cannot install ncdf4_1.6.1 in R-3.0.0 on Cray XE6 HERMIT (R-sig-hpc Digest, Vol 56, Issue 4)
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
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https://stat.ethz.ch/mailman/listinfo/r-sig-hpc or, via email, send a message with subject or body 'help' to r-sig-hpc-request at r-project.org You can reach the person managing the list at r-sig-hpc-owner at r-project.org When replying, please edit your Subject line so it is more specific than "Re: Contents of R-sig-hpc digest..." 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 ------------------------------ _______________________________________________ R-sig-hpc mailing list 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 ****************************************
pragnesh patel Graduate Student | Computer Science Indiana University Bloomington