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 your openblas library
and to R's own shared library before running Python with rpy2.
Something like this:
export LD_LIBRARY_PATH=`R RHOME`/`R CMD config LIBnn`:/uufs/chpc.utah.edu
/sys/installdir/openblas/0.2.19-st/lib
L.
2016-12-07 13:27 GMT-05:00 Wim R. Cardoen <wcard...@gmail.com>:
> 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/inst
> alldir/openblas/0.2.19-st/include "
> setenv CXXFLAGS " -O2 -fPIC -I/uufs/chpc.utah.edu/sys/inst
> alldir/openblas/0.2.19-st/include "
> setenv FFLAGS " -O2 -fPIC -I/uufs/chpc.utah.edu/sys/inst
> alldir/openblas/0.2.19-st/include "
> setenv FCFLAGS " -O2 -fPIC -I/uufs/chpc.utah.edu/sys/inst
> alldir/openblas/0.2.19-st/include "
> setenv LDFLAGS " -Wl,-rpath=/uufs/chpc.utah.edu
> /sys/installdir/openblas/0.2.19-st/lib
> -L/uufs/chpc.utah.edu/sys/inst
> alldir/openblas/0.2.19-st/lib -lopenblas "
>
> # Build executables
> cd /uufs/chpc.utah.edu/sys/builddir/R; mkdir 3.3.2bb; cd 3.3.2bb
>
> # Configure (with BLAS & LAPACK MKL Support)
> ../../../srcdir/R/3.3.2/configure --prefix=/uufs/chpc.utah.edu/s
> ys/installdir/R/3.3.2bb \
> --enable-R-profiling --enable-R-shlib
> --enable-memory-profiling \
> --enable-java --enable-shared=yes
> --with-blas="$LDFLAGS" \
> --with-readline --with-cairo
> --with-tcltk --with-libpng --with-jpeglib --with-libtiff \
> --with-ICU --with-pic --with-x
> --with-lapack
>
> ############################################################
> ################################################
> R is now configured for x86_64-pc-linux-gnu
>
> Source directory: ../../../srcdir/R/3.3.2
> Installation directory: /uufs/chpc.utah.edu/sys/installdir/R/3.3.2bb
>
> C compiler: gcc -std=gnu99 -O2 -fPIC -I/uufs/
> chpc.utah.edu/sys/installdir/openblas/0.2.19-st/include
> Fortran 77 compiler: gfortran -O2 -fPIC -I/uufs/
> chpc.utah.edu/sys/installdir/openblas/0.2.19-st/include
>
> C++ compiler: g++ -O2 -fPIC -I/uufs/
> chpc.utah.edu/sys/installdir/openblas/0.2.19-st/include
> C++11 compiler: g++ -std=c++11 -O2 -fPIC -I/uufs/
> chpc.utah.edu/sys/installdir/openblas/0.2.19-st/include
> Fortran 90/95 compiler: gfortran -O2 -fPIC -I/uufs/
> chpc.utah.edu/sys/installdir/openblas/0.2.19-st/include
> Obj-C compiler: gcc -g -O2 -fobjc-exceptions
>
> Interfaces supported: X11, tcltk
> External libraries: readline, BLAS(OpenBLAS), LAPACK(in blas),
> curl
> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU
> Options enabled: shared R library, R profiling, memory
> profiling
>
> Capabilities skipped:
> Options not enabled: shared BLAS
>
> Recommended packages: yes
>
>
> I have neither set LD_LIBRARY_PATH, nor $R_HOME but the R_LIBS_SITE env.
> variable
> echo $R_LIBS_SITE
> /uufs/chpc.utah.edu/sys/installdir/RLibs/3.3.2bb
> R CMD config BLAS_LIBS
> -Wl,-rpath=/uufs/chpc.utah.edu/sys/installdir/openblas/0.2.19-st/lib
> -L/uufs/chpc.utah.edu/sys/installdir/openblas/0.2.19-st/lib -lopenblas
>
> I installed a whole bunch of packages in the following way:
> install.packages(pkgs=c("ggplot2","htmlwidgets","ggvis"
> ,"rgl","googleVis"),
> lib=c("/uufs/chpc.utah.edu/sys/installdir/RLibs/3.3.2bb")
> ,
> repos=c("http://cran.us.r-project.org";),
> verbose=TRUE)
>
> hpcapps@dirac ~]$ R
>
> R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
> Copyright (C) 2016 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> > .libPaths()
> [1] "/uufs/chpc.utah.edu/sys/installdir/RLibs/3.3.2bb"
> [2] "/uufs/chpc.utah.edu/sys/installdir/R/3.3.2bb/lib64/R/library"
>
>
> PS:
> Note that I have used the same (single threaded) openblas to compile numpy.
> I normally compile R with Intel MKL (threaded). The same is true for
> python.
> When I compiled R and numpy/scipy with the threaded Intel MKL libraries,
> the tests of
> RPy2 were hanging. That's why I went to the single threaded version of
> BLAS/LAPACK.
>
>
> Thanks,
>
> WIm
>
>
>
>
> On Wed, Dec 7, 2016 at 10:43 AM, Laurent Gautier <lgaut...@gmail.com>
> wrote:
>
>> 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 ? What
>> does the shell command "R CMD config BLAS_LIBS" return ?
>>
>> L.
>>
>>
>>
>> 2016-12-07 12:12 GMT-05:00 Wim R. Cardoen <wcard...@gmail.com>:
>>
>>> 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 RPy2 (python 2.7.12) the tests
>>> crashed:
>>>
>>> python -m rpy2.tests -v
>>> rpy2 version: 2.9.0dev
>>> - built against R version: 3-3.2--71607
>>> - running linked to R version: R version 3.3.2 (2016-10-31)
>>> /uufs/chpc.utah.edu/sys/installdir/python/2.7.12bb/lib/pytho
>>> n2.7/site-packages/rpy2-2.9.0.dev0-py2.7-linux-x86_64.egg/
>>> rpy2/robjects/lib/ggplot2.py:67: UserWarning: This was designed againt
>>> ggplot2 version 2.1.0 but you have 2.2.0
>>> warnings.warn('This was designed againt ggplot2 version %s but you
>>> have %s' % (TARGET_VERSION, ggplot2.__version__))
>>> testCallErrorWhenEndedR (rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
>>> ... ok
>>> testConsolePrint (rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
>>> ... ok
>>> testExternalPython (rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
>>> ... ok
>>> testExternalPythonFromExpression
>>> (rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
>>> ... ok
>>> testGet_initoptions (rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
>>> ... ok
>>> testInitr (rinterface.tests.test_EmbeddedR.EmbeddedRTestCase) ... ok
>>> testInterruptR (rinterface.tests.test_EmbeddedR.EmbeddedRTestCase) ...
>>> ok
>>> testParse (rinterface.tests.test_EmbeddedR.EmbeddedRTestCase) ... ok
>>> testParseError (rinterface.tests.test_EmbeddedR.EmbeddedRTestCase) ...
>>> ok
>>> testParseIncompleteError (rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
>>> ... ok
>>> testParseInvalidString (rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
>>> ... ok
>>> testParseUnicode (rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
>>> ... ok
>>> testRpyMemory (rinterface.tests.test_EmbeddedR.EmbeddedRTestCase) ...
>>> Segmentation fault (core dumped)
>>>
>>> Any idea what went wrong? Please let me know if you need more info.
>>>
>>> Thanks,
>>>
>>> Wim
>>>
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>>>
>>
>
>
>
>
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