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rated 0 times [  0] [ 0]  / answers: 1 / hits: 1439  / 1 Year ago, tue, december 20, 2022, 10:33:21

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

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 Answers
7

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.


[#2539] Thursday, December 22, 2022, 1 Year  [reply] [flag answer]
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