> The directory /uufs/chpc.utah.edu/sys/installdir/R/3.3.2bb/lib64/R/lib64
does not exist
Do you end up with the path to the R shared library somewhere in
LD_LIBRARY_PATH ?
Did you check the expected libraries are loaded. For example with:
strace python -m rpy2.tests
2016-12-07 14:56 GMT-05:00
Hi Laurent,
Here are the results of the experiment. As you can see below the issue
remains.
Thanks,
Wim
First lines of MY ORIGINALl python setup.py build:
[hpcapps@dirac 12072016]$ python setup.py build
R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
/uufs/chpc.utah.edu/sys/installdir/R
The command R is doing quite a bit of environment settings before starting
the actual binary. Not all of this is done by rpy2 when starting, and I am
guessing that it is trying to link / use the system's BLAS (and this is
ending in a segfault).
Try setting LD_LIBRARY_PATH to have both the path to
Hi Laurent,
Thanks for your reply.
These are the flags I used to compile R:
setenv CC gcc
setenv CXX g++
setenv F77 gfortran
setenv FC gfortran
setenv CFLAGS " -O2 -fPIC -I/uufs/chpc.utah.edu/sys/
installdir/openblas/0.2.19-st/include "
setenv CXXFLAGS " -O2 -fPIC -I/uufs/chpc.utah.edu/sys/
ins
Hi Wim,
Segfaults can be hard to track without the ability to reproduce (not much
you can do about for now, this seems something specific to your system).
Do you have an environment variable R_HOME defined ? What are your
LD_LIBRARY_PATH like ? Is your customized with ${R_HOME}/etc or ~/.R ? Wha
Hello,
I compiled R v 3.3.2 with openblas (single threaded version).
uname -a
>Linux dirac.chpc.utah.edu 3.10.0-327.36.3.el7.x86_64 #1 SMP Mon Oct 24
16:09:20 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
gcc:
gcc version 4.8.5 20150623 (Red Hat 4.8.5-4) (GCC)
After installing the 2.9.0dev version of
