf.so => not found
libsvml.so => not found
libirng.so => not found
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f9b0b7b9000)
/lib64/ld-linux-x86-64.so.2 (0x000056030ed59000)
libintlc.so.5 => not found

I've installed intel package Intel® Parallel Studio XE | Intel® Software manually (i.e., ./install_gui.sh).

EDIT 2

I tried to reinstall OpenMPI with 

sudo apt-get install --reinstall openmpi-bin libopenmpi-dev

and with 

sudo apt-get purge openmpi-bin libopenmpi-dev
sudo apt-get install openmpi-bin libopenmpi-dev

but none of them had the desired effect, library still links against intel libraries.

Intel libraries are located in /opt/intel.

EDIT 3

ls -l /usr/bin/mpicc.openmpi /usr/bin/opal_wrapper; apt-cache policy openmpi-bin libopenmpi-dev

lrwxrwxrwx 1 root root    12 Feb 25  2016 /usr/bin/mpicc.openmpi -> opal_wrapper
-rwxr-xr-x 1 root root 18928 Feb 25  2016 /usr/bin/opal_wrapper


apt-cache policy openmpi-bin libopenmpi-dev
openmpi-bin:
  Installed: 1.10.2-8ubuntu1
  Candidate: 1.10.2-8ubuntu1
  Version table:
 *** 1.10.2-8ubuntu1 500
        500 http://at.archive.ubuntu.com/ubuntu xenial/universe amd64 Packages
        100 /var/lib/dpkg/status
libopenmpi-dev:
  Installed: 1.10.2-8ubuntu1
  Candidate: 1.10.2-8ubuntu1
  Version table:
 *** 1.10.2-8ubuntu1 500
        500 http://at.archive.ubuntu.com/ubuntu xenial/universe amd64 Packages
        100 /var/lib/dpkg/status
Alexandros Markopoulos
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1 Answers1

3

  • As it seems, the Intel mpicc.openmpi overwrote the official one from repository or one of its linked libraries.

    Here is my output of a official install from repository:

      ~$ dpkg -S /usr/bin/mpicc.openmpi
  libopenmpi-dev: /usr/bin/mpicc.openmpi

  ~$ ldd /usr/bin/mpicc.openmpi
      linux-vdso.so.1 =>  (0x00007ffd785f4000)
      libopen-pal.so.13 => /usr/lib/libopen-pal.so.13 (0x00007ff1d848d000)
      libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007ff1d8270000)
      libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007ff1d7ea6000)
      libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007ff1d7ca2000)
      librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007ff1d7a9a000)
      libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007ff1d7896000)
      libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5 (0x00007ff1d765c000)
      /lib64/ld-linux-x86-64.so.2 (0x000056499326f000)
      libnuma.so.1 => /usr/lib/x86_64-linux-gnu/libnuma.so.1 (0x00007ff1d7450000)
      libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x00007ff1d7246000)

    It does not relay on those missing libraries.

  • To fix it you can reinstall libopenmpi:

      sudo apt-get install --reinstall openmpi-bin libopenmpi-dev

  • Also notice /usr/local/lib/libopen-pal.so.13. It's in /usr/local/lib/ folder so it has higher priority then official one in /usr/lib/, compatibility may be broken.

    Check for all sub-versions using

      ls -l /usr/local/lib/libopen-pal.so.13*

    then rename them, example

      sudo mv /usr/local/lib/libopen-pal.so.13 /usr/local/lib/libopen-pal.so.13.backup
user.dz
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