Re: [R] cannot compile R on Cray XE6 HLRS HERMIT

2013-04-29 Thread Ben Bolker 
Martin Ivanov  abv.bg> writes:

>  Dear All, I am trying to compile R-3.0 on Cray xe6 (HLRS) HERMIT,
>  no success so far.  Here is my experience:

  You might be better off posting this to the r-de...@r-project.org
mailing list (the list is for developer queries: technically this
isn't "development", but queries about compilation on exotic systems
appear more often there, and often require input from R-core members
...)

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[R] cannot compile R on Cray XE6 HLRS HERMIT

2013-04-29 Thread Martin Ivanov 
 Dear All,

I am trying to compile R-3.0 on Cray xe6 (HLRS) HERMIT, no success so far.
Here is my experience:

I use this to configure and make R:

CC="cc" \
CXX="CC" \
F77="ftn" \
FC="ftn" \
CPPFLAGS="-I$PREFIX/include" \
LDFLAGS="-L$PREFIX/lib${LIBDIRSUFFIX}" \
./configure --prefix=$PREFIX \
--exec-prefix=$PREFIX \
--bindir=$PREFIX/bin \
--sbindir=$PREFIX/sbin \
--sysconfdir=$PKG/etc \
--localstatedir=$PKG/var \
--libdir=$PREFIX/lib${LIBDIRSUFFIX} \
--datarootdir=$PREFIX/share \
--datadir=$PREFIX/share \
--infodir=$PREFIX/info \
--mandir=$PREFIX/man \
--docdir=$PREFIX/doc/$PRGNAM-$VERSION \
rdocdir=$PREFIX/doc/$PRGNAM-$VERSION \
rincludedir=$PREFIX/include \
rsharedir=$PREFIX/share \
--disable-BLAS-shlib \
--with-blas \
--with-lapack \
--without-x \
|| exit 1

make || exit 1

My environment is as follows:

  1) modules/3.2.6.7 13) 
udreg/2.3.2-1.0401.5929.3.3.gem 25) 
configuration/1.0-1.0401.35391.1.2.gem
  2) xtpe-network-gemini 14) ugni/4.0-1.0401.5928.9.5.gem   
 26) hosts/1.0-1.0401.35364.1.115.gem
  3) xtpe-interlagos 15) pmi/4.0.1-1..9421.73.3.gem 
 27) lbcd/2.1-1.0401.35360.1.2.gem
  4) cray-mpich2/5.6.4   16) 
dmapp/3.2.1-1.0401.5983.4.5.gem 28) 
nodehealth/5.0-1.0401.38460.12.18.gem
  5) eswrap/1.0.917) 
gni-headers/2.1-1.0401.5675.4.4.gem 29) pdsh/2.26-1.0401.37449.1.1.gem
  6) torque/2.5.918) xpmem/0.1-2.0401.36790.4.3.gem 
 30) shared-root/1.0-1.0401.37253.3.50.gem
  7) moab/6.1.5.s199219) 
job/1.5.5-0.1_2.0401.35380.1.10.gem 31) switch/1.0-1.0401.36779.2.72.gem
  8) system/ws_tools 20) 
csa/3.0.0-1_2.0401.37452.4.50.gem   32) xe-sysroot/4.1.40
  9) system/hlrs-defaults21) 
dvs/1.8.6_0.9.0-1.0401.1401.1.120   33) atp/1.6.2
 10) xt-asyncpe/5.19 22) rca/1.0.0-2.0401.38656.2.2.gem 

 11) gcc/4.7.2   23) 
audit/1.0.0-1.0401.37969.2.32.gem 
 12) xt-libsci/12.0.01   24) ccm/2.2.0-1.0401.37254.2.142

1. PrgEnv-gnu/4.1.40
checking for C libraries of cc -std=gnu99...  
-L/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64 
-L/opt/cray/udreg/2.3.2-1.0401.5929.3.3.gem/lib64 
-L/opt/cray/ugni/4.0-1.0401.5928.9.5.gem/lib64 
-L/opt/cray/pmi/4.0.1-1..9421.73.3.gem/lib64 
-L/opt/cray/dmapp/3.2.1-1.0401.5983.4.5.gem/lib64 
-L/opt/cray/xpmem/0.1-2.0401.36790.4.3.gem/lib64 
-L/opt/cray/rca/1.0.0-2.0401.38656.2.2.gem/lib64 
-L/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/lib 
-L/opt/cray/libsci/12.0.01/gnu/47/interlagos/lib 
-L/opt/cray/xe-sysroot/4.1.40/usr/lib64 -L/opt/cray/xe-sysroot/4.1.40/lib64 
-L/opt/cray/xe-sysroot/4.1.40/usr/lib/alps -L/usr/lib/alps 
-L/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2 
-L/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64 
-L/lib/../lib64 -L/usr/lib/../lib64 
-L/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../.. -lrca 
-L/opt/cray/atp/1.6.2/lib/ -lAtpSigHCommData -lAtpSigHandler -lgfortran 
-lscicpp_gnu -lsci_gnu_mp -lstdc++ -lmpich_gnu_47 -lmpl -lrt 
 -lxpmem -ldmapp -lugni -lpmi -lalpslli -lalpsutil -ludreg -lpthread -lm -lgomp 
-lgcc_eh
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no 
extra underscore
checking whether ftn appends underscores to external names... yes
checking whether ftn appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether ftn and cc -std=gnu99 agree on int and double... configure: 
WARNING: ftn and cc -std=gnu99 disagree on int and double
configure: error: Maybe change CFLAGS or FFLAGS?

2. PrgEnv-gnu/4.1.40 + craype-target-native

R is now configured for x86_64-unknown-linux-gnu

  Source directory:  .
  Installation directory:/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr

  C compiler:cc -std=gnu99  -g -O2
  Fortran 77 compiler:   gfortran  -g -O2

  C++ compiler:  CC  -g -O2
  Fortran 90/95 compiler:ftn -g -O2
  Obj-C compiler:

  Interfaces supported:
  External libraries:readline
  Additional capabilities:   JPEG
  Options enabled:   shared R library, shared BLAS, R profiling, memory 
profiling, strict barrier, static HTML

  Recommended packages:  yes

nmath/*.o` ../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a 
../extra/tre/libtre.a  ../extra/xz/liblzma.a  -L../../lib -lRblas -lgfortran 
-lm -lquadmath   -lreadline -lncurses  -lrt -ldl -lm
make[4]: Entering directory 
`/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/build/tmp/R-3.0.0/src/main'
mkdir -p -- /univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/build/tmp/R-3.0.0/bin/exec
make[4]: Leaving directory 
`/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/build/tmp/R-3.0.0/src/main'
make[3]: