Thanks Adam and Kenneth. I have now a working R 3.3.1 but without ext_lib update and without including some ext_lib that failed to compile, but at least it's compiling and it's fine for me. As I don't have time to upgrade this ext_lib list, I share here my working eb file for R 3.3.1 in case someone want's to use it.
https://github.com/ysagon/easybuild-easyconfigs/blob/R-3.3.1-foss-2016a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb Let me know if you want that I do a PR. Best 2016-06-30 10:17 GMT+02:00 Yann Sagon <[email protected]>: > Hello, > > After some investigation, the error is coming because when the compilation > of Rmpi is done. The script try to load the module to see if it's working. > It seems it's loading without mpirun or orterun or similar and thus fail > with orte_init. > > I have tried to load the compiled module when launching R with mpirun and > it's working fine. > > I didn't wanted to update the non standard exts version, I just wanted to > have a newer version of R. > > Anyway, I have no idea why the installation of Rmpi was working with > previous version of R. > > In the last line of this file, the comment seems to suggest that it might > be needed to launch the compilation with mpirun but I don't know how to do > that with eb. > > > https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/r/rmpi.py > > When compiling manually like that, it'w working: > > mpirun -np 1 R CMD INSTALL > /home/sagon/.local/easybuild/sources/r/R/extensions/Rmpi_0.6-6.tar.gz > > --configure-args="--with-Rmpi-include=/opt/ebsofts/Compiler/GCC/4.9.3-2.25/OpenMPI/1.10.2/include > --with-Rmpi-libpath=/opt/ebsofts/Compiler/GCC/4.9.3-2.25/OpenMPI/1.10.2/lib > --with-mpi=/opt/ebsofts/Compiler/GCC/4.9.3-2.25/OpenMPI/1.10.2 > --with-Rmpi-type=OPENMPI" > > --library=/opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/R/3.3.1/lib64/R/library > --no-clean-on-error > > without mpirun, it' failed with the test. > > > 2016-06-29 18:00 GMT+02:00 Kenneth Hoste <[email protected]>: > >> Hi Yann, >> >> On 29/06/16 17:51, Yann Sagon wrote: >> > Hello, >> > >> > I'm trying to tweak the file >> > >> > R-3.2.3-foss-2016a.eb >> > >> > to install version 3.3.1 of R. >> > >> > In this file, there is a list of non standard exts. >> > >> > Rmpi seems to do some checking once installed and failed with orte_init. >> > >> > Any clue? >> >> Please share the full error message you're running into? >> >> There is an ongoing effort to add an easyconfig for R 3.3.x, but it >> seems like it's stuck in dep hell, see >> https://github.com/hpcugent/easybuild-easyconfigs/pull/3079 . >> >> >> regards, >> >> Kenneth >> > > > > -- > Yann SAGON > Ingénieur système HPC > 24 Rue du Général-Dufour > 1211 Genève 4 - Suisse > Tél. : +41 (0)22 379 7737 > [email protected] - www.unige.ch > -- Yann SAGON Ingénieur système HPC 24 Rue du Général-Dufour 1211 Genève 4 - Suisse Tél. : +41 (0)22 379 7737 [email protected] - www.unige.ch
