[Dune] Problems compiling dune trunk on Cray XT6
Benedikt Oswald
benedikt.oswald at psi.ch
Mon Nov 12 10:10:31 CET 2012
Dear Dune,
I am experiencing problems when compiling the trunk version of Dune on
the Cray XT6. In fact, I am using the Cray environment which I have always used,
i.e. compilers, mpi etc.
Thanks for having a look! Greetings, Benedikt
Below, you find the versions I use and the error messages from the XT6:
URL: https://svn.dune-project.org/svn/dune-common/trunk
Repository Root: https://svn.dune-project.org/svn/dune-common
Repository UUID: 419231ca-4411-0410-aba2-fc6cf8c4f609
Revision: 7058
Node Kind: directory
Schedule: normal
Last Changed Author: gruenich
Last Changed Rev: 7058
Last Changed Date: 2012-11-11 09:17:08 +0100 (Sun, 11 Nov 2012)
Path: .
URL: https://svn.dune-project.org/svn/dune-geometry/trunk
Repository Root: https://svn.dune-project.org/svn/dune-geometry
Repository UUID: e31b3757-9ccd-424d-b11c-a976522ded21
Revision: 350
Node Kind: directory
Schedule: normal
Last Changed Author: sander
Last Changed Rev: 349
Last Changed Date: 2012-11-08 12:54:57 +0100 (Thu, 08 Nov 2012)
Path: .
URL: https://svn.dune-project.org/svn/dune-grid/trunk
Repository Root: https://svn.dune-project.org/svn/dune-grid
Repository UUID: f82f27de-4411-0410-b156-930a902cda50
Revision: 8641
Node Kind: directory
Schedule: normal
Last Changed Author: robertk
Last Changed Rev: 8640
Last Changed Date: 2012-11-09 21:45:32 +0100 (Fri, 09 Nov 2012)
Path: .
URL: https://svn.dune-project.org/svn/dune-istl/trunk
Repository Root: https://svn.dune-project.org/svn/dune-istl
Repository UUID: 8c7282f0-4411-0410-8e4f-cdd3e049afb8
Revision: 1728
Node Kind: directory
Schedule: normal
Last Changed Author: christi
Last Changed Rev: 1728
Last Changed Date: 2012-11-06 14:06:44 +0100 (Tue, 06 Nov 2012)
Path: .
URL: https://svn.dune-project.org/svn/dune-grid-howto/trunk
Repository Root: https://svn.dune-project.org/svn/dune-grid-howto
Repository UUID: 971b7fa1-7d12-0410-b1b7-9c127676b1f7
Revision: 409
Node Kind: directory
Schedule: normal
Last Changed Author: christi
Last Changed Rev: 409
Last Changed Date: 2012-11-06 14:50:07 +0100 (Tue, 06 Nov 2012)
Now run ./configure to setup dune-geometry
--- calling configure for dune-geometry ---
----- using default flags $CONFIGURE_FLAGS from /scratch/rosa/boswald/svnwork/dune-trunk/os.cray.xt6.petsc32p6.opts -----
./configure MPICXX='CC' CXX='CC' CC='cc' F77=ftn LD='CC' CXXFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer -static --no-strict-aliasing -DHAVE_SUPERLU_DIST -I/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC -L/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/lib -lsuperlu_dist_2.5 -L/users/boswald/extlib/parmetis/3.2.0/xt-mpich2/5.5.0/gcc/4.6.2 -lparmetis -lmetis' CPPFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer -static --no-strict-aliasing -DHAVE_SUPERLU_DIST -I/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC -L/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/lib -lsuperlu_dist_2.5 -L/users/boswald/extlib/parmetis/3.2.0/xt-mpich2/5.5.0/gcc/4.6.2 -lparmetis -lmetis' CFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer -static --no-strict-aliasing -DHAVE_SUPERLU_DIST -I/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC -L/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/lib -lsuperlu_dist_2.5 -L/users/boswald/extlib/parmetis/3.2.0/xt-mpich2/5.5.0/gcc/4.6.2 -lparmetis -lmetis' FFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer -static --no-strict-aliasing' LDFLAGS='-static -L/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/lib -lsuperlu_dist_2.5 -lparmetis -lmetis' LTFLAGS=' ' --host=x86_64-unknown-linux-gnu --enable-static --disable-shared --disable-mpiruntest --enable-hades3deltd --enable-hades3dfetd --enable-hades3ddges --enable-hades3ddgfd --enable-hades3dfefd --enable-hades3dfeqs --disable-documentation --enable-parallel --enable-boost --enable-petsc --enable-debug-output --without-gmp --with-boost='/users/boswald/extlib/boost/1.50/gcc/4.6.2' --with-metis='/users/boswald/extlib/metis/4.0.3/gcc/4.6.2' --with-parmetis='/users/boswald/extlib/parmetis/3.2.0/xt-mpich2/5.5.0/gcc/4.6.2' --with-rlog='/users/boswald/extlib/rlog/svn-rev-21/gcc/4.6.2' --with-alugrid='/users/boswald/extlib/ALUGrid/1.94/xt-mpich2/5.5.0/gcc/4.6.2' --with-petsc='/users/boswald/extlib/petsc/3.2-p6/xt-mpich2/5.5.0/gcc/4.6.2' --prefix='/scratch/rosa/boswald/hades3d' "--with-dune-common=/scratch/rosa/boswald/svnwork/dune-trunk/dune-common/" ACLOCAL_AMFLAGS="-I . -I m4 -I /scratch/rosa/boswald/svnwork/dune-trunk/dune-common/m4"
configure: WARNING: unrecognized options: --enable-hades3deltd, --enable-hades3dfetd, --enable-hades3ddges, --enable-hades3ddgfd, --enable-hades3dfefd, --enable-hades3dfeqs, --enable-boost, --enable-petsc, --enable-debug-output, --with-boost, --with-metis, --with-parmetis, --with-rlog, --with-alugrid, --with-petsc
configure: WARNING: if you wanted to set the --build type, don't use --host.
If a cross compiler is detected then cross compile mode will be used
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for x86_64-unknown-linux-gnu-strip... no
checking for strip... strip
checking how to create a pax tar archive... gnutar
checking for x86_64-unknown-linux-gnu-strip... strip
checking how to create a pax tar archive... (cached) gnutar
checking for inkscape... no
checking for doxygen... no
checking for latex... no
checking for bibtex... no
checking for dvipdf... dvipdf
checking for dvips... dvips
checking for wml... no
checking for dot... dot
checking for perl... perl
checking for convert... convert
checking for x86_64-unknown-linux-gnu-pkg-config... no
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for style of include used by make... GNU
checking for x86_64-unknown-linux-gnu-gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking dependency style of cc... gcc3
checking dependency style of cc... (cached) gcc3
checking how to run the C preprocessor... cc -E
checking whether we are using the GNU C++ compiler... yes
checking whether CC accepts -g... yes
checking dependency style of CC... gcc3
checking dependency style of CC... (cached) gcc3
checking how to run the C++ preprocessor... CC -E
configure: Fortran compiler F77 (fortran 77) specified,
while FC (fortran 90) wasn't set.
Trying to use F77 as FC.
checking for x86_64-unknown-linux-gnu-g77... ftn
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether ftn accepts -g... yes
checking for x86_64-unknown-linux-gnu-gfortran... ftn
checking whether we are using the GNU Fortran compiler... yes
checking whether ftn accepts -g... yes
checking build system type... x86_64-suse-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /apps/ela/tools/bin/grep
checking for egrep... /apps/ela/tools/bin/grep -E
checking for fgrep... /apps/ela/tools/bin/grep -F
checking for ld used by cc... CC
checking if the linker (CC) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... no
checking for x86_64-unknown-linux-gnu-dumpbin... no
checking for x86_64-unknown-linux-gnu-link... no
checking for dumpbin... no
checking for link... link -dump -symbols
checking the name lister (link -dump -symbols) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for CC option to reload object files... -r
checking for x86_64-unknown-linux-gnu-objdump... no
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for x86_64-unknown-linux-gnu-ar... no
checking for ar... ar
checking for x86_64-unknown-linux-gnu-strip... (cached) strip
checking for x86_64-unknown-linux-gnu-ranlib... no
checking for ranlib... ranlib
checking command to parse link -dump -symbols output from cc object... failed
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether CC accepts -g... (cached) yes
checking dependency style of CC... (cached) gcc3
checking dependency style of CC... (cached) gcc3
checking how to run the C++ preprocessor... CC -E
checking for x86_64-unknown-linux-gnu-g77... (cached) ftn
checking whether we are using the GNU Fortran 77 compiler... (cached) yes
checking whether ftn accepts -g... (cached) yes
checking for x86_64-unknown-linux-gnu-gfortran... (cached) ftn
checking whether we are using the GNU Fortran compiler... (cached) yes
checking whether ftn accepts -g... (cached) yes
checking for objdir... .libs
checking if cc supports -fno-rtti -fno-exceptions... no
checking for cc option to produce PIC... -fPIC -DPIC
checking if cc PIC flag -fPIC -DPIC works... yes
checking if cc static flag -static works... yes
checking if cc supports -c -o file.o... yes
checking if cc supports -c -o file.o... (cached) yes
checking whether the cc linker (CC -m elf_x86_64) supports shared libraries... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... unsupported
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... no
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for ld used by CC... CC -m elf_x86_64
checking if the linker (CC -m elf_x86_64) is GNU ld... no
checking whether the CC linker (CC -m elf_x86_64) supports shared libraries... yes
checking for CC option to produce PIC... -fPIC -DPIC
checking if CC PIC flag -fPIC -DPIC works... yes
checking if CC static flag -static works... yes
checking if CC supports -c -o file.o... yes
checking if CC supports -c -o file.o... (cached) yes
checking whether the CC linker (CC -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... unsupported
checking if libtool supports shared libraries... no
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for ftn option to produce PIC... -fPIC
checking if ftn PIC flag -fPIC works... yes
checking if ftn static flag -static works... no
checking if ftn supports -c -o file.o... yes
checking if ftn supports -c -o file.o... (cached) yes
checking whether the ftn linker (CC -m elf_x86_64) supports shared libraries... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... unsupported
checking if libtool supports shared libraries... no
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for ftn option to produce PIC... -fPIC
checking if ftn PIC flag -fPIC works... yes
checking if ftn static flag -static works... no
checking if ftn supports -c -o file.o... yes
checking if ftn supports -c -o file.o... (cached) yes
checking whether the ftn linker (CC -m elf_x86_64) supports shared libraries... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... unsupported
checking for x86_64-unknown-linux-gnu-ranlib... ranlib
checking how to get verbose linking output from ftn... -v
checking for Fortran 77 libraries of ftn... -L/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/lib -L/apps/ela/alps/4.0.2-2.0400.7033.0/lib/alps -L/opt/cray/udreg/2.3.2-1.0400.4691.4.1.gem/lib64 -L/opt/cray/ugni/2.3-1.0400.4374.4.88.gem/lib64 -L/opt/cray/pmi/3.0.1-1.0000.8917.33.1.gem/lib64 -L/opt/cray/dmapp/3.2.1-1.0400.4255.2.159.gem/lib64 -L/opt/cray/xpmem/0.1-2.0400.31280.3.1.gem/lib64 -L/opt/cray/mpt/5.5.0/gni/mpich2-gnu/46/lib -L/opt/xt-libsci/11.1.00/gnu/46/interlagos/lib -L/usr/lib/alps -L/apps/ela/opt/gcc/4.6.2/snos/bin/../lib/gcc/x86_64-suse-linux/4.6.2 -L/apps/ela/opt/gcc/4.6.2/snos/bin/../lib/gcc -L/apps/ela/opt/gcc/4.6.2/snos/bin/../lib/gcc/x86_64-suse-linux/4.6.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/apps/ela/opt/gcc/4.6.2/snos/bin/../lib/gcc/x86_64-suse-linux/4.6.2/../../.. -lsuperlu_dist_2.5 -lparmetis -lmetis -L/opt/cray/atp/1.4.4/lib/ -lAtpSigHCommData -lAtpSigHandler -lscicpp_gnu -lsci_gnu_mp -lstdc++ -lgfortran -lm -lmpichf90_gnu_46 -lmpich_gnu_46 -lmpl -lrt -lxpmem -ldmapp -lugni -lpmi -lalpslli -lalpsutil -ludreg -lpthread -lgomp -lquadmath
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 for sgemm_... yes
checking for cheev_... yes
checking how to get verbose linking output from ftn... -v
checking for Fortran libraries of ftn... -L/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/lib -L/apps/ela/alps/4.0.2-2.0400.7033.0/lib/alps -L/opt/cray/udreg/2.3.2-1.0400.4691.4.1.gem/lib64 -L/opt/cray/ugni/2.3-1.0400.4374.4.88.gem/lib64 -L/opt/cray/pmi/3.0.1-1.0000.8917.33.1.gem/lib64 -L/opt/cray/dmapp/3.2.1-1.0400.4255.2.159.gem/lib64 -L/opt/cray/xpmem/0.1-2.0400.31280.3.1.gem/lib64 -L/opt/cray/mpt/5.5.0/gni/mpich2-gnu/46/lib -L/opt/xt-libsci/11.1.00/gnu/46/interlagos/lib -L/usr/lib/alps -L/apps/ela/opt/gcc/4.6.2/snos/bin/../lib/gcc/x86_64-suse-linux/4.6.2 -L/apps/ela/opt/gcc/4.6.2/snos/bin/../lib/gcc -L/apps/ela/opt/gcc/4.6.2/snos/bin/../lib/gcc/x86_64-suse-linux/4.6.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/apps/ela/opt/gcc/4.6.2/snos/bin/../lib/gcc/x86_64-suse-linux/4.6.2/../../.. -lsuperlu_dist_2.5 -lparmetis -lmetis -L/opt/cray/atp/1.4.4/lib/ -lAtpSigHCommData -lAtpSigHandler -lscicpp_gnu -lsci_gnu_mp -lstdc++ -lgfortran -lm -lmpichf90_gnu_46 -lmpich_gnu_46 -lmpl -lrt -lxpmem -ldmapp -lugni -lpmi -lalpslli -lalpsutil -ludreg -lpthread -lgomp -lquadmath
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking whether compiler is officially supported by DUNE... yes
checking whether CC accepts -std=c++11... no
checking whether CC accepts -std=c++0x... yes
checking whether static_assert is supported... yes
checking whether nullptr is supported... yes
checking type_traits usability... yes
checking type_traits presence... yes
checking for type_traits... yes
checking tr1/type_traits usability... yes
checking tr1/type_traits presence... yes
checking for tr1/type_traits... yes
checking tuple usability... yes
checking tuple presence... yes
checking for tuple... yes
checking tr1/tuple usability... yes
checking tr1/tuple presence... yes
checking for tr1/tuple... yes
checking whether <array> C++0x is supported... yes
checking whether integral_constant conforming to C++11 is supported... yes
checking memory usability... yes
checking memory presence... yes
checking for memory... yes
checking tr1/memory usability... yes
checking tr1/memory presence... yes
checking for tr1/memory... yes
checking boost/shared_ptr.hpp usability... no
checking boost/shared_ptr.hpp presence... no
checking for boost/shared_ptr.hpp... no
checking the location of shared_ptr header file...
checking whether SHARED_PTR_NAMESPACE (std) provides make_shared... yes
checking whether compiling C++ code works... yes
checking whether linking C++ objects works... yes
checking for __attribute__((deprecated))... yes
checking for __attribute__((deprecated("message")))... yes
checking for __attribute__((unused))... yes
checking rpc/rpc.h usability... yes
checking rpc/rpc.h presence... yes
checking for rpc/rpc.h... yes
checking for mpicc... no
checking for hcc... no
checking for mpcc... no
checking for mpcc_r... no
checking for mpxlc... no
checking for cmpicc... no
checking for MPI_Init... yes
checking for mpi.h... yes
configure: Trying to identify the version of MPI compiler cc
checking for lam... no
checking for mpich... no
checking for OpenMPI... no
checking for MVAPICH... no
checking for MVAPICH2... no
checking for mpich2... yes
checking whether compiling with MPICH2 works... yes
configure: WARNING: Disabled test whether running with MPICH2 works.
checking for MPI_Finalized in -lm... yes
checking sys/mman.h usability... yes
checking sys/mman.h presence... yes
checking for sys/mman.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
configure: skipping check for GMP
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for string.h... (cached) yes
checking for pow in -lm... yes
checking for sqrt... yes
checking for strchr... yes
configure: creating ./config.lt
config.lt: creating libtool
checking for dune-common installation or source tree... found in /scratch/rosa/boswald/svnwork/dune-trunk/dune-common
checking dune/common/stdstreams.hh usability... yes
checking dune/common/stdstreams.hh presence... yes
checking for dune/common/stdstreams.hh... yes
checking for libdunecommon... no
configure: WARNING: /scratch/rosa/boswald/svnwork/dune-trunk/dune-common does not seem to contain a valid dune-common (failed to link with libdunecommon.la)
configure: error: could not find required module dune-common
--- Failed to build dune-geometry ---
Terminating dunecontrol due to previous errors!
56.083u 166.214s 5:00.48 73.9% 0+0k 3224+448224io 0pf+0w
Linux ela3 2.6.32.59-0.7-default #1 SMP 2012-07-13 15:50:56 +0200 x86_64 x86_64 x86_64 GNU/Linux
ela3 svnwork/dune-trunk> module li
Currently Loaded Modulefiles:
1) ela 5) alps/4.0.2-2.0400.7033.0 9) totalview-support/1.1.3 13) pmi/3.0.1-1.0000.8917.33.1.gem 17) xt-asyncpe/5.11
2) slurm 6) udreg/2.3.2-1.0400.4691.4.1.gem 10) xt-totalview/8.10.0 14) dmapp/3.2.1-1.0400.4255.2.159.gem 18) atp/1.4.4
3) xtpe-interlagos 7) rosa 11) xt-libsci/11.1.00 15) gni-headers/2.1-1.0400.4351.3.1.gem 19) PrgEnv-gnu/4.0.46
4) xt-mpich2/5.5.0 8) xtpe-network-gemini 12) ugni/2.3-1.0400.4374.4.88.gem 16) xpmem/0.1-2.0400.31280.3.1.gem 20) gcc/4.6.2
--------------------------------------------------------------------------------------------------------------------------------------------------------------------
Benedikt Oswald, Dr. sc. techn., dipl. El. Ing. ETH, www.psi.ch, GFA
Paul Scherrer Institute (PSI), CH-5232 Villigen, Suisse, benedikt.oswald at psi.ch, +41(0)56 310 32 12
"Passion is required for any great work, and for the revolution passion and audacity are required in big doses.",
Ernesto 'Che' Guevara, Letter to his parents.
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