[MOAB-dev] problem building MOAB

Tue Mar 13 09:30:46 CDT 2012

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'