This is on a Mac Pro laptop, and GCC 4.9 is used.
The configure log is attached. Thanks
Xujun
On Fri, Sep 25, 2015 at 1:06 PM, Dmitry Karpeyev <karp...@mcs.anl.gov>
wrote:
> Xujun,
> Can you send the output of configure and config.log.
> Dmitry
>
> On Fri, Sep 25, 2015, 13:02 Cody Permann <codyperm...@gmail.com> wrote:
>
>> What operating system are you on? What compiler are you using?
>>
>> On Fri, Sep 25, 2015 at 11:58 AM Xujun Zhao <xzha...@gmail.com> wrote:
>>
>> > Hi all,
>> >
>> > I try to update my installation of libMesh. This is directly pulled from
>> > github.
>> > The configure log shows everything is good, but errors occur during make
>> > Here it is:
>> >
>> > Making all in sfcurves
>> >
>> > make[2]: Nothing to be done for `all'.
>> >
>> > Making all in fparser
>> >
>> > /Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive
>> >
>> > Making all in extrasrc
>> >
>> > /Applications/Xcode.app/Contents/Developer/usr/bin/make all-am
>> >
>> > make[5]: Nothing to be done for `all-am'.
>> >
>> > CXX libdbg_la-fparser.lo
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:36049:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -2960(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:36403:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -2960(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:36461:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -2960(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:36811:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -2960(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:36869:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -2960(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:39346:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -2960(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:92956:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -272(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:92988:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -272(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:93020:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -272(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:93052:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -272(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:93084:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -272(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:93116:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -272(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:98179:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -1040(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:98481:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -1040(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:98617:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -1040(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:98939:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -1040(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:99008:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -1040(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:101122:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -1040(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:148403:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -994(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:148439:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -994(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:148475:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -994(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:148511:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -994(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:148547:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -994(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:148583:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -994(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:166176:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -26(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:167621:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -18(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:167669:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -26(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:189247:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -10(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:189269:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -10(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:189304:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -18(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:189340:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -18(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:189553:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -10(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:189575:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -10(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:189610:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -18(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:189646:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -18(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:201255:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -18(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:201538:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -18(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:201572:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -18(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:201619:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -26(%rbp)
>> >
>> > * ^*
>> >
>> > */var/folders/ld/l3h41k4x0t33lycdjbx9sw300000gn/T//ccuccREq.s:201667:2:
>> > **error:
>> > **ambiguous instructions require an explicit suffix (could be 'filds',
>> or
>> > 'fildl')*
>> >
>> > fild -26(%rbp)
>> >
>> > * ^*
>> >
>> > make[4]: *** [libdbg_la-fparser.lo] Error 1
>> >
>> > make[3]: *** [all-recursive] Error 1
>> >
>> > make[2]: *** [all] Error 2
>> >
>> > make[1]: *** [all-recursive] Error 1
>> >
>> > make: *** [all-recursive] Error 1
>> >
>> >
>> ------------------------------------------------------------------------------
>> > _______________________________________________
>> > Libmesh-users mailing list
>> > Libmesh-users@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/libmesh-users
>> >
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Libmesh-users mailing list
>> Libmesh-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>
>
---------------------------------------------
----------- Configuring libMesh -------------
---------------------------------------------
checking build system type... x86_64-apple-darwin14.5.0
checking host system type... x86_64-apple-darwin14.5.0
checking target system type... x86_64-apple-darwin14.5.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... build-aux/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... yes
checking for src/base/libmesh.C... yes
checking for perl... /usr/bin/perl
checking for style of include used by make... GNU
checking for mpicxx... mpicxx
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 mpicxx accepts -g... yes
checking dependency style of mpicxx... gcc3
<<< C++ compiler is gcc-4.9 >>>
checking for mpicc... mpicc
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 for mpif90... mpif90
checking whether we are using the GNU Fortran compiler... yes
checking whether mpif90 accepts -g... yes
checking for mpif77... mpif77
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether mpif77 accepts -g... yes
checking whether mpicxx supports C++11 features by default... yes
<<< Disabling GLIBCXX debugging on Darwin >>>
<<< Configuring libMesh with methods "opt dbg" >>>
checking for C++11 std::move support... yes
checking for C++11 std::shared_ptr support with opt flags... yes
checking for C++11 std::shared_ptr support with dbg flags... yes
checking for C++11 std::unique_ptr support... yes
checking for C++11 std::regex support... yes
checking for C++11 override keyword support... yes
checking for C++11 initializer list support... yes
checking for C++11 variadic template support... yes
checking for C++11 <thread> support... yes
checking for C++11 <type_traits> support... yes
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by mpicc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
checking the name lister (/usr/bin/nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-apple-darwin14.5.0 file names to
x86_64-apple-darwin14.5.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin14.5.0 file names to toolchain
format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... no
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... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm output from mpicc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking how to run the C preprocessor... mpicc -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 for dlfcn.h... yes
checking for objdir... .libs
checking if mpicc supports -fno-rtti -fno-exceptions... no
checking for mpicc option to produce PIC... -fno-common -DPIC
checking if mpicc PIC flag -fno-common -DPIC works... yes
checking if mpicc static flag -static works... no
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) supports shared libraries... yes
checking dynamic linker characteristics... darwin14.5.0 dyld
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... no
checking how to run the C++ preprocessor... mpicxx -E
checking for ld used by mpicxx... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking whether the mpicxx linker (/usr/bin/ld) supports shared libraries...
yes
checking for mpicxx option to produce PIC... -fno-common -DPIC
checking if mpicxx PIC flag -fno-common -DPIC works... yes
checking if mpicxx static flag -static works... no
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) supports shared libraries...
yes
checking dynamic linker characteristics... darwin14.5.0 dyld
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... no
checking for mpif77 option to produce PIC... -fno-common
checking if mpif77 PIC flag -fno-common works... yes
checking if mpif77 static flag -static works... no
checking if mpif77 supports -c -o file.o... yes
checking if mpif77 supports -c -o file.o... (cached) yes
checking whether the mpif77 linker (/usr/bin/ld) supports shared libraries...
yes
checking dynamic linker characteristics... darwin14.5.0 dyld
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... no
checking for mpif90 option to produce PIC... -fno-common
checking if mpif90 PIC flag -fno-common works... yes
checking if mpif90 static flag -static works... no
checking if mpif90 supports -c -o file.o... yes
checking if mpif90 supports -c -o file.o... (cached) yes
checking whether the mpif90 linker (/usr/bin/ld) supports shared libraries...
yes
checking dynamic linker characteristics... darwin14.5.0 dyld
checking how to hardcode library paths into programs... immediate
checking Major version... 1
checking Minor version... 0
checking Point version... 0
checking whether ln -s works... yes
checking whether mpicc and cc understand -c and -o together... yes
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for pkg-config... no
checking whether the compiler implements namespaces... yes
---------------------------------------------
------- Configuring compiler features -------
---------------------------------------------
<<< Default floating point is double precision (double) >>>
checking for C/C++ restrict keyword... __restrict
<<< Configuring library with getpwuid >>>
<<< Configuring library with exception throwing support >>>
<<< Configuring library with compile timestamps >>>
checking size of short int... 2
checking size of int... 4
checking size of unsigned int... 4
checking size of long int... 8
checking size of float... 4
checking size of double... 8
checking size of void *... 8
checking size of function_pointer... 8
checking whether the compiler supports Run-Time Type Identification... yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking csignal usability... yes
checking csignal presence... yes
checking for csignal... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking whether the compiler has locale... yes
checking whether the compiler has stringstream... yes
checking fenv.h usability... yes
checking fenv.h presence... yes
checking for fenv.h... yes
checking xmmintrin.h usability... yes
checking xmmintrin.h presence... yes
checking for xmmintrin.h... yes
checking whether the compiler supports std::unordered_multimap... yes
checking whether the compiler supports std::unordered_map... yes
checking whether the compiler supports std::unordered_set... yes
checking whether the compiler supports std::hash... yes
checking for library containing dlopen... none required
checking whether the c++ compiler supports dlopen/dlsym/dlclose... yes
checking whether the compiler supports GCC C++ ABI name demangling... yes
checking whether the c++ compiler supports glibc backtrace... yes
checking for OpenMP flag of C++ compiler... -fopenmp
<<< Configuring library with OpenMP support >>>
---------------------------------------------
----- Done configuring compiler features ----
---------------------------------------------
---------------------------------------------
----- Configuring core library features -----
---------------------------------------------
configuring gdb command... "gdb"
<<< Configuring library with warnings >>>
<<< Configuring library to disable libMesh::CommWorld >>>
<<< Configuring library to require ``include "libmesh/etc.h"'' style >>>
<<< Configuring library to keep names in libMesh namespace >>>
configuring size of boundary_id... 2
configuring size of dof_id... 4
configuring size of processor_id... 2
configuring size of subdomain_id... 2
<<< Configuring library with unique id support >>>
configuring size of unique_id... 8
<<< Configuring library with stack trace file support >>>
<<< Configuring library with AMR support >>>
<<< Configuring library with variational smoother support >>>
<<< Configuring library with periodic BC support >>>
<<< Configuring library with Dirichlet constraint support >>>
<<< Configuring library with node constraints support >>>
<<< Configuring library to use ParallelMesh >>>
<<< Configuring library to use ghosted local vectors >>>
<<< Configuring library to store node valence >>>
<<< Configuring library with higher order p-FEM shapes >>>
<<< Configuring library with infinite elements >>>
<<< Configuring library with second derivatives >>>
checking rpc/rpc.h usability... yes
checking rpc/rpc.h presence... yes
checking for rpc/rpc.h... yes
checking for xdrstdio_create... yes
<<< Configuring library with XDR support >>>
<<< Configuring library with real number support >>>
<<< Configuring library with reference counting support >>>
<<< Configuring library with performance logging support >>>
<<< Configuring library example suite support >>>
---------------------------------------------
-- Done configuring core library features ---
---------------------------------------------
---------------------------------------------
----- Configuring for optional packages -----
---------------------------------------------
checking for boostlib >= 1.55.0... yes
<<< Using external boost installation >>>
checking if Howard Hinnant's C++03 unique_ptr implementation can be compiled...
yes
<<< Installing Howard Hinnant's unique_ptr implementation >>>
checking /Users/xzhao/software/petsc/petsc-3.5.4/include/petscversion.h
usability... yes
checking /Users/xzhao/software/petsc/petsc-3.5.4/include/petscversion.h
presence... yes
checking for /Users/xzhao/software/petsc/petsc-3.5.4/include/petscversion.h...
yes
grep: /Users/xzhao/software/petsc/petsc-3.5.4/include/petscconf.h: No such file
or directory
./configure: line 30155: test: -gt: unary operator expected
<<< Attempting to configure library with MPI from PETSC config... >>>
<<< Found PETSc 3.5.4 installation in /Users/xzhao/software/petsc/petsc-3.5.4
... >>>
<<< Configuring library with Hypre support >>>
checking whether we can compile a trivial PETSc program... yes
checking for TAO support via PETSc... yes
checking /Users/xzhao/software/slepc/slepc-3.5.4/include/slepcversion.h
usability... yes
checking /Users/xzhao/software/slepc/slepc-3.5.4/include/slepcversion.h
presence... yes
checking for /Users/xzhao/software/slepc/slepc-3.5.4/include/slepcversion.h...
yes
checking
/Users/xzhao/software/slepc/slepc-3.5.4/arch-darwin-c-opt/include/slepcconf.h
usability... yes
checking
/Users/xzhao/software/slepc/slepc-3.5.4/arch-darwin-c-opt/include/slepcconf.h
presence... yes
checking for
/Users/xzhao/software/slepc/slepc-3.5.4/arch-darwin-c-opt/include/slepcconf.h...
yes
<<< Querying SLEPc configuration from
/Users/xzhao/software/slepc/slepc-3.5.4/conf/slepc_variables >>>
checking whether we can compile a trivial SLEPc program... yes
<<< Configuring library with SLEPc version 3.5.4 support >>>
checking /usr/include/tbb/task_scheduler_init.h usability... no
checking /usr/include/tbb/task_scheduler_init.h presence... no
checking for /usr/include/tbb/task_scheduler_init.h... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... -D_THREAD_SAFE
checking for PTHREAD_PRIO_INHERIT... yes
<<< Configuring library with pthread support >>>
checking whether the compiler supports std::thread... yes
<<< Configuring library with Laspack support >>>
<<< Configuring library with SFC support >>>
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for gzopen in -lz... yes
<<< Configuring library with gzstreams support >>>
checking for bzip2... bzip2
checking for bunzip2... bunzip2
<<< Using bzip2/bunzip2 for writing/reading compressed .bz2 files >>>
checking for xz... xz
<<< Using xz for writing/reading compressed .xz files >>>
checking X11/Intrinsic.h usability... no
checking X11/Intrinsic.h presence... no
checking for X11/Intrinsic.h... no
<<< Configuring library with Metis support >>>
checking for thread local storage (TLS) class... __thread
<<< Configuring library with Parmetis support >>>
checking for doxygen... no
<<< Configuring library with Tetgen support >>>
<<< Configuring library with Triangle support >>>
checking for library containing sqrt... none required
checking for library containing trunc... none required
checking for library containing cos... none required
<<< Configuring library with Qhull version 2012.1 support >>>
<<< Configuring library with GMV support >>>
checking /usr/local/include/vtk-6.2/vtkConfigure.h usability... yes
checking /usr/local/include/vtk-6.2/vtkConfigure.h presence... yes
checking for /usr/local/include/vtk-6.2/vtkConfigure.h... yes
<<< Configuring library with VTK version 6.2.0 support >>>
Testing EIGEN_INC=/usr/include
checking /usr/include/Eigen/Eigen usability... no
checking /usr/include/Eigen/Eigen presence... no
checking for /usr/include/Eigen/Eigen... no
<<< external Eigen header files not found, using Eigen from ./contrib >>>
checking Eigen/Dense usability... yes
checking Eigen/Dense presence... yes
checking for Eigen/Dense... yes
checking Eigen/Sparse usability... yes
checking Eigen/Sparse presence... yes
checking for Eigen/Sparse... yes
checking for eigen - version >= 3.1.2... yes
<<< Configuring library with Eigen support >>>
checking /usr/include/glpk.h usability... no
checking /usr/include/glpk.h presence... no
checking for /usr/include/glpk.h... no
GLPK header files not found!
checking for valid nlopt installation... no
<<< Required header files not found, Cap'n Proto support disabled. >>>
checking hdf5.h usability... yes
checking hdf5.h presence... yes
checking for hdf5.h... yes
checking for hdf5 - version >= 1.8.0... yes
checking for H5Fopen in -lhdf5... yes
<<< Configuring library with HDF5 support >>>
<<< Configuring library with NetCDF version 4 support >>>
<<< Configuring library with Exodus version v5.22 support >>>
<<< Configuring library with Exodus Fortran API >>>
<<< Configuring library with Nemesis version v5.22 support >>>
<<< Configuring library with libHilbert support >>>
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for bison... bison -y
<<< Configuring library with fparser support (release version) >>>
checking for dlopen support... (cached) yes
<<< Configuring library with fparser JIT compilation support >>>
checking for cppunit-config... no
checking for Cppunit - version >= 1.10.0... no
<<< Configuring library with nanoflann KDtree support >>>
checking /usr/include/curl/curl.h usability... yes
checking /usr/include/curl/curl.h presence... yes
checking for /usr/include/curl/curl.h... yes
<<< Configuring library with CURL version 7.43 support >>>
checking for main in -lcurl... no
----------------------------------------------
--- Done configuring for optional packages ---
----------------------------------------------
removing duplicate include paths...
removing duplicate libraries...
checking for git... /usr/bin/git
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating include/Makefile
config.status: creating include/libmesh/Makefile
config.status: creating contrib/Makefile
config.status: creating contrib/utils/Makefile
config.status: creating contrib/utils/Make.common
config.status: creating tests/Makefile
config.status: creating tests/base/getpot_test.C
config.status: creating contrib/utils/libmesh.pc
config.status: creating contrib/utils/libmesh-opt.pc
config.status: creating contrib/utils/libmesh-dbg.pc
config.status: creating contrib/utils/libmesh-devel.pc
config.status: creating contrib/utils/libmesh-prof.pc
config.status: creating contrib/utils/libmesh-oprof.pc
config.status: creating doc/Doxyfile
config.status: creating doc/Makefile
config.status: creating doc/html/Makefile
config.status: creating contrib/bin/libmesh-config
config.status: creating contrib/bin/xda2mgf
config.status: creating contrib/bin/create_libmesh_release
config.status: creating doc/dot
config.status: creating tests/run_unit_tests.sh
config.status: creating contrib/boost/include/Makefile
config.status: creating contrib/unique_ptr/Makefile
config.status: creating contrib/laspack/Makefile
config.status: creating contrib/sfcurves/Makefile
config.status: creating contrib/gzstream/Makefile
config.status: creating contrib/tecplot/tecio/Makefile
config.status: creating contrib/tecplot/binary/Makefile
config.status: creating contrib/metis/Makefile
config.status: creating contrib/parmetis/Makefile
config.status: creating contrib/tetgen/Makefile
config.status: creating contrib/triangle/Makefile
config.status: creating contrib/qhull/qhull/Makefile
config.status: creating contrib/gmv/Makefile
config.status: creating contrib/eigen/eigen/Makefile
config.status: creating contrib/capnproto/Makefile
config.status: creating contrib/netcdf/v3/Makefile
config.status: creating contrib/exodusii/v5.09/Makefile
config.status: creating contrib/exodusii/v5.22/exodus/Makefile
config.status: creating contrib/nemesis/v3.09/Makefile
config.status: creating contrib/nemesis/v5.22/nemesis/Makefile
config.status: creating contrib/libHilbert/Makefile
config.status: creating contrib/fparser/Makefile
config.status: creating contrib/fparser/extrasrc/Makefile
config.status: creating contrib/nanoflann/Makefile
config.status: creating examples/introduction/introduction_ex1/Makefile
config.status: creating examples/introduction/introduction_ex2/Makefile
config.status: creating examples/introduction/introduction_ex3/Makefile
config.status: creating examples/introduction/introduction_ex4/Makefile
config.status: creating examples/introduction/introduction_ex5/Makefile
config.status: creating examples/adaptivity/adaptivity_ex1/Makefile
config.status: creating examples/adaptivity/adaptivity_ex2/Makefile
config.status: creating examples/adaptivity/adaptivity_ex3/Makefile
config.status: creating examples/adaptivity/adaptivity_ex4/Makefile
config.status: creating examples/adaptivity/adaptivity_ex5/Makefile
config.status: creating examples/adjoints/adjoints_ex1/Makefile
config.status: creating examples/adjoints/adjoints_ex2/Makefile
config.status: creating examples/adjoints/adjoints_ex3/Makefile
config.status: creating examples/adjoints/adjoints_ex4/Makefile
config.status: creating examples/adjoints/adjoints_ex5/Makefile
config.status: creating examples/eigenproblems/eigenproblems_ex1/Makefile
config.status: creating examples/eigenproblems/eigenproblems_ex2/Makefile
config.status: creating examples/eigenproblems/eigenproblems_ex3/Makefile
config.status: creating examples/fem_system/fem_system_ex1/Makefile
config.status: creating examples/fem_system/fem_system_ex2/Makefile
config.status: creating examples/fem_system/fem_system_ex3/Makefile
config.status: creating examples/fem_system/fem_system_ex4/Makefile
config.status: creating
examples/solution_transfer/solution_transfer_ex1/Makefile
config.status: creating examples/miscellaneous/miscellaneous_ex1/Makefile
config.status: creating examples/miscellaneous/miscellaneous_ex2/Makefile
config.status: creating examples/miscellaneous/miscellaneous_ex3/Makefile
config.status: creating examples/miscellaneous/miscellaneous_ex4/Makefile
config.status: creating examples/miscellaneous/miscellaneous_ex5/Makefile
config.status: creating examples/miscellaneous/miscellaneous_ex6/Makefile
config.status: creating examples/miscellaneous/miscellaneous_ex7/Makefile
config.status: creating examples/miscellaneous/miscellaneous_ex8/Makefile
config.status: creating examples/miscellaneous/miscellaneous_ex9/Makefile
config.status: creating examples/miscellaneous/miscellaneous_ex10/Makefile
config.status: creating examples/miscellaneous/miscellaneous_ex11/Makefile
config.status: creating examples/optimization/optimization_ex1/Makefile
config.status: creating examples/optimization/optimization_ex2/Makefile
config.status: creating examples/subdomains/subdomains_ex1/Makefile
config.status: creating examples/subdomains/subdomains_ex2/Makefile
config.status: creating examples/subdomains/subdomains_ex3/Makefile
config.status: creating
examples/systems_of_equations/systems_of_equations_ex1/Makefile
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config.status: creating examples/transient/transient_ex1/Makefile
config.status: creating examples/transient/transient_ex2/Makefile
config.status: creating examples/vector_fe/vector_fe_ex1/Makefile
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config.status: creating examples/vector_fe/vector_fe_ex3/Makefile
config.status: creating examples/vector_fe/vector_fe_ex4/Makefile
config.status: creating examples/Makefile
config.status: creating include/libmesh_config.h.tmp
config.status: executing include/libmesh_config.h commands
config.status: creating include/libmesh_config.h - prefix LIBMESH for
include/libmesh_config.h.tmp defines
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in contrib/netcdf/v4
(/Users/xzhao/software/SourceCodes/libmesh-1.0.0-pre/contrib/netcdf/v4)
configure: running /bin/sh ./configure --disable-option-checking
'--prefix=/Users/xzhao/software/libmesh/libmesh-1.0.0-pre' '--with-methods=opt
dbg' '--enable-everything' '--enable-slepc' '--enable-parmesh'
'--enable-nodeconstraint' '--enable-reference-counting' '--disable-strict-lgpl'
'--with-vtk-include=/usr/local/include/vtk-6.2' '--with-vtk-lib=/usr/local/lib'
'PETSC_DIR=/Users/xzhao/software/petsc/petsc-3.5.4'
'PETSC_ARCH=arch-darwin-c-opt'
'SLEPC_DIR=/Users/xzhao/software/slepc/slepc-3.5.4' '--disable-testsets'
'CXX=mpicxx' 'CC=mpicc' 'F77=mpif77' 'FC=mpif90' 'CPPFLAGS= ' 'LIBS= '
--cache-file=/dev/null --srcdir=.
configure: netCDF 4.3.1
checking build system type... x86_64-apple-darwin14.5.0
checking host system type... x86_64-apple-darwin14.5.0
checking target system type... x86_64-apple-darwin14.5.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
configure: checking user options
checking whether a win32 DLL is desired... no
checking whether a NCIO_MINBLOCKSIZE was specified... 256
checking if fsync support is enabled... no
checking whether extra valgrind tests should be run... no
checking whether we should try to build netCDF-4... yes
checking do we require hdf5 dynamic-loading support... xno
checking whether reading of HDF4 SD files is to be enabled... no
checking whether to fetch some sample HDF4 files from Unidata ftp site to test
HDF4 reading (requires wget)... no
checking whether parallel I/O for classic and 64-bit offset files using
parallel-netcdf is to be enabled... no
checking whether extra example tests should be run... no
checking whether parallel IO tests should be run... no
checking whether a default chunk size in bytes was specified... 4194304
checking whether a maximum per-variable cache size for HDF5 was specified...
67108864
checking whether a number of chunks for the default per-variable cache was
specified... 10
checking whether a default file cache size for HDF5 was specified... 4194304
checking whether a default file cache maximum number of elements for HDF5 was
specified... 1009
checking whether a default cache preemption for HDF5 was specified... 0.75
checking whether netCDF-4 logging is enabled... no
checking whether cdmremote client is to be built... no
checking whether DAP client is to be built... yes
checking for style of include used by make... GNU
checking for gcc... mpicc
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 mpicc accepts -g... yes
checking for mpicc option to accept ISO C89... none needed
checking dependency style of mpicc... gcc3
checking for curl_easy_setopt in -lcurl... yes
checking for library containing curl_easy_setopt... -lcurl
checking whether dap remote testing should be enabled (default off)... no
checking whether netcdf4 group names should be enabled (default on)... yes
checking whether the time-consuming dap tests should be enabled (default
off)... no
checking whether netCDF extra tests should be run (developers only)... no
checking whether FFIO will be used... no
checking whether examples should be built... yes
checking whether v2 netCDF API should be built... yes
checking whether the ncgen/ncdump/nccopy should be built... yes
checking whether test should be built and run... no
checking whether large file (> 2GB) tests should be run... no
checking whether benchmaks should be run (experimental)... no
checking whether extreme numbers should be used in tests... yes
checking where to put large temp files if large file tests are run... .
configure: finding C compiler
checking for gcc... (cached) mpicc
checking whether we are using the GNU C compiler... (cached) yes
checking whether mpicc accepts -g... (cached) yes
checking for mpicc option to accept ISO C89... (cached) none needed
checking dependency style of mpicc... (cached) gcc3
checking whether mpicc and cc understand -c and -o together... yes
checking for an ANSI C-conforming const... yes
checking whether a CURLOPT_KEYPASSWD is defined... yes
configure: setting up libtool
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by mpicc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
checking the name lister (/usr/bin/nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-apple-darwin14.5.0 file names to
x86_64-apple-darwin14.5.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin14.5.0 file names to toolchain
format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... no
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... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm output from mpicc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking how to run the C preprocessor... mpicc -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 for dlfcn.h... yes
checking for objdir... .libs
checking if mpicc supports -fno-rtti -fno-exceptions... no
checking for mpicc option to produce PIC... -fno-common -DPIC
checking if mpicc PIC flag -fno-common -DPIC works... yes
checking if mpicc static flag -static works... no
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) supports shared libraries... yes
checking dynamic linker characteristics... darwin14.5.0 dyld
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
configure: finding other utilities
checking for doxygen... no
configure: WARNING: Doxygen not found - documentation will not be built
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
configure: displaying some results
checking CPPFLAGS...
checking CC CFLAGS... mpicc -g -O2
checking type mpicc... mpicc is hashed
(/Users/xzhao/software/petsc/petsc-3.5.4/arch-darwin-c-opt/bin/mpicc)
checking CXX... mpicxx
checking CXXFLAGS...
checking type mpicxx... mpicxx is
/Users/xzhao/software/petsc/petsc-3.5.4/arch-darwin-c-opt/bin/mpicxx
checking FC... mpif90
checking FFLAGS...
checking type mpif90... mpif90 is
/Users/xzhao/software/petsc/petsc-3.5.4/arch-darwin-c-opt/bin/mpif90
checking F90... unset
checking AR... ar
checking AR_FLAGS... cru
checking type ar... ar is hashed (/usr/bin/ar)
checking NM... /usr/bin/nm
checking NMFLAGS...
configure: checking types, headers, and functions
checking for stdlib.h... (cached) yes
checking for sys/types.h... (cached) yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for ANSI C header files... (cached) yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking whether time.h and sys/time.h may both be included... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking ctype.h usability... yes
checking ctype.h presence... yes
checking for ctype.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking malloc.h usability... no
checking malloc.h presence... no
checking for malloc.h... no
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for vprintf... yes
checking for _doprnt... no
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for strlcat... yes
checking for strerror... yes
checking for snprintf... yes
checking for strchr... yes
checking for strrchr... yes
checking for strcat... yes
checking for strcpy... yes
checking for strdup... yes
checking for strcasecmp... yes
checking for strtod... yes
checking for strtoll... yes
checking for strtoull... yes
checking for strstr... yes
checking for mkstemp... yes
checking for rand... yes
checking for getrlimit... yes
checking for gettimeofday... yes
checking for fsync... yes
checking for MPI_Comm_f2c... no
checking whether in-memory files are enabled... configure: --enable-dap
requires --enable-diskless
yes
checking for memmove... yes
checking for getpagesize... yes
checking for sysconf... yes
checking whether mmap is enabled for in-memory files... no
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for getpagesize... (cached) yes
checking for working mmap... yes
checking for mremap... no
mmap function or mremap function is not available: disabling mmap
checking for size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether isnan is declared... yes
checking whether isinf is declared... yes
checking whether isfinite is declared... yes
checking whether signbit is declared... yes
checking for struct stat.st_blksize... yes
checking for IEEE floating point format... yes
checking for size_t... (cached) yes
checking for off_t... yes
checking for ssize_t... yes
checking for ptrdiff_t... yes
checking for uchar... no
checking for longlong... no
checking whether char is unsigned... no
checking whether byte ordering is bigendian... no
checking size of short... 2
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of float... 4
checking size of double... 8
checking size of off_t... 8
checking size of size_t... 8
checking for library containing deflate... none required
checking for floor in -lm... yes
checking for library containing H5Fflush... -lhdf5
checking for library containing H5DSis_scale... -lhdf5_hl
checking hdf5.h usability... yes
checking hdf5.h presence... yes
checking for hdf5.h... yes
checking for H5Pget_fapl_mpiposix... no
checking for H5Pget_fapl_mpio... no
checking for H5Pset_deflate... yes
checking for H5Z_SZIP... yes
checking whether parallel I/O features are to be included... no
checking for library containing SZ_Compress... none required
checking for unsigned long long int... yes
checking for long long int... yes
checking for unsigned long long int... (cached) yes
checking what to call the output of the ftpbin target...
binary-netcdf-4.3.1.tar mpif90 mpicxx
checking value of LIBS... -lhdf5_hl -lhdf5 -lm -lcurl
configure: generating header files and makefiles
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating nc-config
config.status: creating netcdf.pc
config.status: creating include/Makefile
config.status: creating h5_test/Makefile
config.status: creating man4/Makefile
config.status: creating man4/images/Makefile
config.status: creating libsrc/Makefile
config.status: creating libsrc4/Makefile
config.status: creating libsrc5/Makefile
config.status: creating nctest/Makefile
config.status: creating nc_test4/Makefile
config.status: creating nc_test/Makefile
config.status: creating ncdump/Makefile
config.status: creating ncgen3/Makefile
config.status: creating ncgen/Makefile
config.status: creating examples/Makefile
config.status: creating examples/C/Makefile
config.status: creating examples/CDL/Makefile
config.status: creating oc2/Makefile
config.status: creating libdap2/Makefile
config.status: creating libdispatch/Makefile
config.status: creating liblib/Makefile
config.status: creating ncdump/cdl4/Makefile
config.status: creating ncdump/expected4/Makefile
config.status: creating ncdap_test/Makefile
config.status: creating ncdap_test/testdata3/Makefile
config.status: creating ncdap_test/expected3/Makefile
config.status: creating ncdap_test/expected4/Makefile
config.status: creating ncdap_test/expectremote3/Makefile
config.status: creating ncdap_test/expectremote4/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
----------------------------------- SUMMARY -----------------------------------
Package version.................... : libmesh-1.0.0-pre
C++ compiler type.................. : gcc4.9
C++ compiler....................... : mpicxx
C compiler......................... : mpicc
Fortran compiler................... : mpif90
Build Methods...................... : opt dbg
CPPFLAGS...(opt)................... : -DNDEBUG
CXXFLAGS...(opt)................... : -O2 -felide-constructors -funroll-loops
-fstrict-aliasing -Wdisabled-optimization -fopenmp
CFLAGS.....(opt)................... : -O2 -funroll-loops -fstrict-aliasing
-fopenmp
CPPFLAGS...(dbg)................... : -DDEBUG
CXXFLAGS...(dbg)................... : -O0 -felide-constructors -g -pedantic -W
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat -Wparentheses
-Woverloaded-virtual -fopenmp
CFLAGS.....(dbg)................... : -g -Wimplicit -fopenmp
Install dir........................ :
/Users/xzhao/software/libmesh/libmesh-1.0.0-pre
Build user......................... : xzhao
Build host......................... : mcswl109.mcs.anl.gov
Build architecture................. : x86_64-apple-darwin14.5.0
Git revision....................... : fba9c8675ba4c216cc27f6782b776e8f69ba091e
Library Features:
library warnings................. : yes
adaptive mesh refinement......... : yes
blocked matrix/vector storage.... : no
complex variables................ : no
example suite.................... : yes
ghosted vectors.................. : yes
high-order shape functions....... : yes
unique-id support................ : yes
id size (boundaries)............. : 2 bytes
id size (dofs)................... : 4 bytes
id size (unique)................. : 8 bytes
id size (processors)............. : 2 bytes
id size (subdomains)............. : 2 bytes
infinite elements................ : yes
Dirichlet constraints............ : yes
node constraints................. : yes
parallel mesh.................... : yes
performance logging.............. : yes
periodic boundary conditions..... : yes
reference counting............... : yes
shape function 2nd derivatives... : yes
stack trace files................ : yes
track node valence............... : yes
variational smoother............. : yes
xdr binary I/O................... : yes
Optional Packages:
boost............................ : yes
capnproto........................ : no
cppunit.......................... : no
curl............................. : no
eigen............................ : yes
exodus........................... : yes
version....................... : v5.22
fparser.......................... : yes
build from version............ : release
glpk............................. : no
gmv.............................. : yes
gzstream......................... : yes
hdf5............................. : yes
laspack.......................... : yes
libhilbert....................... : yes
metis............................ : yes
mpi.............................. : yes
nanoflann........................ : yes
nemesis.......................... : yes
version....................... : v5.22
netcdf........................... : yes
version....................... : 4
nlopt............................ : no
openmp........................... : yes
parmetis......................... : yes
petsc............................ : yes
version....................... : 3.5.4
pthreads......................... : yes
qhull............................ : yes
sfcurves......................... : yes
slepc............................ : yes
version....................... : 3.5.4
tbb.............................. : no
c++ threads...................... : yes
flavor........................ : std::thread
c++ rtti ........................ : yes
tecio............................ : no
tecplot...(vendor binaries)...... : no
tetgen........................... : yes
triangle......................... : yes
trilinos......................... : no
vtk.............................. : yes
version....................... : 6.2.0
libmesh_optional_INCLUDES........ : -I/usr/local/include/vtk-6.2
-D_THREAD_SAFE -pthread -I/Users/xzhao/software/slepc/slepc-3.5.4/include
-I/Users/xzhao/software/slepc/slepc-3.5.4/arch-darwin-c-opt/include
-I/Users/xzhao/software/petsc/petsc-3.5.4/include
-I/Users/xzhao/software/petsc/petsc-3.5.4/arch-darwin-c-opt/include
-I/usr/local/include
libmesh_optional_LIBS............ : -Wl,-rpath,/usr/local/lib
-L/usr/local/lib -lvtkIOCore-6.2 -lvtkCommonCore-6.2 -lvtkCommonDataModel-6.2
-lvtkFiltersCore-6.2 -lvtkIOXML-6.2 -lvtkImagingCore-6.2 -lvtkIOImage-6.2
-lvtkImagingMath-6.2 -lvtkIOParallelXML-6.2 -lz
-L/Users/xzhao/software/slepc/slepc-3.5.4/arch-darwin-c-opt/lib -lslepc
-lBLOPEX -L/Users/xzhao/software/petsc/petsc-3.5.4/arch-darwin-c-opt/lib
-L/usr/local/Cellar/gcc49/4.9.3/lib/gcc/4.9/gcc/x86_64-apple-darwin14.4.0/4.9.3
-L/usr/local/Cellar/gcc49/4.9.3/lib/gcc/4.9 -lpetsc -lelemental -lpmrrr
-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack
-lsuperlu_dist_3.3 -lHYPRE -lml -lflapack -lfblas -lparmetis -lmetis -ltriangle
-lchaco -lssl -lcrypto -lmpichf90 -lpthread -lgfortran -lquadmath -lm
-lmpichcxx -lstdc++ -lpmpich -lmpich -lopa -lmpl -lSystem -lgcc_ext.10.5 -ldl
-------------------------------------------------------------------------------
Configure complete, now type 'make' and then 'make install'.
---------------------------------------------
--------- Done Configuring libMesh ----------
---------------------------------------------
------------------------------------------------------------------------------
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