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/
installdir/openblas/0.2.19-st/include "
setenv FFLAGS " -O2 -fPIC -I/uufs/chpc.utah.edu/sys/
installdir/openblas/0.2.19-st/include "
setenv FCFLAGS " -O2 -fPIC -I/uufs/chpc.utah.edu/sys/
installdir/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/installdir/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/
sys/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/
>> python2.7/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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