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I tried installing version 4.0.5.tar.gz on an Ubuntu 18.04 LTS server at school but it failed following instructions here that say:

shell$ gunzip -c openmpi-4.0.5.tar.gz | tar xf -
shell$ cd openmpi-4.0.5
shell$ ./configure --prefix=/usr/local
<...lots of output...>
shell$ make all install

So I tried version 3.1.6 and it failed again.

The error was:

  make[2]: Nothing to be done for 'install-exec-am'.
 /bin/mkdir -p '/usr/local/share/openmpi/amca-param-sets'
 /usr/bin/install -c -m 644 amca-param-sets/example.conf '/usr/local/share/openmpi/amca-param-sets'
/usr/bin/install: cannot remove '/usr/local/share/openmpi/amca-param-sets/example.conf': Permission denied
Makefile:1806: recipe for target 'install-dist_amca_paramDATA' failed
make[2]: *** [install-dist_amca_paramDATA] Error 1
make[2]: Leaving directory '/home/T00057442/openmpi31/openmpi-3.1.6/contrib'
Makefile:1897: recipe for target 'install-am' failed
make[1]: *** [install-am] Error 2
make[1]: Leaving directory '/home/T00057442/openmpi31/openmpi-3.1.6/contrib'
Makefile:1896: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1

for version 3.1.6 on the server and locally:

make[2]: Nothing to be done for 'install-exec-am'.
 /bin/mkdir -p '/usr/local/share/openmpi/amca-param-sets'
/bin/mkdir: cannot create directory ‘/usr/local/share/openmpi’: Permission denied
Makefile:1789: recipe for target 'install-dist_amca_paramDATA' failed
make[2]: *** [install-dist_amca_paramDATA] Error 1
make[2]: Leaving directory '/media/nobu/UbuntuFiles/Downloads/openmpi-4.0.5/contrib'
Makefile:1880: recipe for target 'install-am' failed
make[1]: *** [install-am] Error 2
make[1]: Leaving directory '/media/nobu/UbuntuFiles/Downloads/openmpi-4.0.5/contrib'
Makefile:1879: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1

so both times it is install-am? What is that and has anyone successfully installed openmpi or mpich? I need it for Ray Surveyor: http://zorino.github.io/raysurveyor-tutorial/#/42

Edit: I run

base) nobu@gold3forever:~/Desktop/BioInformatics/RA/kover/ray$ mpiexec --version
mpiexec: error while loading shared libraries: libopen-rte.so.40: cannot open shared object file: No such file or directory

then I tried:

(base) nobu@gold3forever:~/Desktop/BioInformatics/RA/kover/ray$ mpirun --version
mpirun: error while loading shared libraries: libopen-rte.so.40: cannot open shared object file: No such file or directory

Finally

(base) nobu@gold3forever:~/Desktop/BioInformatics/RA/kover/ray$ mpicxx --showme:version
mpicxx: error while loading shared libraries: libopen-pal.so.40: cannot open shared object file: No such file or directory

I thought I was okay, following directions from @NOrbert in his answer but when I try to install Ray Surveyor I get

(base) nobu@gold3forever:~/Desktop/BioInformatics/RA/kover/ray$ make PREFIX=`pwd`/BUILD MAXKMERLENGTH=64 HAVE_LIBZ=y HAVE_LIBBZ2=y ASSERT=n;
  CXX code/application_core/ray_main.o
mpicxx: error while loading shared libraries: libopen-pal.so.40: cannot open shared object file: No such file or directory
Makefile:160: recipe for target 'code/application_core/ray_main.o' failed
make: *** [code/application_core/ray_main.o] Error 127
mLstudent33
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  • This appears to be a simple permissions issue - you are running make install as a non-privileged user and therefore it does not have permission to write to the /usr/local/share/ directory – steeldriver Oct 16 '20 at 09:16
  • @steeldriver I will try this. sudo make install all or is it sudo make install? – mLstudent33 Oct 16 '20 at 21:25
  • First make all; if that succeeds you can then proceed to sudo make install – steeldriver Oct 16 '20 at 21:43
  • command: ompi_info returns ompi_info: error while loading shared libraries: libmpi.so.40: cannot open shared object file: No such file or directory – mLstudent33 Oct 17 '20 at 02:22

3 Answers3

1

Per the comment above, sudo ldconfig I read on that link after the steps provided by @NOrbert.

mLstudent33
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0

You do not need to compile OpenMPI by yourself.

This package is presented in Ubuntu repositories.

Simply install it with:

sudo apt-add-repository universe
sudo apt-get install libopenmpi-dev

and then continue with compilation of only Ray Surveyor.

N0rbert
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  • I got libopenmpi-dev is already the newest version (2.1.1-8). 0 upgraded, 0 newly installed, 0 to remove and 70 not upgraded. so I guess it is installed. I ran instructions here before trying any of the above: https://zoomadmin.com/HowToInstall/UbuntuPackage/openmpi-bin – mLstudent33 Oct 16 '20 at 21:25
  • When I tried to install Ray Surveyor following instructions here: https://github.com/zorino/RaySurveyor-Tutorial, I get (base) nobu@gold3forever:~/Desktop/BioInformatics/RA/kover/ray$ make PREFIX=`pwd`/BUILD MAXKMERLENGTH=64 HAVE_LIBZ=y HAVE_LIBBZ2=y ASSERT=n; CXX code/application_core/ray_main.o mpicxx: error while loading shared libraries: libopen-pal.so.40: cannot open shared object file: No such file or directory Makefile:160: recipe for target 'code/application_core/ray_main.o' failed make: *** [code/application_core/ray_main.o] Error 127 – mLstudent33 Oct 19 '20 at 05:16
  • Actually running sudo ldconfig I found here: https://askubuntu.com/a/784120/1118094 and now that last step is executing. – mLstudent33 Oct 19 '20 at 05:22
0

I got this error while trying to install OpenMPI 4.0.0 in Ubuntu 18.04. I wanted this particular version for another library. I solved this by running sudo make all install instead of make all install. You can notice this error in the error logs in the question too (Permission denied).

Gautam Sreekumar
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