[R-sig-hpc] cannot install ncdf4_1.6.1 in R-3.0.0 on Cray XE6 HERMIT (R-sig-hpc Digest, Vol 56, Issue 4)
Martin Ivanov
martin.ivanov at ifg.uni-tuebingen.de
Tue May 7 19:04:29 CEST 2013
Hello, Pragnesh,
Thank You very much for Your responsiveness.
Now I am trying to compile hdf5, but unsuccessfully.
Here is my setting:
if [ "$ARCH" = "i486" ]; then
SLKCFLAGS="-O2 -march=i486 -mtune=i686"
LIBDIRSUFFIX=""
elif [ "$ARCH" = "i686" ]; then
SLKCFLAGS="-O2 -march=i686 -mtune=i686"
LIBDIRSUFFIX=""
elif [ "$ARCH" = "x86_64" ]; then
SLKCFLAGS="-O2 -fPIC"
LIBDIRSUFFIX="64"
else
SLKCFLAGS="-O2"
LIBDIRSUFFIX=""
fi
CC="cc" \
CXX="CC" \
FCC="ftn" \
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CPPFLAGS="-DgFortran -I$PREFIX/include" \
LDFLAGS="-L$PREFIX/lib${LIBDIRSUFFIX}" \
./configure \
--prefix=$PREFIX \
--sysconfdir=$PKG/etc \
--localstatedir=$PKG/var \
--libdir=$PREFIX/lib${LIBDIRSUFFIX} \
--infodir=$PREFIX/info \
--mandir=$PREFIX/man \
--docdir=$PREFIX/doc/$PRGNAM-$VERSION \
--program-prefix="" \
--program-suffix="" \
--disable-fortran \
--disable-cxx \
--enable-shared \
--disable-static \
--enable-largefile \
--enable-parallel \
--disable-linux-lfs \
--with-zlib \
--with-pthread \
My environment is:
ipmiva at eslogin001:/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/build/source>
module list
Currently Loaded Modulefiles:
1) modules/3.2.6.7 13)
ugni/4.0-1.0401.5928.9.5.gem 25) hosts/1.0-1.0401.35364.1.115.gem
2) xtpe-network-gemini 14)
pmi/4.0.1-1.0000.9421.73.3.gem 26) lbcd/2.1-1.0401.35360.1.2.gem
3) xtpe-interlagos 15)
dmapp/3.2.1-1.0401.5983.4.5.gem 27)
nodehealth/5.0-1.0401.38460.12.18.gem
4) eswrap/1.0.9 16)
gni-headers/2.1-1.0401.5675.4.4.gem 28) pdsh/2.26-1.0401.37449.1.1.gem
5) torque/2.5.9 17)
xpmem/0.1-2.0401.36790.4.3.gem 29)
shared-root/1.0-1.0401.37253.3.50.gem
6) moab/6.1.5.s1992 18)
job/1.5.5-0.1_2.0401.35380.1.10.gem 30) switch/1.0-1.0401.36779.2.72.gem
7) system/ws_tools 19)
csa/3.0.0-1_2.0401.37452.4.50.gem 31) xe-sysroot/4.1.40
8) system/hlrs-defaults 20)
dvs/1.8.6_0.9.0-1.0401.1401.1.120 32) atp/1.6.2
9) xt-asyncpe/5.19 21)
rca/1.0.0-2.0401.38656.2.2.gem 33) PrgEnv-gnu/4.1.40
10) gcc/4.7.2 22)
audit/1.0.0-1.0401.37969.2.32.gem 34) cray-mpich2/5.6.4
11) xt-libsci/12.0.01 23)
ccm/2.2.0-1.0401.37254.2.142
12) udreg/2.3.2-1.0401.5929.3.3.gem 24)
configuration/1.0-1.0401.35391.1.2.gem
I had to unload the module craype-target-native, because with it hdf5's
configure does not find mpi. And here is the compilation error now:
from H5detect.c:57:
/opt/cray/xe-sysroot/4.1.40/usr/include/string.h:64:14: note: expected
'void *' but argument is of type 'volatile long double *'
H5detect.c:1533:5: warning: passing argument 1 of 'memset' discards
'volatile' qualifier from pointer target type [enabled by default]
In file included from H5private.h:51:0,
from H5detect.c:57:
/opt/cray/xe-sysroot/4.1.40/usr/include/string.h:64:14: note: expected
'void *' but argument is of type 'volatile long double *'
H5detect.c:1533:5: warning: passing argument 1 of 'memset' discards
'volatile' qualifier from pointer target type [enabled by default]
In file included from H5private.h:51:0,
from H5detect.c:57:
/opt/cray/xe-sysroot/4.1.40/usr/include/string.h:64:14: note: expected
'void *' but argument is of type 'volatile long double *'
H5detect.c:1533:5: warning: cast discards '__attribute__((noreturn))'
qualifier from pointer target type [-Wcast-qual]
H5detect.c:1533:5: warning: cast discards '__attribute__((noreturn))'
qualifier from pointer target type [-Wcast-qual]
H5detect.c:1533:5: warning: to be safe all intermediate pointers in cast
from 'char **' to 'const char **' must be 'const' qualified [-Wcast-qual]
H5detect.c:1533:5: warning: passing argument 3 of 'imp_bit' discards
'volatile' qualifier from pointer target type [enabled by default]
H5detect.c:1054:1: note: expected 'void *' but argument is of type
'volatile long double *'
H5detect.c:1533:5: warning: passing argument 4 of 'imp_bit' discards
'volatile' qualifier from pointer target type [enabled by default]
H5detect.c:1054:1: note: expected 'void *' but argument is of type
'volatile long double *'
H5detect.c:1533:5: warning: passing argument 3 of 'bit_cmp' discards
'volatile' qualifier from pointer target type [enabled by default]
H5detect.c:933:1: note: expected 'void *' but argument is of type
'volatile long double *'
H5detect.c:1533:5: warning: passing argument 4 of 'bit_cmp' discards
'volatile' qualifier from pointer target type [enabled by default]
H5detect.c:933:1: note: expected 'void *' but argument is of type
'volatile long double *'
H5detect.c:1533:5: warning: passing argument 3 of 'bit_cmp' discards
'volatile' qualifier from pointer target type [enabled by default]
H5detect.c:933:1: note: expected 'void *' but argument is of type
'volatile long double *'
H5detect.c:1533:5: warning: passing argument 4 of 'bit_cmp' discards
'volatile' qualifier from pointer target type [enabled by default]
H5detect.c:933:1: note: expected 'void *' but argument is of type
'volatile long double *'
H5detect.c:1533:5: warning: passing argument 4 of 'find_bias' discards
'volatile' qualifier from pointer target type [enabled by default]
H5detect.c:1104:1: note: expected 'void *' but argument is of type
'volatile long double *'
H5detect.c:1533:5: warning: cast discards '__attribute__((noreturn))'
qualifier from pointer target type [-Wcast-qual]
H5detect.c:1533:5: warning: cast discards '__attribute__((noreturn))'
qualifier from pointer target type [-Wcast-qual]
mv -f .deps/H5detect-H5detect.Tpo .deps/H5detect-H5detect.Po
/bin/sh ../libtool --tag=CC --mode=link cc -g -ansi -pedantic -Wall -W
-Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual
-Wcast-align -Wwrite-strings -Wconversion -Waggregate-return
-Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations
-Wredundant-decls -Wnested-externs -Winline -O3 -fomit-frame-pointer
-finline-functions -O2 -fPIC -o H5detect H5detect-H5detect.o
-lpthread -lz -lm
libtool: link: cc -g -ansi -pedantic -Wall -W -Wundef -Wshadow
-Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align
-Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes
-Wmissing-prototypes -Wmissing-declarations -Wredundant-decls
-Wnested-externs -Winline -O3 -fomit-frame-pointer -finline-functions
-O2 -fPIC -o H5detect H5detect-H5detect.o -lpthread -lz -lm
H5detect-H5detect.o: In function `print_header':
/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/build/tmp/hdf5-1.8.5/src/H5detect.c:1203:
warning: Using 'getpwuid' in statically linked applications requires at
runtime the shared libraries from the glibc version used for linking
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \
sed -e 's/-L/:/g' -e 's/
//g'`" \
./H5detect > H5Tinit.c || \
(test $HDF5_Make_Ignore && echo "*** Error ignored")
|| \
(rm -f H5Tinit.c ; exit 1)
/bin/sh: line 4: 29860 Illegal instruction
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | sed -e 's/-L/:/g' -e 's/
//g'`" ./H5detect > H5Tinit.c
make[2]: *** [H5Tinit.c] Error 1
make[2]: Leaving directory
`/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/build/tmp/hdf5-1.8.5/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory
`/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/build/tmp/hdf5-1.8.5/src'
make: *** [all-recursive] Error 1
Any ideas?
I would be very thankful to you if you provide
detailed installation instructions of hdf5, netcdf, ncdf4 and pbdNCDF4 on Cray XE6 machine. I could use it as a guide.
Best regrds,
Martin
On 05/07/2013 03:35 PM, Pragnesh Patel wrote:
> Hi Martin,
>
> It looks like you need to recompile hdf5 and netcdf with
> "--enable-shared" option (either in your home directory or lustre
> directory(I assume you use lustre file system)). Once you have those,
> you should be able to install pbdNCDF4 and ncdf4 packages.
>
> Please let me know, if you need detail installation instructions of
> hdf5, netcdf, ncdf4 and pbdNCDF4 on Cray XE6 machine.
>
> (TO run: you need to copy all *.so files(from hdf5 and netcdf lib
> directory) to lustre file system so compute nodes can access those).
>
>
> Thanks
> Pragnesh
>
>
>
> On 5/5/13, r-sig-hpc-request at r-project.org
> <r-sig-hpc-request at r-project.org> wrote:
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>> Today's Topics:
>>
>> 1. cannot install ncdf4_1.6.1 in R-3.0.0 on Cray XE6 HERMIT
>> (Martin Ivanov)
>> 2. Re: Trouble compiling R-3.0.0 an a Linux Cluster (Martin
>> Ivanov) (Martin Ivanov)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Sat, 04 May 2013 15:25:53 +0200
>> From: Martin Ivanov <martin.ivanov at ifg.uni-tuebingen.de>
>> To: "R-sig-hpc at r-project.org" <r-sig-hpc at r-project.org>
>> Subject: [R-sig-hpc] cannot install ncdf4_1.6.1 in R-3.0.0 on Cray XE6
>> HERMIT
>> Message-ID: <51850C61.10201 at ifg.uni-tuebingen.de>
>> Content-Type: text/plain; charset=UTF-8; format=flowed
>>
>> Dear All,
>>
>> I am working on Cray xe6 (HLRS) HERMIT. Recently I had a problem
>> compiling R-3.0.0.
>> Finally the problem is solved, I had to use PrgEnv-gnu/4.1.40 together
>> with craype-target-native, and also supply
>> LDFLAGS="-L$PREFIX/lib64 -Wl,-rpath -Wl,$PREFIX/lib64
>> -L/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/build/tmp/R-3.0.0/lib",
>> where PREFIX=/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr.
>>
>> Now that I have R, I also need to work with netcdf data files, so I need
>> to use the netcdf library. I want
>> netcdf-4.1.1 and hdf5-1.8.5. I see both are available as modules, so I
>> loaded hdf5-parallel/1.8.5.0 and
>> netcdf-hdf5parallel/4.1.1.0. To use netcdf from within R I have to
>> compile the ncdf4_1.6.1.tar.gz package.
>> And here is my problem. This package uses the nc-config file to tune the
>> compilation environment. However,
>> the
>> /opt/cray/netcdf-hdf5parallel/4.1.1.0/netcdf-hdf5parallel-gnu/bin/nc-config
>>
>> contains obsolete information:
>>
>> prefix=/tmp/ulib/netcdf/4.1.1.0/netcdf-hdf5parallel/netcdf-hdf5parallel-gnu
>> exec_prefix=${prefix}
>> libdir=${exec_prefix}/lib
>> includedir=${prefix}/include
>> cc="cc"
>> cxx="CC"
>> fc="ftn"
>> cflags=" -I${includedir}"
>> fflags="-g -O2 -I${includedir}"
>> libs="-L${libdir} -lnetcdf
>> -L/tmp/ulib/hdf5/1.8.5.0/hdf5-parallel/hdf5-parallel-gnu/lib -lhdf5_hl
>> -lhdf5 -L/usr/lib64/lib -lz -lm "
>> flibs="-L${libdir} -lnetcdff -lnetcdf
>> -L/tmp/ulib/hdf5/1.8.5.0/hdf5-parallel/hdf5-parallel-gnu/lib -lhdf5_hl
>> -lhdf5 -L/usr/lib64/lib -lz -lm "
>>
>> the prefix as well as
>> /tmp/ulib/hdf5/1.8.5.0/hdf5-parallel/hdf5-parallel-gnu do not exist any
>> more. That is why I copied the nc-config to
>> my home directory and modified it with the correct paths like this:
>>
>> prefix=/opt/cray/netcdf-hdf5parallel/4.1.1.0/netcdf-hdf5parallel-gnu
>> exec_prefix=${prefix}
>> libdir=${exec_prefix}/lib
>> includedir=${prefix}/include
>>
>> cc="cc"
>> cxx="CC"
>> fc="ftn"
>> cflags=" -I${includedir}"
>> fflags="-g -O2 -I${includedir}"
>> libs="-L${libdir} -lnetcdf
>> -L/opt/cray/hdf5-parallel/1.8.5.0/hdf5-parallel-gnu/lib -lhdf5_hl
>> -lhdf5 -L/usr/lib64/lib -lz -lm "
>> flibs="-L${libdir} -lnetcdff -lnetcdf
>> -L/opt/cray/hdf5-parallel/1.8.5.0/hdf5-parallel-gnu/lib -lhdf5_hl
>> -lhdf5 -L/usr/lib64/lib -lz -lm "
>>
>> Compilation failed with the message that mpi.h is not found. So I
>> modified the cflags like this:
>>
>> cflags=" -I${includedir}
>> -I/opt/cray/mpt/5.6.4/gni/mpich2-cray64/74/include" and now the
>> compilation fails with this message:
>>
>> ********************** Results of ncdf4 package configure
>> *******************
>>
>> netCDF v4 CPP flags =
>> -I/opt/cray/netcdf-hdf5parallel/4.1.1.0/netcdf-hdf5parallel-gnu/include
>> -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include
>> netCDF v4 LD flags =
>> -Wl,-rpath,/opt/cray/netcdf-hdf5parallel/4.1.1.0/netcdf-hdf5parallel-gnu/lib
>>
>> -Wl,-rpath,/opt/cray/hdf5-parallel/1.8.5.0/hdf5-parallel-gnu/lib
>> -Wl,-rpath,/usr/lib64/lib
>> -L/opt/cray/netcdf-hdf5parallel/4.1.1.0/netcdf-hdf5parallel-gnu/lib
>> -lnetcdf -L/opt/cray/hdf5-parallel/1.8.5.0/hdf5-parallel-gnu/lib
>> -lhdf5_hl -lhdf5 -L/usr/lib64/lib -lz -lm
>> netCDF v4 runtime path =
>> -Wl,-rpath,/opt/cray/netcdf-hdf5parallel/4.1.1.0/netcdf-hdf5parallel-gnu/lib
>>
>> -Wl,-rpath,/opt/cray/hdf5-parallel/1.8.5.0/hdf5-parallel-gnu/lib
>> -Wl,-rpath,/usr/lib64/lib
>>
>> ******************************************************************************
>>
>> ** libs
>> gcc -std=gnu99
>> -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG
>> -I/opt/cray/netcdf-hdf5parallel/4.1.1.0/netcdf-hdf5parallel-gnu/include
>> -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -I/usr/local/include
>> -fpic -g -O2 -c ncdf.c -o ncdf.o
>> gcc -std=gnu99
>> -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG
>> -I/opt/cray/netcdf-hdf5parallel/4.1.1.0/netcdf-hdf5parallel-gnu/include
>> -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -I/usr/local/include
>> -fpic -g -O2 -c ncdf2.c -o ncdf2.o
>> gcc -std=gnu99
>> -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG
>> -I/opt/cray/netcdf-hdf5parallel/4.1.1.0/netcdf-hdf5parallel-gnu/include
>> -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -I/usr/local/include
>> -fpic -g -O2 -c ncdf3.c -o ncdf3.o
>> gcc -std=gnu99
>> -I/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/include -DNDEBUG
>> -I/opt/cray/netcdf-hdf5parallel/4.1.1.0/netcdf-hdf5parallel-gnu/include
>> -I/opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include -I/usr/local/include
>> -fpic -g -O2 -c src_ncdf4.c -o src_ncdf4.o
>> gcc -std=gnu99 -shared
>> -L/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64 -Wl,-rpath
>> -Wl,/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64
>> -L/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/build/tmp/R-3.0.0/lib -o
>> ncdf4.so ncdf.o ncdf2.o ncdf3.o src_ncdf4.o
>> -Wl,-rpath,/opt/cray/netcdf-hdf5parallel/4.1.1.0/netcdf-hdf5parallel-gnu/lib
>>
>> -Wl,-rpath,/opt/cray/hdf5-parallel/1.8.5.0/hdf5-parallel-gnu/lib
>> -Wl,-rpath,/usr/lib64/lib
>> -L/opt/cray/netcdf-hdf5parallel/4.1.1.0/netcdf-hdf5parallel-gnu/lib
>> -lnetcdf -L/opt/cray/hdf5-parallel/1.8.5.0/hdf5-parallel-gnu/lib
>> -lhdf5_hl -lhdf5 -L/usr/lib64/lib -lz -lm
>> -L/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0/system/usr/lib64/R/lib -lR
>> /usr/bin/ld:
>> /opt/cray/netcdf-hdf5parallel/4.1.1.0/netcdf-hdf5parallel-gnu/lib/libnetcdf.a(nc4attr.o):
>>
>> relocation R_X86_64_32 against `.rodata' can not be used when making a
>> shared object; recompile with -fPIC
>> /opt/cray/netcdf-hdf5parallel/4.1.1.0/netcdf-hdf5parallel-gnu/lib/libnetcdf.a:
>>
>> could not read symbols: Bad value
>> collect2: error: ld returned 1 exit status
>> make: *** [ncdf4.so] Error 1
>> ERROR: compilation failed for package ?ncdf4?
>>
>>
>> I have tried instead -I/opt/cray/mpt/5.6.4/gni/mpich2-cray64/74/include
>> to also use /opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/include and
>> /opt/cray/mpt/5.6.4/gni/mpich2-cray/74/include, but I always get the
>> same error message. I have found this:
>> http://www.gentoo.org/proj/en/base/amd64/howtos/?part=1&chap=3
>> on this topic, but I get confused, because as one can see -fpic is
>> already used as a flag.
>>
>> By the way my environment is as follows:
>> ipmiva at eslogin001:/univ_2/ws3/ws/ipmiva-WRF_331_CORDEX-0> module list
>> Currently Loaded Modulefiles:
>> 1) modules/3.2.6.7 14)
>> ugni/4.0-1.0401.5928.9.5.gem 27) lbcd/2.1-1.0401.35360.1.2.gem
>> 2) xtpe-network-gemini 15)
>> pmi/4.0.1-1.0000.9421.73.3.gem 28)
>> nodehealth/5.0-1.0401.38460.12.18.gem
>> 3) xtpe-interlagos 16)
>> dmapp/3.2.1-1.0401.5983.4.5.gem 29) pdsh/2.26-1.0401.37449.1.1.gem
>> 4) cray-mpich2/5.6.4 17)
>> gni-headers/2.1-1.0401.5675.4.4.gem 30)
>> shared-root/1.0-1.0401.37253.3.50.gem
>> 5) eswrap/1.0.9 18)
>> xpmem/0.1-2.0401.36790.4.3.gem 31)
>> switch/1.0-1.0401.36779.2.72.gem
>> 6) torque/2.5.9 19)
>> job/1.5.5-0.1_2.0401.35380.1.10.gem 32) xe-sysroot/4.1.40
>> 7) moab/6.1.5.s1992 20)
>> csa/3.0.0-1_2.0401.37452.4.50.gem 33) atp/1.6.2
>> 8) system/ws_tools 21)
>> dvs/1.8.6_0.9.0-1.0401.1401.1.120 34) PrgEnv-gnu/4.1.40
>> 9) system/hlrs-defaults 22)
>> rca/1.0.0-2.0401.38656.2.2.gem 35) craype-target-native
>> 10) xt-asyncpe/5.19 23)
>> audit/1.0.0-1.0401.37969.2.32.gem 36) hdf5-parallel/1.8.5.0
>> 11) gcc/4.7.2 24)
>> ccm/2.2.0-1.0401.37254.2.142 37) netcdf-hdf5parallel/4.1.1.0
>> 12) xt-libsci/12.0.01 25)
>> configuration/1.0-1.0401.35391.1.2.gem
>> 13) udreg/2.3.2-1.0401.5929.3.3.gem 26)
>> hosts/1.0-1.0401.35364.1.115.gem
>>
>>
>> Any suggestions will be appreciated.
>>
>> Best regards,
>>
>> Martin
>>
>>
>>
>>
>>
>> --
>> Dr. Martin Ivanov
>> Eberhard-Karls-Universit?t T?bingen
>> Mathematisch-Naturwissenschaftliche Fakult?t
>> Fachbereich Geowissenschaften
>> Water & Earth System Science (WESS)
>> H?lderlinstra?e 12, 72074 T?bingen, Deutschland
>> Tel. +4970712974213
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Sat, 04 May 2013 15:30:40 +0200
>> From: Martin Ivanov <martin.ivanov at ifg.uni-tuebingen.de>
>> To: Rodney Sparapani <rsparapa at mcw.edu>
>> Cc: Martin Ivanov
>> <public-martin.ivanov-qUHYnPI9w1ZN1tXVncjlcWfrygkm6VTR at plane.gmane.org>,
>> r-sig-hpc at r-project.org,
>> public-r-sig-hpc-0bNBQ1PAWB4BXFe83j6qeQ at plane.gmane.org
>> Subject: Re: [R-sig-hpc] Trouble compiling R-3.0.0 an a Linux Cluster
>> (Martin Ivanov)
>> Message-ID: <51850D80.5060606 at ifg.uni-tuebingen.de>
>> Content-Type: text/plain; charset=UTF-8; format=flowed
>>
>> Dear Dr Sparapani,
>>
>>
>> Thank You very much for Your suggestion, it worked like a charm. Finally
>> I have R-3.0.0 on Cray XE6.
>> Now I have another problem: I cannot install ncdf4, which I have
>> described in another thread, called
>> "cannot install ncdf4_1.6.1 in R-3.0.0 on Cray XE6 HERMIT".
>>
>> Best regards,
>> Martin
>>
>> On 04/30/2013 06:26 PM, Rodney Sparapani wrote:
>>> On 04/29/2013 04:54 PM, Pragnesh Patel wrote:
>>>> export LD_LIBRARY_PATH=$R_WORK_HOME/lib64/R/lib:$LD_LIBRARY_PATH
>>> Good catch. But, instead of fooling around with LD_LIBRARY_PATH,
>>> which can cause all kinds of headaches, you might be better off
>>> trying something like...
>>>
>>> LDFLAGS="-L$PREFIX/lib${LIBDIRSUFFIX} -Wl,-rpath \
>>> -Wl,$PREFIX/lib${LIBDIRSUFFIX}"
>>>
>>> Rodney
>>>
>>> _______________________________________________
>>> R-sig-hpc mailing list
>>> R-sig-hpc at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>
>> --
>> Dr. Martin Ivanov
>> Eberhard-Karls-Universit?t T?bingen
>> Mathematisch-Naturwissenschaftliche Fakult?t
>> Fachbereich Geowissenschaften
>> Water & Earth System Science (WESS)
>> H?lderlinstra?e 12, 72074 T?bingen, Deutschland
>> Tel. +4970712974213
>>
>>
>>
>> ------------------------------
>>
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>> R-sig-hpc at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>
>>
>> End of R-sig-hpc Digest, Vol 56, Issue 4
>> ****************************************
>>
>
--
Dr. Martin Ivanov
Eberhard-Karls-Universität Tübingen
Mathematisch-Naturwissenschaftliche Fakultät
Fachbereich Geowissenschaften
Water & Earth System Science (WESS)
Hölderlinstraße 12, 72074 Tübingen, Deutschland
Tel. +4970712974213
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