[MOAB-dev] problem building MOAB
Lorenzo Alessio Botti
ihabiamx at yahoo.it
Tue Mar 13 09:57:08 CDT 2012
Sorry, it seems that the libtool versions I got with apt-get were outdated...
Installing the latest version
http://ftpmirror.gnu.org/libtool/libtool-2.4.2.tar.gz
solves the problem.
Thanks
Lorenzo
> On Mar 13, 2012, at 3:53 PM, Iulian Grindeanu wrote:
>
>> Hi ,
>> I would suggest doing a very clean build after updating libtool. It seems to be an autotools problem, not moab.
>> Can you send the output of autoreconf -fi and the config.log?
>> I did not see this error before, and searching online did not offer any fixes except libtool updates, as you found out too.
>>
>> Iulian
>> Hi all,
>> sorry to bother you but I have a problem building MOAB on a debian cluster.
>> I've tried different versions of libtool but I always get the same error running make.
>>
>> The problem seems to be related with
>> ./libtool: line 835: X--tag=CXX: command not found
>>
>> I found different different bug reports related to this command e.g.
>> http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=526585
>> but I really don't know how to solve it.
>>
>> Thanks in advance.
>> Lorenzo
>>
>>
>>
>>
>> botti at frontend:~/src2/moab-4.1.0$ autoreconf -fi
>> configure.ac:33: warning: macro `AM_SILENT_RULES' not found in library
>> configure.ac:35: warning: macro `AM_SILENT_RULES' not found in library
>> You should update your `aclocal.m4' by running aclocal.
>> Putting files in AC_CONFIG_AUX_DIR, `config'.
>> configure.ac:33: warning: macro `AM_SILENT_RULES' not found in library
>> configure.ac:35: warning: macro `AM_SILENT_RULES' not found in library
>> test/parallel/Makefile.am:17: `:='-style assignments are not portable
>>
>>
>>
>> botti at frontend:~/src2/moab-4.1.0$ ./configure --with-szip=/home/botti/src2/szip-2.1/szip/ --with-zlib=/home/botti/src2/zlib-1.2.6/ --with-hdf5=/home/botti/src2/hdf5-1.8.8/ --with-mpi=/home/botti/src2/mpich2-install/ --disable-imesh --with-zoltan=/home/botti/src2/Zoltan_v3.6/build_dir --with-metis=/home/botti/src2/ParMETIS3_1/METISLib/ --with-zoltan-arch=gcc --enable-mbzoltan --with-parmetis=/home/botti/src2/ParMETIS3_1/
>> checking build system type... x86_64-unknown-linux-gnu
>> checking host system type... x86_64-unknown-linux-gnu
>> checking target system type... x86_64-unknown-linux-gnu
>> 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 sed... sed
>> checking for style of include used by make... GNU
>> checking for gcc... mpicc
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether mpicc accepts -g... yes
>> checking for mpicc option to accept ISO C89... none needed
>> checking dependency style of mpicc... gcc3
>> checking how to run the C preprocessor... mpicc -E
>> checking whether we are using the GNU C++ compiler... yes
>> checking whether mpicxx accepts -g... yes
>> checking dependency style of mpicxx... gcc3
>> checking how to run the C++ preprocessor... mpicxx -E
>> checking whether we are using the GNU Fortran compiler... yes
>> checking whether /home/botti/src2/mpich2-install//bin/mpif90 accepts -g... yes
>> checking whether we are using the GNU Fortran 77 compiler... yes
>> checking whether /home/botti/src2/mpich2-install//bin/mpif77 accepts -g... yes
>> checking whether ln -s works... yes
>> checking whether make sets $(MAKE)... (cached) yes
>> checking for a sed that does not truncate output... sed
>> checking for grep that handles long lines and -e... /bin/grep
>> checking for egrep... /bin/grep -E
>> checking for fgrep... /bin/grep -F
>> checking for ld used by mpicc... /usr/bin/ld
>> checking if the linker (/usr/bin/ld) is GNU ld... yes
>> checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
>> checking the name lister (/usr/bin/nm -B) interface... BSD nm
>> checking the maximum length of command line arguments... 98304
>> checking whether the shell understands some XSI constructs... yes
>> checking whether the shell understands "+="... yes
>> checking for /usr/bin/ld option to reload object files... -r
>> checking for objdump... objdump
>> checking how to recognize dependent libraries... pass_all
>> checking for ar... ar
>> checking for strip... strip
>> checking for ranlib... ranlib
>> checking command to parse /usr/bin/nm -B output from mpicc object... ok
>> 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 mpicxx accepts -g... (cached) yes
>> checking dependency style of mpicxx... (cached) gcc3
>> checking how to run the C++ preprocessor... mpicxx -E
>> checking whether we are using the GNU Fortran 77 compiler... (cached) yes
>> checking whether /home/botti/src2/mpich2-install//bin/mpif77 accepts -g... (cached) yes
>> checking whether we are using the GNU Fortran compiler... (cached) yes
>> checking whether /home/botti/src2/mpich2-install//bin/mpif90 accepts -g... (cached) yes
>> checking for objdir... .libs
>> checking if mpicc supports -fno-rtti -fno-exceptions... no
>> checking for mpicc option to produce PIC... -fPIC -DPIC
>> checking if mpicc PIC flag -fPIC -DPIC works... yes
>> checking if mpicc static flag -static works... yes
>> checking if mpicc supports -c -o file.o... yes
>> checking if mpicc supports -c -o file.o... (cached) yes
>> checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
>> checking dynamic linker characteristics... GNU/Linux ld.so
>> checking how to hardcode library paths into programs... immediate
>> checking whether stripping libraries is possible... yes
>> checking if libtool supports shared libraries... yes
>> checking whether to build shared libraries... no
>> checking whether to build static libraries... yes
>> checking for ld used by mpicxx... /usr/bin/ld -m elf_x86_64
>> checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
>> checking whether the mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
>> checking for mpicxx option to produce PIC... -fPIC -DPIC
>> checking if mpicxx PIC flag -fPIC -DPIC works... yes
>> checking if mpicxx static flag -static works... yes
>> checking if mpicxx supports -c -o file.o... yes
>> checking if mpicxx supports -c -o file.o... (cached) yes
>> checking whether the mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
>> checking dynamic linker characteristics... GNU/Linux ld.so
>> checking how to hardcode library paths into programs... immediate
>> checking if libtool supports shared libraries... yes
>> checking whether to build shared libraries... no
>> checking whether to build static libraries... yes
>> checking for /home/botti/src2/mpich2-install//bin/mpif77 option to produce PIC... -fPIC
>> checking if /home/botti/src2/mpich2-install//bin/mpif77 PIC flag -fPIC works... yes
>> checking if /home/botti/src2/mpich2-install//bin/mpif77 static flag -static works... yes
>> checking if /home/botti/src2/mpich2-install//bin/mpif77 supports -c -o file.o... yes
>> checking if /home/botti/src2/mpich2-install//bin/mpif77 supports -c -o file.o... (cached) yes
>> checking whether the /home/botti/src2/mpich2-install//bin/mpif77 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
>> checking dynamic linker characteristics... GNU/Linux ld.so
>> checking how to hardcode library paths into programs... immediate
>> checking if libtool supports shared libraries... yes
>> checking whether to build shared libraries... no
>> checking whether to build static libraries... yes
>> checking for /home/botti/src2/mpich2-install//bin/mpif90 option to produce PIC... -fPIC
>> checking if /home/botti/src2/mpich2-install//bin/mpif90 PIC flag -fPIC works... yes
>> checking if /home/botti/src2/mpich2-install//bin/mpif90 static flag -static works... yes
>> checking if /home/botti/src2/mpich2-install//bin/mpif90 supports -c -o file.o... yes
>> checking if /home/botti/src2/mpich2-install//bin/mpif90 supports -c -o file.o... (cached) yes
>> checking whether the /home/botti/src2/mpich2-install//bin/mpif90 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
>> checking dynamic linker characteristics... GNU/Linux ld.so
>> checking how to hardcode library paths into programs... immediate
>> checking for known C compilers... GNU
>> checking for known compiler/OS combinations... GNU:x86_64
>> checking for known c++ compilers... GNU
>> checking for known compiler/OS combinations... GNU:x86_64
>> checking if platform is IBM BlueGene... no
>> checking for gunzip... gunzip -c
>> checking for gzip... (cached) gunzip -c
>> checking for zcat... (cached) gunzip -c
>> checking if C++ compiler supports template class specialization... yes
>> checking if C++ compiler supports template function specialization... yes
>> checking if mpicxx works... yes
>> checking how to get verbose linking output from /home/botti/src2/mpich2-install//bin/mpif90... -v
>> checking for Fortran libraries of /home/botti/src2/mpich2-install//bin/mpif90... -L/home/botti/src2/mpich2-install/lib -L/usr/lib/gcc/x86_64-linux-gnu/4.3.2 -L/usr/lib/gcc/x86_64-linux-gnu/4.3.2/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.3.2/../../.. -lgfortranbegin -lgfortran -lm -lmpichf90 -lmpich -lopa -lmpl -lrt -lpthread
>> checking for dummy main to link with Fortran libraries... none
>> checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
>> checking for vsnprintf... yes
>> checking if std::vector has templatized insert method... yes
>> checking if std::copy must be old SGI format... no
>> checking for inttypes.h... (cached) yes
>> checking for stdint.h... (cached) yes
>> checking for sys/types.h... (cached) yes
>> checking stddef.h usability... yes
>> checking stddef.h presence... yes
>> checking for stddef.h... yes
>> checking for stdlib.h... (cached) yes
>> checking for void *... yes
>> checking size of void *... 8
>> checking for size_t... yes
>> checking for ptrdiff_t... yes
>> checking size of EntityHandle... 8
>> checking if iMesh support is to be built... no
>> checking if iGeom support is to be built... no
>> configure: creating ./config.lt
>> config.lt: creating libtool
>> ./libtool: line 835: X--tag=CXX: command not found
>> ./libtool: line 868: libtool: ignoring unknown tag : command not found
>> ./libtool: line 835: X--tag=CXX: command not found
>> ./libtool: line 868: libtool: ignoring unknown tag : command not found
>> checking ieeefp.h usability... no
>> checking ieeefp.h presence... no
>> checking for ieeefp.h... no
>> checking for C++ unordered_map... std::tr1
>> checking mpi.h usability... yes
>> checking mpi.h presence... yes
>> checking for mpi.h... yes
>> checking If mpi.h conflicts with C headers in C++... no
>> checking for mpiexec... mpiexec
>> checking for deflate in -lz... yes
>> checking for SZ_Decompress in -lsz... yes
>> checking if HDF5 support is enabled... yes
>> checking hdf5.h usability... yes
>> checking hdf5.h presence... yes
>> checking for hdf5.h... yes
>> checking for gpfs_stat in -lgpfs... no
>> checking for H5Fopen in -lhdf5... yes
>> checking for H5Pset_fapl_mpio in -lhdf5... yes
>> checking for H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS... yes
>> checking if CCMIO support is enabled... yes
>> checking if CCMIO support available...
>> checking ccmio.h usability... no
>> checking ccmio.h presence... no
>> checking for ccmio.h... no
>> checking ccmioutility.h usability... no
>> checking ccmioutility.h presence... no
>> checking for ccmioutility.h... no
>> checking ccmiocore.h usability... no
>> checking ccmiocore.h presence... no
>> checking for ccmiocore.h... no
>> checking unsuccessful, Ccmio support disabled...
>> checking if NetCDF support is enabled... yes
>> checking netcdf.h usability... no
>> checking netcdf.h presence... no
>> checking for netcdf.h... no
>> configure: WARNING: NetCDF header not found.
>> checking for nc_create in -lnetcdf... no
>> checking for nc_create in -lnetcdf... no
>> checking for nc_create in -lnetcdf... no
>> configure: WARNING: "NetCDF support disabled"
>> checking if Pnetcdf support is enabled... yes
>> checking pnetcdf.h usability... no
>> checking pnetcdf.h presence... no
>> checking for pnetcdf.h... no
>> checking for ncmpi_create in -lpnetcdf... no
>> checking if mbconvert is to be built... yes
>> checking if hexmodops is to be built... yes
>> checking if qvdual is to be built... no
>> checking if vtkMOABReader is to be built... no
>> checking if mbsize is to be built... yes
>> checking if mbskin is to be built... yes
>> checking if mbtagprop is to be built... yes
>> checking if mbmem is to be built... yes
>> checking if mcnpmit is to be built... no
>> checking if mbcoupler is to be built... no
>> checking if spheredecomp is to be built... yes
>> checking if mbsurfplot is to be built... yes
>> checking if mbzoltan is to be built... yes
>> checking if dagmc is to be built... yes
>> checking if gsets is to be built... yes
>> checking if mbdepth is to be built... yes
>> checking if refiner is to be built... no
>> checking if h5mtools is to be built... yes
>> checking for zoltan_cpp.h... yes
>> checking for Zoltan_LB_Partition in -lzoltan... no
>> checking for Zoltan_LB_Partition in -lzoltan... yes
>> configure: creating ./config.status
>> config.status: creating Makefile
>> config.status: creating moab.make
>> config.status: creating src/Makefile
>> config.status: creating src/io/Makefile
>> config.status: creating src/io/mhdf/Makefile
>> config.status: creating src/parallel/Makefile
>> config.status: creating src/oldinc/Makefile
>> config.status: creating test/Makefile
>> config.status: creating test/h5file/Makefile
>> config.status: creating test/dual/Makefile
>> config.status: creating test/obb/Makefile
>> config.status: creating test/perf/Makefile
>> config.status: creating test/io/Makefile
>> config.status: creating test/parallel/Makefile
>> config.status: creating test/oldinc/Makefile
>> config.status: creating itaps/Makefile
>> config.status: creating itaps/imesh/Makefile
>> config.status: creating itaps/imesh/iMesh-Defs.inc
>> config.status: creating itaps/igeom/Makefile
>> config.status: creating itaps/igeom/iGeom-Defs.inc
>> config.status: creating tools/Makefile
>> config.status: creating tools/refiner/Makefile
>> config.status: creating tools/mbcoupler/Makefile
>> config.status: creating tools/mbzoltan/Config.moab
>> config.status: creating tools/mbzoltan/Makefile
>> config.status: creating tools/mcnpmit/Makefile
>> config.status: creating tools/qvdual/Makefile
>> config.status: creating tools/vtkMOABReader/Makefile
>> config.status: creating tools/dagmc/Makefile
>> config.status: creating doc/Makefile
>> config.status: creating doc/user.dox
>> config.status: creating examples/Makefile
>> config.status: creating examples/examples.make
>> config.status: creating examples/simple/makefile
>> config.status: creating MeshFiles/Makefile
>> config.status: creating MeshFiles/unittest/Makefile
>> config.status: creating MeshFiles/unittest/io/Makefile
>> config.status: creating config.h
>> config.status: config.h is unchanged
>> config.status: creating src/moab/Version.h
>> config.status: src/moab/Version.h is unchanged
>> config.status: creating src/moab/EntityHandle.hpp
>> config.status: src/moab/EntityHandle.hpp is unchanged
>> config.status: creating src/parallel/moab_mpi_config.h
>> config.status: src/parallel/moab_mpi_config.h is unchanged
>> config.status: creating src/FCDefs.h
>> config.status: src/FCDefs.h is unchanged
>> config.status: executing depfiles commands
>> config.status: executing libtool commands
>> config.status: executing src/MOAB_FCDefs.h commands
>> C: mpicc -Wall -pipe -pedantic -Wno-long-long -O2 -DNDEBUG -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map
>> C++: mpicxx -Wall -pipe -pedantic -Wno-long-long -O2 -DNDEBUG -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map
>> Fortran: /home/botti/src2/mpich2-install//bin/mpif90 -g -O2 -O2
>> configure: WARNING:
>> *************************************************************************
>> * MOAB has been configured w/out the NetCDF library.
>> * Support for ExodusII/Genesis and other file formats is disabled!
>> *************************************************************************
>>
>>
>>
>> botti at frontend:~/src2/moab-4.1.0$ make
>> make all-recursive
>> make[1]: Entering directory `/home/botti/src2/moab-4.1.0'
>> Making all in src
>> make[2]: Entering directory `/home/botti/src2/moab-4.1.0/src'
>> cd .. && /bin/sh /home/botti/src2/moab-4.1.0/config/missing --run autoheader
>> rm -f stamp-h5
>> touch FCDefs.h.in
>> cd .. && /bin/sh ./config.status src/FCDefs.h
>> config.status: creating src/FCDefs.h
>> config.status: src/FCDefs.h is unchanged
>> make all-recursive
>> make[3]: Entering directory `/home/botti/src2/moab-4.1.0/src'
>> Making all in parallel
>> make[4]: Entering directory `/home/botti/src2/moab-4.1.0/src/parallel'
>> cd ../.. && /bin/sh /home/botti/src2/moab-4.1.0/config/missing --run autoheader
>> rm -f stamp-h4
>> touch moab_mpi_config.h.in
>> cd ../.. && /bin/sh ./config.status src/parallel/moab_mpi_config.h
>> config.status: creating src/parallel/moab_mpi_config.h
>> config.status: src/parallel/moab_mpi_config.h is unchanged
>> make all-am
>> make[5]: Entering directory `/home/botti/src2/moab-4.1.0/src/parallel'
>> /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src -I/home/botti/src2/hdf5-1.8.8/ -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DIS_BUILDING_MB -DSRCDIR=. -I./.. -I.. -I./../io -I./../io/mhdf/include -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -Wall -pipe -pedantic -Wno-long-long -O2 -DNDEBUG -MT ParallelComm.lo -MD -MP -MF .deps/ParallelComm.Tpo -c -o ParallelComm.lo ParallelComm.cpp
>> ../../libtool: line 835: X--tag=CXX: command not found
>> ../../libtool: line 868: libtool: ignoring unknown tag : command not found
>> ../../libtool: line 835: X--mode=compile: command not found
>> ../../libtool: line 1002: *** Warning: inferring the mode of operation is deprecated.: command not found
>> ../../libtool: line 1003: *** Future versions of Libtool will require --mode=MODE be specified.: command not found
>> ../../libtool: line 1033: libtool: warning: cannot infer operation mode from `mpicxx': command not found
>> ../../libtool: line 7096: libtool: you must specify a MODE: command not found
>> ../../libtool: line 7097: Try `libtool --help' for more information.: command not found
>> make[5]: *** [ParallelComm.lo] Error 1
>> make[5]: Leaving directory `/home/botti/src2/moab-4.1.0/src/parallel'
>> make[4]: *** [all] Error 2
>> make[4]: Leaving directory `/home/botti/src2/moab-4.1.0/src/parallel'
>> make[3]: *** [all-recursive] Error 1
>> make[3]: Leaving directory `/home/botti/src2/moab-4.1.0/src'
>> make[2]: *** [all] Error 2
>> make[2]: Leaving directory `/home/botti/src2/moab-4.1.0/src'
>> make[1]: *** [all-recursive] Error 1
>> make[1]: Leaving directory `/home/botti/src2/moab-4.1.0'
>
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