On 02/07/16 10:34, Yann Sagon wrote:
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.
FYI: easyconfigs for R 3.3.1 with the new foss/2016b and intel/2016b
toolchains and with updated dependencies & extension were merged via
https://github.com/hpcugent/easybuild-easyconfigs/pull/3314.
I did not run into the Rmpi issue Yann described...
regards,
Kenneth
Best
2016-06-30 10:17 GMT+02:00 Yann Sagon <[email protected]
<mailto:[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]
<mailto:[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 <tel:%2B41%20%280%2922%20379%207737>
[email protected] <mailto:[email protected]> - www.unige.ch
<http://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] <mailto:[email protected]> - www.unige.ch
<http://www.unige.ch>
