Configure Error

[astron...@gmail.com]

Dear Prof. Griffith

My operating system is Ubuntu 12.4 x64. I got IBAMR source code through “git clone https://github.com/IBAMR/IBAMR.git”. When I entered IBAMR folder and typed the command: "./configure", I faced the following error:

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 whether make supports nested variables... yes

checking whether make supports nested variables... (cached) yes

checking whether to enable maintainer-specific portions of Makefiles... no

checking for gcc... gcc

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 gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking for style of include used by make... GNU

checking dependency style of gcc... gcc3

checking how to run the C preprocessor... gcc -E

checking for g++... g++

checking whether we are using the GNU C++ compiler... yes

checking whether g++ accepts -g... yes

checking dependency style of g++... gcc3

checking how to run the C++ preprocessor... g++ -E

checking for gfortran... gfortran

checking whether we are using the GNU Fortran compiler... yes

checking whether gfortran accepts -g... yes

checking build system type... x86_64-unknown-linux-gnu

checking host system type... x86_64-unknown-linux-gnu

checking how to get verbose linking output from gfortran... -v

checking for Fortran libraries of gfortran...  -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../.. -lgfortran -lm -lquadmath

checking for dummy main to link with Fortran libraries... none

checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore

checking for Fortran flag to compile .f files... none

checking for gcc... (cached) gcc

checking whether we are using the GNU C compiler... (cached) yes

checking whether gcc accepts -g... (cached) yes

checking for gcc option to accept ISO C89... (cached) none needed

checking dependency style of gcc... (cached) gcc3

checking for function MPI_Init... no

checking for function MPI_Init in -lmpi... yes

checking for mpi.h... no

checking whether we are using the GNU C++ compiler... (cached) yes

checking whether g++ accepts -g... (cached) yes

checking dependency style of g++... (cached) gcc3

checking for function MPI_Init... yes

checking for mpi.h... no

checking for grep that handles long lines and -e... /bin/grep

checking for egrep... /bin/grep -E

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 whether sys/types.h defines makedev... yes

checking for ANSI C header files... (cached) yes

checking how to print strings... printf

checking for a sed that does not truncate output... /bin/sed

checking for fgrep... /bin/grep -F

checking for ld used by gcc... /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 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 how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop

checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop

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 dlltool... no

checking how to associate runtime and link libraries... printf %s\n

checking for ar... ar

checking for archiver @FILE support... @

checking for strip... strip

checking for ranlib... ranlib

checking command to parse /usr/bin/nm -B output from gcc object... ok

checking for sysroot... no

checking for mt... mt

checking if mt is a manifest tool... no

checking for dlfcn.h... yes

checking for objdir... .libs

checking if gcc supports -fno-rtti -fno-exceptions... no

checking for gcc option to produce PIC... -fPIC -DPIC

checking if gcc PIC flag -fPIC -DPIC works... yes

checking if gcc static flag -static works... no

checking if gcc supports -c -o file.o... yes

checking if gcc supports -c -o file.o... (cached) yes

checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

checking whether -lc should be explicitly linked in... no

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... yes

checking whether to build static libraries... yes

checking how to run the C++ preprocessor... g++ -E

checking for ld used by g++... /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 g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

checking for g++ option to produce PIC... -fPIC -DPIC

checking if g++ PIC flag -fPIC -DPIC works... yes

checking if g++ static flag -static works... no

checking if g++ supports -c -o file.o... yes

checking if g++ supports -c -o file.o... (cached) yes

checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

checking dynamic linker characteristics... (cached) 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... yes

checking whether to build static libraries... yes

checking for gfortran option to produce PIC... -fPIC

checking if gfortran PIC flag -fPIC works... yes

checking if gfortran static flag -static works... no

checking if gfortran supports -c -o file.o... yes

checking if gfortran supports -c -o file.o... (cached) yes

checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

checking dynamic linker characteristics... (cached) GNU/Linux ld.so

checking how to hardcode library paths into programs... immediate

checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes

checking for gm4... no

checking for m4... m4

checking for grep that handles long lines and -e... (cached) /bin/grep

checking for a sed that does not truncate output... (cached) /bin/sed

checking whether compiler supports __builtin_expect keyword... yes

checking whether compiler supports __builtin_prefetch keyword... yes

checking for doxygen... /usr/bin/doxygen

checking for dot... /usr/bin/dot

checking for ld used by gcc... /usr/bin/ld -m elf_x86_64

checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... (cached) yes

checking for shared library run path origin... done

====================================

Configuring optional package libMesh

====================================

configure: Optional package libMesh is DISABLED

==================================

Configuring required package Boost

==================================

first check for a system Boost library; if not found, revert to bundled Boost library

checking for Boost headers version >= 1.46.1... yes

checking for Boost's header version... 1_46_1

checking boost/array.hpp usability... yes

checking boost/array.hpp presence... yes

checking for boost/array.hpp... yes

checking boost/multi_array.hpp usability... yes

checking boost/multi_array.hpp presence... yes

checking for boost/multi_array.hpp... yes

==================================

Configuring required package Eigen

==================================

first check for a system Eigen library; if not found, revert to bundled Eigen library

checking Eigen/Eigen usability... no

checking Eigen/Eigen presence... no

checking for Eigen/Eigen... no

configure: could not find system Eigen library, using bundled Eigen library

checking Eigen/Eigen usability... yes

checking Eigen/Eigen presence... yes

checking for Eigen/Eigen... yes

checking for Eigen version >= 3.1.0... yes

=================================

Configuring required package HDF5

=================================

grep: //conf/petscvariables: No such file or directory

./configure: line 26386: test: !=: unary operator expected

checking hdf5.h usability... no

checking hdf5.h presence... no

checking for hdf5.h... no

configure: error: could not find header file hdf5.h

I would be so pleased if you could guide me through this problem.

Sincerely Yours,

Omid Atlaschian

[Boyce Griffith]

Do you have PETSC_DIR and PETSC_ARCH environment variables set? They are used by configure to determine where PETSc is located and how it is configured.

-- Boyce

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