(view as text)
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by PyLith configure 1.7.0, which was
generated by GNU Autoconf 2.59. Invocation command line was
$ ./configure --prefix=/home/buildbot/install/pylith_centos_x86_64_binbot LDFLAGS=-L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/pylith_deps/lib CPPFLAGS=-I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include --enable-testing --enable-cubit --enable-hdf5 --enable-swig PETSC_DIR=/home/buildbot/install/pylith_centos_x86_64_binbot PETSC_DIR=/home/buildbot/install/pylith_centos_x86_64_binbot
## --------- ##
## Platform. ##
## --------- ##
hostname = kale.geodynamics.org
uname -m = x86_64
uname -r = 2.6.18-274.3.1.el5
uname -s = Linux
uname -v = #1 SMP Tue Sep 6 20:13:52 EDT 2011
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = x86_64
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /home/buildbot/install/pylith_centos_x86_64_binbot/bin
PATH: /home/buildbot/install/pylith_centos_x86_64_binbot/bin
PATH: /home/buildbot/install/pylith_centos_x86_64_binbot/bin
PATH: /home/buildbot/pylith_deps/bin
PATH: /home/buildbot/buildbot/bin
PATH: /usr/kerberos/bin
PATH: /usr/local/bin
PATH: /bin
PATH: /usr/bin
PATH: /home/buildbot/bin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:1598: checking for a BSD-compatible install
configure:1653: result: /usr/bin/install -c
configure:1664: checking whether build environment is sane
configure:1707: result: yes
configure:1772: checking for gawk
configure:1788: found /bin/gawk
configure:1798: result: gawk
configure:1808: checking whether make sets $(MAKE)
configure:1828: result: yes
configure:2048: checking build system type
configure:2066: result: x86_64-redhat-linux-gnu
configure:2074: checking host system type
configure:2088: result: x86_64-redhat-linux-gnu
configure:2343: checking for C++ compiler version
configure:2346: mpicxx --version </dev/null >&5
g++ (GCC) 4.5.2
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:2349: $? = 0
configure:2351: mpicxx -v </dev/null >&5
mpicxx for MPICH2 version 1.3.2p1
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/home/buildbot/install/pylith_centos_x86_64_binbot/libexec/gcc/x86_64-unknown-linux-gnu/4.5.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../gcc-4.5.2/configure --prefix=/home/buildbot/install/pylith_centos_x86_64_binbot --enable-languages=c,c++,fortran --disable-multilib
Thread model: posix
gcc version 4.5.2 (GCC)
configure:2354: $? = 0
configure:2356: mpicxx -V </dev/null >&5
g++: error trying to exec 'x86_64-unknown-linux-gnu-gcc--I/home/buildbot/install/pylith_centos_x86_64_binbot/include': execvp: No such file or directory
configure:2359: $? = 0
configure:2382: checking for C++ compiler default output file name
configure:2385: mpicxx -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/pylith_deps/lib conftest.cc >&5
configure:2388: $? = 0
configure:2434: result: a.out
configure:2439: checking whether the C++ compiler works
configure:2445: ./a.out
configure:2448: $? = 0
configure:2465: result: yes
configure:2472: checking whether we are cross compiling
configure:2474: result: no
configure:2477: checking for suffix of executables
configure:2479: mpicxx -o conftest -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/pylith_deps/lib conftest.cc >&5
configure:2482: $? = 0
configure:2507: result:
configure:2513: checking for suffix of object files
configure:2534: mpicxx -c -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:2537: $? = 0
configure:2559: result: o
configure:2563: checking whether we are using the GNU C++ compiler
configure:2587: mpicxx -c -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:2593: $? = 0
configure:2597: test -z
|| test ! -s conftest.err
configure:2600: $? = 0
configure:2603: test -s conftest.o
configure:2606: $? = 0
configure:2619: result: yes
configure:2625: checking whether mpicxx accepts -g
configure:2646: mpicxx -c -g -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:2652: $? = 0
configure:2656: test -z
|| test ! -s conftest.err
configure:2659: $? = 0
configure:2662: test -s conftest.o
configure:2665: $? = 0
configure:2676: result: yes
configure:2718: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:2724: $? = 0
configure:2728: test -z
|| test ! -s conftest.err
configure:2731: $? = 0
configure:2734: test -s conftest.o
configure:2737: $? = 0
configure:2763: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
conftest.cc: In function 'int main()':
conftest.cc:15:9: error: 'exit' was not declared in this scope
configure:2769: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "PyLith"
| #define PACKAGE_TARNAME "pylith"
| #define PACKAGE_VERSION "1.7.0"
| #define PACKAGE_STRING "PyLith 1.7.0"
| #define PACKAGE_BUGREPORT "cig-short@geodynamics.org"
| #define PACKAGE "pylith"
| #define VERSION "1.7.0"
| /* end confdefs.h. */
|
| int
| main ()
| {
| exit (42);
| ;
| return 0;
| }
configure:2718: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
conftest.cc:11:40: error: 'void std::exit(int)' should have been declared inside 'std'
configure:2724: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "PyLith"
| #define PACKAGE_TARNAME "pylith"
| #define PACKAGE_VERSION "1.7.0"
| #define PACKAGE_STRING "PyLith 1.7.0"
| #define PACKAGE_BUGREPORT "cig-short@geodynamics.org"
| #define PACKAGE "pylith"
| #define VERSION "1.7.0"
| /* end confdefs.h. */
| extern "C" void std::exit (int) throw (); using std::exit;
| #include <stdlib.h>
| int
| main ()
| {
| exit (42);
| ;
| return 0;
| }
configure:2718: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
conftest.cc:11:31: error: 'void std::exit(int)' should have been declared inside 'std'
In file included from conftest.cc:12:0:
/usr/include/stdlib.h:646:70: error: declaration of 'void std::exit(int) throw ()' throws different exceptions
conftest.cc:11:17: error: from previous declaration 'void std::exit(int)'
configure:2724: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "PyLith"
| #define PACKAGE_TARNAME "pylith"
| #define PACKAGE_VERSION "1.7.0"
| #define PACKAGE_STRING "PyLith 1.7.0"
| #define PACKAGE_BUGREPORT "cig-short@geodynamics.org"
| #define PACKAGE "pylith"
| #define VERSION "1.7.0"
| /* end confdefs.h. */
| extern "C" void std::exit (int); using std::exit;
| #include <stdlib.h>
| int
| main ()
| {
| exit (42);
| ;
| return 0;
| }
configure:2718: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:2724: $? = 0
configure:2728: test -z
|| test ! -s conftest.err
configure:2731: $? = 0
configure:2734: test -s conftest.o
configure:2737: $? = 0
configure:2763: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:2769: $? = 0
configure:2773: test -z
|| test ! -s conftest.err
configure:2776: $? = 0
configure:2779: test -s conftest.o
configure:2782: $? = 0
configure:2816: checking for style of include used by make
configure:2844: result: GNU
configure:2872: checking dependency style of mpicxx
configure:2962: result: gcc3
configure:3025: checking for gcc
configure:3051: result: mpicc
configure:3295: checking for C compiler version
configure:3298: mpicc --version </dev/null >&5
gcc (GCC) 4.5.2
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:3301: $? = 0
configure:3303: mpicc -v </dev/null >&5
mpicc for MPICH2 version 1.3.2p1
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/home/buildbot/install/pylith_centos_x86_64_binbot/libexec/gcc/x86_64-unknown-linux-gnu/4.5.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../gcc-4.5.2/configure --prefix=/home/buildbot/install/pylith_centos_x86_64_binbot --enable-languages=c,c++,fortran --disable-multilib
Thread model: posix
gcc version 4.5.2 (GCC)
configure:3306: $? = 0
configure:3308: mpicc -V </dev/null >&5
gcc: error trying to exec 'x86_64-unknown-linux-gnu-gcc--I/home/buildbot/install/pylith_centos_x86_64_binbot/include': execvp: No such file or directory
configure:3311: $? = 0
configure:3314: checking whether we are using the GNU C compiler
configure:3338: mpicc -c -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:3344: $? = 0
configure:3348: test -z
|| test ! -s conftest.err
configure:3351: $? = 0
configure:3354: test -s conftest.o
configure:3357: $? = 0
configure:3370: result: yes
configure:3376: checking whether mpicc accepts -g
configure:3397: mpicc -c -g -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:3403: $? = 0
configure:3407: test -z
|| test ! -s conftest.err
configure:3410: $? = 0
configure:3413: test -s conftest.o
configure:3416: $? = 0
configure:3427: result: yes
configure:3444: checking for mpicc option to accept ANSI C
configure:3514: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:3520: $? = 0
configure:3524: test -z
|| test ! -s conftest.err
configure:3527: $? = 0
configure:3530: test -s conftest.o
configure:3533: $? = 0
configure:3551: result: none needed
configure:3569: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
conftest.c:2:9: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'me'
configure:3575: $? = 1
configure: failed program was:
| #ifndef __cplusplus
| choke me
| #endif
configure:3710: checking dependency style of mpicc
configure:3800: result: gcc3
configure:3891: checking for a sed that does not truncate output
configure:3947: result: /bin/sed
configure:3950: checking for egrep
configure:3960: result: grep -E
configure:3976: checking for ld used by mpicc
configure:4043: result: /usr/bin/ld
configure:4052: checking if the linker (/usr/bin/ld) is GNU ld
configure:4067: result: yes
configure:4072: checking for /usr/bin/ld option to reload object files
configure:4079: result: -r
configure:4097: checking for BSD-compatible nm
configure:4146: result: /usr/bin/nm -B
configure:4150: checking whether ln -s works
configure:4154: result: yes
configure:4161: checking how to recognise dependent libraries
configure:4337: result: pass_all
configure:4425: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:4428: $? = 0
configure:4574: checking how to run the C preprocessor
configure:4609: mpicc -E -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c
configure:4615: $? = 0
configure:4647: mpicc -E -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c
conftest.c:14:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:4653: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "PyLith"
| #define PACKAGE_TARNAME "pylith"
| #define PACKAGE_VERSION "1.7.0"
| #define PACKAGE_STRING "PyLith 1.7.0"
| #define PACKAGE_BUGREPORT "cig-short@geodynamics.org"
| #define PACKAGE "pylith"
| #define VERSION "1.7.0"
| #ifdef __cplusplus
| extern "C" void exit (int) throw ();
| #endif
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4692: result: mpicc -E
configure:4716: mpicc -E -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c
configure:4722: $? = 0
configure:4754: mpicc -E -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c
conftest.c:14:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:4760: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "PyLith"
| #define PACKAGE_TARNAME "pylith"
| #define PACKAGE_VERSION "1.7.0"
| #define PACKAGE_STRING "PyLith 1.7.0"
| #define PACKAGE_BUGREPORT "cig-short@geodynamics.org"
| #define PACKAGE "pylith"
| #define VERSION "1.7.0"
| #ifdef __cplusplus
| extern "C" void exit (int) throw ();
| #endif
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4804: checking for ANSI C header files
configure:4829: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:4835: $? = 0
configure:4839: test -z
|| test ! -s conftest.err
configure:4842: $? = 0
configure:4845: test -s conftest.o
configure:4848: $? = 0
configure:4937: mpicc -o conftest -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/pylith_deps/lib conftest.c >&5
conftest.c: In function 'main':
conftest.c:31:7: warning: incompatible implicit declaration of built-in function 'exit'
configure:4940: $? = 0
configure:4942: ./conftest
configure:4945: $? = 0
configure:4960: result: yes
configure:4984: checking for sys/types.h
configure:5000: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:5006: $? = 0
configure:5010: test -z
|| test ! -s conftest.err
configure:5013: $? = 0
configure:5016: test -s conftest.o
configure:5019: $? = 0
configure:5030: result: yes
configure:4984: checking for sys/stat.h
configure:5000: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:5006: $? = 0
configure:5010: test -z
|| test ! -s conftest.err
configure:5013: $? = 0
configure:5016: test -s conftest.o
configure:5019: $? = 0
configure:5030: result: yes
configure:4984: checking for stdlib.h
configure:5000: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:5006: $? = 0
configure:5010: test -z
|| test ! -s conftest.err
configure:5013: $? = 0
configure:5016: test -s conftest.o
configure:5019: $? = 0
configure:5030: result: yes
configure:4984: checking for string.h
configure:5000: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:5006: $? = 0
configure:5010: test -z
|| test ! -s conftest.err
configure:5013: $? = 0
configure:5016: test -s conftest.o
configure:5019: $? = 0
configure:5030: result: yes
configure:4984: checking for memory.h
configure:5000: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:5006: $? = 0
configure:5010: test -z
|| test ! -s conftest.err
configure:5013: $? = 0
configure:5016: test -s conftest.o
configure:5019: $? = 0
configure:5030: result: yes
configure:4984: checking for strings.h
configure:5000: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:5006: $? = 0
configure:5010: test -z
|| test ! -s conftest.err
configure:5013: $? = 0
configure:5016: test -s conftest.o
configure:5019: $? = 0
configure:5030: result: yes
configure:4984: checking for inttypes.h
configure:5000: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:5006: $? = 0
configure:5010: test -z
|| test ! -s conftest.err
configure:5013: $? = 0
configure:5016: test -s conftest.o
configure:5019: $? = 0
configure:5030: result: yes
configure:4984: checking for stdint.h
configure:5000: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:5006: $? = 0
configure:5010: test -z
|| test ! -s conftest.err
configure:5013: $? = 0
configure:5016: test -s conftest.o
configure:5019: $? = 0
configure:5030: result: yes
configure:4984: checking for unistd.h
configure:5000: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:5006: $? = 0
configure:5010: test -z
|| test ! -s conftest.err
configure:5013: $? = 0
configure:5016: test -s conftest.o
configure:5019: $? = 0
configure:5030: result: yes
configure:5056: checking dlfcn.h usability
configure:5068: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:5074: $? = 0
configure:5078: test -z
|| test ! -s conftest.err
configure:5081: $? = 0
configure:5084: test -s conftest.o
configure:5087: $? = 0
configure:5097: result: yes
configure:5101: checking dlfcn.h presence
configure:5111: mpicc -E -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c
configure:5117: $? = 0
configure:5137: result: yes
configure:5172: checking for dlfcn.h
configure:5179: result: yes
configure:5202: checking how to run the C++ preprocessor
configure:5233: mpicxx -E -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc
configure:5239: $? = 0
configure:5271: mpicxx -E -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc
conftest.cc:25:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:5277: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "PyLith"
| #define PACKAGE_TARNAME "pylith"
| #define PACKAGE_VERSION "1.7.0"
| #define PACKAGE_STRING "PyLith 1.7.0"
| #define PACKAGE_BUGREPORT "cig-short@geodynamics.org"
| #define PACKAGE "pylith"
| #define VERSION "1.7.0"
| #ifdef __cplusplus
| extern "C" void exit (int) throw ();
| #endif
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:5316: result: mpicxx -E
configure:5340: mpicxx -E -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc
configure:5346: $? = 0
configure:5378: mpicxx -E -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc
conftest.cc:25:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:5384: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "PyLith"
| #define PACKAGE_TARNAME "pylith"
| #define PACKAGE_VERSION "1.7.0"
| #define PACKAGE_STRING "PyLith 1.7.0"
| #define PACKAGE_BUGREPORT "cig-short@geodynamics.org"
| #define PACKAGE "pylith"
| #define VERSION "1.7.0"
| #ifdef __cplusplus
| extern "C" void exit (int) throw ();
| #endif
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:5522: checking for Fortran 77 compiler version
configure:5525: mpif77 --version </dev/null >&5
GNU Fortran (GCC) 4.5.2
Copyright (C) 2010 Free Software Foundation, Inc.
GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING
configure:5528: $? = 0
configure:5530: mpif77 -v </dev/null >&5
mpif77 for MPICH2 version 1.3.2p1
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/home/buildbot/install/pylith_centos_x86_64_binbot/libexec/gcc/x86_64-unknown-linux-gnu/4.5.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../gcc-4.5.2/configure --prefix=/home/buildbot/install/pylith_centos_x86_64_binbot --enable-languages=c,c++,fortran --disable-multilib
Thread model: posix
gcc version 4.5.2 (GCC)
configure:5533: $? = 0
configure:5535: mpif77 -V </dev/null >&5
gfortran: error trying to exec 'x86_64-unknown-linux-gnu-gcc--I/home/buildbot/install/pylith_centos_x86_64_binbot/include': execvp: No such file or directory
configure:5538: $? = 0
configure:5546: checking whether we are using the GNU Fortran 77 compiler
configure:5560: mpif77 -c conftest.F >&5
configure:5566: $? = 0
configure:5570: test -z
|| test ! -s conftest.err
configure:5573: $? = 0
configure:5576: test -s conftest.o
configure:5579: $? = 0
configure:5592: result: yes
configure:5598: checking whether mpif77 accepts -g
configure:5610: mpif77 -c -g conftest.f >&5
configure:5616: $? = 0
configure:5620: test -z
|| test ! -s conftest.err
configure:5623: $? = 0
configure:5626: test -s conftest.o
configure:5629: $? = 0
configure:5641: result: yes
configure:5671: checking the maximum length of command line arguments
configure:5780: result: 32768
configure:5791: checking command to parse /usr/bin/nm -B output from mpicc object
configure:5896: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:5899: $? = 0
configure:5903: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm
configure:5906: $? = 0
configure:5958: mpicc -o conftest -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/pylith_deps/lib conftest.c conftstm.o >&5
configure:5961: $? = 0
configure:5999: result: ok
configure:6003: checking for objdir
configure:6018: result: .libs
configure:6108: checking for ar
configure:6124: found /usr/bin/ar
configure:6135: result: ar
configure:6188: checking for ranlib
configure:6204: found /usr/bin/ranlib
configure:6215: result: ranlib
configure:6268: checking for strip
configure:6284: found /usr/bin/strip
configure:6295: result: strip
configure:6567: checking if mpicc supports -fno-rtti -fno-exceptions
configure:6585: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -fno-rtti -fno-exceptions conftest.c >&5
cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C
configure:6589: $? = 0
configure:6602: result: no
configure:6617: checking for mpicc option to produce PIC
configure:6827: result: -fPIC
configure:6835: checking if mpicc PIC flag -fPIC works
configure:6853: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -fPIC -DPIC conftest.c >&5
configure:6857: $? = 0
configure:6870: result: yes
configure:6898: checking if mpicc static flag -static works
configure:6926: result: no
configure:6936: checking if mpicc supports -c -o file.o
configure:6957: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -o out/conftest2.o conftest.c >&5
configure:6961: $? = 0
configure:6983: result: yes
configure:7009: checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:7967: result: yes
configure:7988: checking whether -lc should be explicitly linked in
configure:7993: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:7996: $? = 0
configure:8011: mpicc -shared conftest.o -v -Wl,-soname -Wl,conftest -o conftest 2\>\&1 \| grep -lc \>/dev/null 2\>\&1
configure:8014: $? = 0
configure:8026: result: no
configure:8034: checking dynamic linker characteristics
configure:8427: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:8430: $? = 0
configure:8643: result: GNU/Linux ld.so
configure:8652: checking how to hardcode library paths into programs
configure:8677: result: immediate
configure:8691: checking whether stripping libraries is possible
configure:8696: result: yes
configure:9530: checking if libtool supports shared libraries
configure:9532: result: yes
configure:9535: checking whether to build shared libraries
configure:9556: result: yes
configure:9559: checking whether to build static libraries
configure:9563: result: no
configure:9655: creating libtool
configure:10246: checking for ld used by mpicxx
configure:10313: result: /usr/bin/ld -m elf_x86_64
configure:10322: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld
configure:10337: result: yes
configure:10388: checking whether the mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:11326: result: yes
configure:11344: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cpp >&5
configure:11347: $? = 0
configure:11466: checking for mpicxx option to produce PIC
configure:11740: result: -fPIC
configure:11748: checking if mpicxx PIC flag -fPIC works
configure:11766: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -fPIC -DPIC conftest.cpp >&5
configure:11770: $? = 0
configure:11783: result: yes
configure:11811: checking if mpicxx static flag -static works
configure:11839: result: no
configure:11849: checking if mpicxx supports -c -o file.o
configure:11870: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -o out/conftest2.o conftest.cpp >&5
configure:11874: $? = 0
configure:11896: result: yes
configure:11922: checking whether the mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:11947: result: yes
configure:12014: checking dynamic linker characteristics
configure:12407: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cpp >&5
configure:12410: $? = 0
configure:12623: result: GNU/Linux ld.so
configure:12632: checking how to hardcode library paths into programs
configure:12657: result: immediate
configure:13186: checking if libtool supports shared libraries
configure:13188: result: yes
configure:13191: checking whether to build shared libraries
configure:13211: result: yes
configure:13214: checking whether to build static libraries
configure:13218: result: no
configure:13228: checking for mpif77 option to produce PIC
configure:13438: result: -fPIC
configure:13446: checking if mpif77 PIC flag -fPIC works
configure:13464: mpif77 -c -g -O2 -fPIC conftest.f >&5
configure:13468: $? = 0
configure:13481: result: yes
configure:13509: checking if mpif77 static flag -static works
configure:13537: result: no
configure:13547: checking if mpif77 supports -c -o file.o
configure:13568: mpif77 -c -g -O2 -o out/conftest2.o conftest.f >&5
configure:13572: $? = 0
configure:13594: result: yes
configure:13620: checking whether the mpif77 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:14558: result: yes
configure:14625: checking dynamic linker characteristics
configure:15018: mpif77 -c -g -O2 conftest.f >&5
Warning: conftest.f:1: Illegal preprocessor directive
configure:15021: $? = 0
configure:15234: result: GNU/Linux ld.so
configure:15243: checking how to hardcode library paths into programs
configure:15268: result: immediate
configure:18890: checking for a BSD-compatible install
configure:18945: result: /usr/bin/install -c
configure:18963: checking for nemesis
configure:18981: found /home/buildbot/install/pylith_centos_x86_64_binbot/bin/nemesis
configure:18994: result: /home/buildbot/install/pylith_centos_x86_64_binbot/bin/nemesis
configure:19013: checking whether /home/buildbot/install/pylith_centos_x86_64_binbot/bin/nemesis version >= 2.4
configure:19022: /home/buildbot/install/pylith_centos_x86_64_binbot/bin/nemesis -c import sys, string # split strings by '.' and convert to numeric. Append some zeros # because we need at least 4 digits for the hex conversion. minver = map(int, string.split('2.4', '.')) + [0, 0, 0] minverhex = 0 for i in xrange(0, 4): minverhex = (minverhex << 8) + minver[i] sys.exit(sys.hexversion < minverhex)
configure:19025: $? = 0
configure:19027: result: yes
configure:19121: checking for /home/buildbot/install/pylith_centos_x86_64_binbot/bin/nemesis version
configure:19128: result: 2.6
configure:19140: checking for /home/buildbot/install/pylith_centos_x86_64_binbot/bin/nemesis platform
configure:19147: result: linux2
configure:19154: checking for /home/buildbot/install/pylith_centos_x86_64_binbot/bin/nemesis script directory
configure:19162: result: ${prefix}/lib/python2.6/site-packages
configure:19171: checking for /home/buildbot/install/pylith_centos_x86_64_binbot/bin/nemesis extension module directory
configure:19179: result: ${exec_prefix}/lib/python2.6/site-packages
configure:19195: checking /home/buildbot/install/pylith_centos_x86_64_binbot/bin/nemesis sysconfig
configure:19276: result: ok
configure:19337: checking for PETSc dir
configure:19364: result: /home/buildbot/install/pylith_centos_x86_64_binbot
configure:19371: checking for PETSc arch
configure:19401: result: pylith-linux-gnu-cxx-opt
configure:19404: checking for PETSc config
configure:19456: result: /home/buildbot/install/pylith_centos_x86_64_binbot/conf/petscvariables
configure:19459: checking for PETSc version == 3.2.0
configure:19507: /home/buildbot/install/pylith_centos_x86_64_binbot/bin/nemesis petsc.py >conftest.sh 2>&5
configure:19510: $? = 0
configure:19536: result: yes
configure:19573: checking for PetscInitialize
configure:19597: mpicxx -o conftest -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/pylith_deps/lib conftest.cc -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lpetsc -lpthread -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lml -lchaco -lflapack -lfblas -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lhdf5_fortran -lhdf5 -lz -lm -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib/gcc/x86_64-unknown-linux-gnu/4.5.2 -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib/gcc/x86_64-unknown-linux-gnu/4.5.2 -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib64 -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib64 -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -lmpichf90 -lgfortran -lm -lm -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -ldl >&5
configure:19603: $? = 0
configure:19607: test -z
|| test ! -s conftest.err
configure:19610: $? = 0
configure:19613: test -s conftest
configure:19616: $? = 0
configure:19619: result: yes (C++)
configure:19898: checking for petsc.h
configure:19918: mpicxx -c -g -O2 -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/install/pylith_centos_x86_64_binbot/include/sieve -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:19924: $? = 0
configure:19928: test -z
|| test ! -s conftest.err
configure:19931: $? = 0
configure:19934: test -s conftest.o
configure:19937: $? = 0
configure:19940: result: yes
configure:20061: checking whether we can link a trivial C++ PETSc program
configure:20093: mpicxx -o conftest -g -O2 -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/install/pylith_centos_x86_64_binbot/include/sieve -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/pylith_deps/lib conftest.cc -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lpetsc -lpthread -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lml -lchaco -lflapack -lfblas -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lhdf5_fortran -lhdf5 -lz -lm -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib/gcc/x86_64-unknown-linux-gnu/4.5.2 -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib/gcc/x86_64-unknown-linux-gnu/4.5.2 -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib64 -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib64 -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -lmpichf90 -lgfortran -lm -lm -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -ldl -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lpetsc -lpthread -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lml -lchaco -lflapack -lfblas -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lhdf5_fortran -lhdf5 -lz -lm -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib/gcc/x86_64-unknown-linux-gnu/4.5.2 -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib/gcc/x86_64-unknown-linux-gnu/4.5.2 -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib64 -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib64 -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -lmpichf90 -lgfortran -lm -lm -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -ldl >&5
configure:20099: $? = 0
configure:20103: test -z
|| test ! -s conftest.err
configure:20106: $? = 0
configure:20109: test -s conftest
configure:20112: $? = 0
configure:20116: result: yes
configure:20235: checking for PetscInitialize
configure:20259: mpicxx -o conftest -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/pylith_deps/lib conftest.cc -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lpetsc -lpthread -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lml -lchaco -lflapack -lfblas -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lhdf5_fortran -lhdf5 -lz -lm -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib/gcc/x86_64-unknown-linux-gnu/4.5.2 -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib/gcc/x86_64-unknown-linux-gnu/4.5.2 -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib64 -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib64 -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -lmpichf90 -lgfortran -lm -lm -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -ldl >&5
configure:20265: $? = 0
configure:20269: test -z
|| test ! -s conftest.err
configure:20272: $? = 0
configure:20275: test -s conftest
configure:20278: $? = 0
configure:20281: result: yes (C++)
configure:20552: checking for PETSc/Sieve
configure:20585: mpicxx -o conftest -g -O2 -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/install/pylith_centos_x86_64_binbot/include/sieve -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/pylith_deps/lib conftest.cc -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lpetsc -lpthread -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lml -lchaco -lflapack -lfblas -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lhdf5_fortran -lhdf5 -lz -lm -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib/gcc/x86_64-unknown-linux-gnu/4.5.2 -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib/gcc/x86_64-unknown-linux-gnu/4.5.2 -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib64 -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib64 -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -lmpichf90 -lgfortran -lm -lm -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -ldl >&5
configure:20591: $? = 0
configure:20595: test -z
|| test ! -s conftest.err
configure:20598: $? = 0
configure:20601: test -s conftest
configure:20604: $? = 0
configure:20607: result: yes
configure:20656: Generating Python egg info
configure:20659: /home/buildbot/install/pylith_centos_x86_64_binbot/bin/nemesis setup.py egg_info >&5 2>&5
/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/merlin-1.7.egg/merlin/__init__.py:175: DeprecationWarning: the sets module is deprecated
from sets import ImmutableSet
/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/merlin-1.7.egg/merlin/__init__.py:2709: UserWarning: Module pkg_resources was already imported from /home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/setuptools-0.6c9-py2.6.egg/pkg_resources.py, but /home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/merlin-1.7.egg is being added to sys.path
import pkg_resources as x
/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/merlin-1.7.egg/merlin/__init__.py:2709: UserWarning: Module site was already imported from /home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site.pyc, but /home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/merlin-1.7.egg is being added to sys.path
import pkg_resources as x
running egg_info
creating PyLith.egg-info
writing requirements to PyLith.egg-info/requires.txt
writing PyLith.egg-info/PKG-INFO
writing top-level names to PyLith.egg-info/top_level.txt
writing dependency_links to PyLith.egg-info/dependency_links.txt
writing manifest file 'PyLith.egg-info/SOURCES.txt'
writing manifest file 'PyLith.egg-info/SOURCES.txt'
configure:20662: $? = 0
configure:20674: checking for egg-related flags
configure:20677: /home/buildbot/install/pylith_centos_x86_64_binbot/bin/nemesis setup.py egg_flags >&5 2>&5
/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/merlin-1.7.egg/merlin/__init__.py:175: DeprecationWarning: the sets module is deprecated
from sets import ImmutableSet
/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/merlin-1.7.egg/merlin/__init__.py:2709: UserWarning: Module pkg_resources was already imported from /home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/setuptools-0.6c9-py2.6.egg/pkg_resources.py, but /home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/merlin-1.7.egg is being added to sys.path
import pkg_resources as x
/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/merlin-1.7.egg/merlin/__init__.py:2709: UserWarning: Module site was already imported from /home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site.pyc, but /home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/merlin-1.7.egg is being added to sys.path
import pkg_resources as x
running egg_flags
configure:20680: $? = 0
configure:20682: result: ok
configure:20719: checking for special C compiler options needed for large files
configure:20818: result: no
configure:20824: checking for _FILE_OFFSET_BITS value needed for large files
configure:20855: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:20861: $? = 0
configure:20865: test -z
|| test ! -s conftest.err
configure:20868: $? = 0
configure:20871: test -s conftest.o
configure:20874: $? = 0
configure:20939: result: no
configure:20949: checking for _LARGE_FILES value needed for large files
configure:20980: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:20986: $? = 0
configure:20990: test -z
|| test ! -s conftest.err
configure:20993: $? = 0
configure:20996: test -s conftest.o
configure:20999: $? = 0
configure:21064: result: no
configure:21080: checking for numpy python module
configure:21084: result: found
configure:21096: checking for numpy include directory
configure:21103: result: /home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/numpy/core/include
configure:21112: checking for python module FIAT
configure:21117: result: found /home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/FIAT/__init__.pyc
configure:21127: checking for FIAT version
configure:21151: result: 0.9.9
configure:21170: checking for swig
configure:21188: found /home/buildbot/pylith_deps/bin/swig
configure:21200: result: /home/buildbot/pylith_deps/bin/swig
configure:21215: checking for SWIG version
configure:21218: result: 2.0.2
configure:21275: SWIG executable is '/home/buildbot/pylith_deps/bin/swig'
configure:21278: SWIG library directory is '/home/buildbot/pylith_deps/share/swig/2.0.2'
configure:21314: checking cppunit/TestRunner.h usability
configure:21326: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:21332: $? = 0
configure:21336: test -z
|| test ! -s conftest.err
configure:21339: $? = 0
configure:21342: test -s conftest.o
configure:21345: $? = 0
configure:21355: result: yes
configure:21359: checking cppunit/TestRunner.h presence
configure:21369: mpicxx -E -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc
configure:21375: $? = 0
configure:21395: result: yes
configure:21430: checking for cppunit/TestRunner.h
configure:21437: result: yes
configure:21459: checking for CppUnit::TestRunner in -lcppunit
configure:21478: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:21484: $? = 0
configure:21488: test -z
|| test ! -s conftest.err
configure:21491: $? = 0
configure:21494: test -s conftest.o
configure:21497: $? = 0
configure:21499: result: yes
configure:21534: checking netcdfcpp.h usability
configure:21546: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:21552: $? = 0
configure:21556: test -z
|| test ! -s conftest.err
configure:21559: $? = 0
configure:21562: test -s conftest.o
configure:21565: $? = 0
configure:21575: result: yes
configure:21579: checking netcdfcpp.h presence
configure:21589: mpicxx -E -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc
configure:21595: $? = 0
configure:21615: result: yes
configure:21650: checking for netcdfcpp.h
configure:21657: result: yes
configure:21680: checking for NcFile in -lnetcdfc++
configure:21698: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:21704: $? = 0
configure:21708: test -z
|| test ! -s conftest.err
configure:21711: $? = 0
configure:21714: test -s conftest.o
configure:21717: $? = 0
configure:21719: result: yes
configure:21969: checking hdf5.h usability
configure:21981: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:21987: $? = 0
configure:21991: test -z
|| test ! -s conftest.err
configure:21994: $? = 0
configure:21997: test -s conftest.o
configure:22000: $? = 0
configure:22010: result: yes
configure:22014: checking hdf5.h presence
configure:22024: mpicxx -E -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc
configure:22030: $? = 0
configure:22050: result: yes
configure:22085: checking for hdf5.h
configure:22092: result: yes
configure:22115: checking for H5Fopen in -lhdf5
configure:22133: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:22139: $? = 0
configure:22143: test -z
|| test ! -s conftest.err
configure:22146: $? = 0
configure:22149: test -s conftest.o
configure:22152: $? = 0
configure:22154: result: yes
configure:22176: checking for library containing H5Pset_dxpl_mpio
configure:22206: mpicxx -o conftest -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/pylith_deps/lib conftest.cc >&5
/tmp/cccF8VsW.o: In function `main':
/home/buildbot/slave/build/pylith_centos_x86_64_binbot/PyLith/trunk/binaries/conftest.cc:36: undefined reference to `H5Pset_dxpl_mpio'
collect2: ld returned 1 exit status
configure:22212: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "PyLith"
| #define PACKAGE_TARNAME "pylith"
| #define PACKAGE_VERSION "1.7.0"
| #define PACKAGE_STRING "PyLith 1.7.0"
| #define PACKAGE_BUGREPORT "cig-short@geodynamics.org"
| #define PACKAGE "pylith"
| #define VERSION "1.7.0"
| #ifdef __cplusplus
| extern "C" void exit (int) throw ();
| #endif
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| /* end confdefs.h. */
|
| /* Override any gcc2 internal prototype to avoid an error. */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
| builtin and then its argument prototype would still apply. */
| char H5Pset_dxpl_mpio ();
| int
| main ()
| {
| H5Pset_dxpl_mpio ();
| ;
| return 0;
| }
configure:22261: mpicxx -o conftest -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/pylith_deps/lib conftest.cc -lhdf5 >&5
configure:22267: $? = 0
configure:22271: test -z
|| test ! -s conftest.err
configure:22274: $? = 0
configure:22277: test -s conftest
configure:22280: $? = 0
configure:22295: result: -lhdf5
configure:22599: checking proj_api.h usability
configure:22611: mpicc -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c >&5
configure:22617: $? = 0
configure:22621: test -z
|| test ! -s conftest.err
configure:22624: $? = 0
configure:22627: test -s conftest.o
configure:22630: $? = 0
configure:22640: result: yes
configure:22644: checking proj_api.h presence
configure:22654: mpicc -E -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.c
configure:22660: $? = 0
configure:22680: result: yes
configure:22715: checking for proj_api.h
configure:22722: result: yes
configure:22745: checking for pj_init_plus in -lproj
configure:22775: mpicc -o conftest -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/pylith_deps/lib conftest.c -lproj -lhdf5 >&5
configure:22781: $? = 0
configure:22785: test -z
|| test ! -s conftest.err
configure:22788: $? = 0
configure:22791: test -s conftest
configure:22794: $? = 0
configure:22807: result: yes
configure:22843: checking spatialdata/spatialdb/SpatialDB.hh usability
configure:22855: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:22861: $? = 0
configure:22865: test -z
|| test ! -s conftest.err
configure:22868: $? = 0
configure:22871: test -s conftest.o
configure:22874: $? = 0
configure:22884: result: yes
configure:22888: checking spatialdata/spatialdb/SpatialDB.hh presence
configure:22898: mpicxx -E -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc
configure:22904: $? = 0
configure:22924: result: yes
configure:22959: checking for spatialdata/spatialdb/SpatialDB.hh
configure:22966: result: yes
configure:22989: checking for SimpleDB in -lspatialdata
configure:23008: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:23014: $? = 0
configure:23018: test -z
|| test ! -s conftest.err
configure:23021: $? = 0
configure:23024: test -s conftest.o
configure:23027: $? = 0
configure:23029: result: yes
configure:23099: checking whether C++ compiler defines __PRETTY_FUNCTION__
configure:23117: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:23123: $? = 0
configure:23127: test -z
|| test ! -s conftest.err
configure:23130: $? = 0
configure:23133: test -s conftest.o
configure:23136: $? = 0
configure:23138: result: yes
configure:23273: checking whether byte ordering is bigendian
configure:23300: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
configure:23306: $? = 0
configure:23310: test -z
|| test ! -s conftest.err
configure:23313: $? = 0
configure:23316: test -s conftest.o
configure:23319: $? = 0
configure:23343: mpicxx -c -g -O2 -DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include conftest.cc >&5
conftest.cc: In function 'int main()':
conftest.cc:34:6: error: 'big' was not declared in this scope
conftest.cc:34:10: error: expected ';' before 'endian'
configure:23349: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "PyLith"
| #define PACKAGE_TARNAME "pylith"
| #define PACKAGE_VERSION "1.7.0"
| #define PACKAGE_STRING "PyLith 1.7.0"
| #define PACKAGE_BUGREPORT "cig-short@geodynamics.org"
| #define PACKAGE "pylith"
| #define VERSION "1.7.0"
| #ifdef __cplusplus
| extern "C" void exit (int) throw ();
| #endif
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_LIBPROJ 1
| #define __FUNCTION_NAME__ __PRETTY_FUNCTION__
| /* end confdefs.h. */
| #include <sys/types.h>
| #include <sys/param.h>
|
| int
| main ()
| {
| #if BYTE_ORDER != BIG_ENDIAN
| not big endian
| #endif
|
| ;
| return 0;
| }
configure:23484: result: no
configure:23694: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by PyLith config.status 1.7.0, which was
generated by GNU Autoconf 2.59. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on kale.geodynamics.org
config.status:927: creating Makefile
config.status:927: creating pylith/Makefile
config.status:927: creating libsrc/Makefile
config.status:927: creating libsrc/pylith/Makefile
config.status:927: creating libsrc/pylith/bc/Makefile
config.status:927: creating libsrc/pylith/feassemble/Makefile
config.status:927: creating libsrc/pylith/faults/Makefile
config.status:927: creating libsrc/pylith/friction/Makefile
config.status:927: creating libsrc/pylith/materials/Makefile
config.status:927: creating libsrc/pylith/meshio/Makefile
config.status:927: creating libsrc/pylith/problems/Makefile
config.status:927: creating libsrc/pylith/topology/Makefile
config.status:927: creating libsrc/pylith/utils/Makefile
config.status:927: creating modulesrc/Makefile
config.status:927: creating modulesrc/include/Makefile
config.status:927: creating modulesrc/bc/Makefile
config.status:927: creating modulesrc/faults/Makefile
config.status:927: creating modulesrc/feassemble/Makefile
config.status:927: creating modulesrc/friction/Makefile
config.status:927: creating modulesrc/materials/Makefile
config.status:927: creating modulesrc/meshio/Makefile
config.status:927: creating modulesrc/mpi/Makefile
config.status:927: creating modulesrc/problems/Makefile
config.status:927: creating modulesrc/topology/Makefile
config.status:927: creating modulesrc/utils/Makefile
config.status:927: creating applications/Makefile
config.status:927: creating applications/utilities/Makefile
config.status:927: creating unittests/Makefile
config.status:927: creating unittests/libtests/Makefile
config.status:927: creating unittests/libtests/bc/Makefile
config.status:927: creating unittests/libtests/bc/data/Makefile
config.status:927: creating unittests/libtests/faults/Makefile
config.status:927: creating unittests/libtests/faults/data/Makefile
config.status:927: creating unittests/libtests/feassemble/Makefile
config.status:927: creating unittests/libtests/feassemble/data/Makefile
config.status:927: creating unittests/libtests/friction/Makefile
config.status:927: creating unittests/libtests/friction/data/Makefile
config.status:927: creating unittests/libtests/materials/Makefile
config.status:927: creating unittests/libtests/materials/data/Makefile
config.status:927: creating unittests/libtests/meshio/Makefile
config.status:927: creating unittests/libtests/meshio/data/Makefile
config.status:927: creating unittests/libtests/topology/Makefile
config.status:927: creating unittests/libtests/topology/data/Makefile
config.status:927: creating unittests/libtests/utils/Makefile
config.status:927: creating unittests/pytests/Makefile
config.status:927: creating unittests/pytests/bc/Makefile
config.status:927: creating unittests/pytests/bc/data/Makefile
config.status:927: creating unittests/pytests/faults/Makefile
config.status:927: creating unittests/pytests/faults/data/Makefile
config.status:927: creating unittests/pytests/feassemble/Makefile
config.status:927: creating unittests/pytests/feassemble/data/Makefile
config.status:927: creating unittests/pytests/friction/Makefile
config.status:927: creating unittests/pytests/friction/data/Makefile
config.status:927: creating unittests/pytests/materials/Makefile
config.status:927: creating unittests/pytests/materials/data/Makefile
config.status:927: creating unittests/pytests/meshio/Makefile
config.status:927: creating unittests/pytests/meshio/data/Makefile
config.status:927: creating unittests/pytests/mpi/Makefile
config.status:927: creating unittests/pytests/problems/Makefile
config.status:927: creating unittests/pytests/problems/data/Makefile
config.status:927: creating unittests/pytests/topology/Makefile
config.status:927: creating unittests/pytests/topology/data/Makefile
config.status:927: creating unittests/pytests/utils/Makefile
config.status:927: creating tests_auto/Makefile
config.status:927: creating tests_auto/1d/Makefile
config.status:927: creating tests_auto/1d/line2/Makefile
config.status:927: creating tests_auto/1d/line3/Makefile
config.status:927: creating tests_auto/2d/Makefile
config.status:927: creating tests_auto/2d/tri3/Makefile
config.status:927: creating tests_auto/2d/quad4/Makefile
config.status:927: creating tests_auto/petsc/Makefile
config.status:927: creating tests/Makefile
config.status:927: creating tests/2d/Makefile
config.status:927: creating tests/2d/maxwell/Makefile
config.status:927: creating tests/2d/slipdir/Makefile
config.status:927: creating tests/2d/frictionslide/Makefile
config.status:927: creating tests/3d/Makefile
config.status:927: creating tests/3d/matprops/Makefile
config.status:927: creating tests/3d/slipdir/Makefile
config.status:927: creating tests/3d/cyclicfriction/Makefile
config.status:927: creating tests/3d/cyclicfriction/output/Makefile
config.status:927: creating tests/3d/plasticity/Makefile
config.status:927: creating tests/3d/plasticity/threehex27/Makefile
config.status:927: creating tests/3d/plasticity/threehex27/config/Makefile
config.status:927: creating tests/3d/plasticity/threehex27/mesh/Makefile
config.status:927: creating tests/3d/plasticity/threehex27/results/Makefile
config.status:927: creating tests/3d/plasticity/threehex27/spatialdb/Makefile
config.status:927: creating tests/3d/plasticity/threehex8/Makefile
config.status:927: creating tests/3d/plasticity/threehex8/config/Makefile
config.status:927: creating tests/3d/plasticity/threehex8/mesh/Makefile
config.status:927: creating tests/3d/plasticity/threehex8/results/Makefile
config.status:927: creating tests/3d/plasticity/threehex8/spatialdb/Makefile
config.status:927: creating tests/topology/Makefile
config.status:927: creating tests/refinefaulttip/Makefile
config.status:927: creating doc/Makefile
config.status:927: creating doc/developer/Makefile
config.status:927: creating doc/install/Makefile
config.status:927: creating doc/refguide/Makefile
config.status:927: creating doc/releasenotes/Makefile
config.status:927: creating doc/userguide/Makefile
config.status:927: creating doc/presentations/Makefile
config.status:927: creating examples/Makefile
config.status:927: creating examples/3d/Makefile
config.status:927: creating examples/3d/tet4/Makefile
config.status:927: creating examples/3d/tet4/output/Makefile
config.status:927: creating examples/3d/hex8/Makefile
config.status:927: creating examples/3d/hex8/output/Makefile
config.status:927: creating examples/2d/Makefile
config.status:927: creating examples/2d/subduction/Makefile
config.status:927: creating examples/2d/subduction/output/Makefile
config.status:927: creating examples/bar_shearwave/Makefile
config.status:927: creating examples/twocells/Makefile
config.status:927: creating examples/bar_shearwave/hex8/Makefile
config.status:927: creating examples/bar_shearwave/hex8/output/Makefile
config.status:927: creating examples/bar_shearwave/quad4/Makefile
config.status:927: creating examples/bar_shearwave/quad4/output/Makefile
config.status:927: creating examples/bar_shearwave/tet4/Makefile
config.status:927: creating examples/bar_shearwave/tet4/output/Makefile
config.status:927: creating examples/bar_shearwave/tri3/Makefile
config.status:927: creating examples/bar_shearwave/tri3/output/Makefile
config.status:927: creating examples/greensfns/Makefile
config.status:927: creating examples/greensfns/hex8/Makefile
config.status:927: creating examples/greensfns/hex8/gfimpulses/Makefile
config.status:927: creating examples/greensfns/hex8/gfresponses/Makefile
config.status:927: creating examples/greensfns/hex8/gfspatialdb/Makefile
config.status:927: creating examples/twocells/twohex8/Makefile
config.status:927: creating examples/twocells/twohex27-cubit/Makefile
config.status:927: creating examples/twocells/twoquad4/Makefile
config.status:927: creating examples/twocells/twotet4/Makefile
config.status:927: creating examples/twocells/twotet4-geoproj/Makefile
config.status:927: creating examples/twocells/twotri3/Makefile
config.status:927: creating examples/meshing/Makefile
config.status:927: creating examples/meshing/surface_nurbs/Makefile
config.status:927: creating examples/meshing/surface_nurbs/contours/Makefile
config.status:927: creating examples/meshing/surface_nurbs/contours/journal/Makefile
config.status:927: creating examples/meshing/surface_nurbs/dem/Makefile
config.status:927: creating examples/meshing/surface_nurbs/dem/ulines/Makefile
config.status:927: creating examples/meshing/surface_nurbs/dem/vlines/Makefile
config.status:927: creating examples/meshing/surface_nurbs/triangles/Makefile
config.status:927: creating templates/Makefile
config.status:927: creating share/Makefile
config.status:1031: creating portinfo
config.status:1323: executing depfiles commands
## ---------------- ##
## Cache variables. ##
## ---------------- ##
_cv_numpy_incdir=/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/numpy/core/include
ac_cv_build=x86_64-redhat-linux-gnu
ac_cv_build_alias=x86_64-redhat-linux-gnu
ac_cv_c_bigendian=no
ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CC_set=set
ac_cv_env_CC_value=mpicc
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=set
ac_cv_env_CPPFLAGS_value='-I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include'
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=set
ac_cv_env_CXX_value=mpicxx
ac_cv_env_F77_set=set
ac_cv_env_F77_value=mpif77
ac_cv_env_FFLAGS_set=
ac_cv_env_FFLAGS_value=
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value='-L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/pylith_deps/lib'
ac_cv_env_PETSC_ARCH_set=set
ac_cv_env_PETSC_ARCH_value=pylith-linux-gnu-cxx-opt
ac_cv_env_PETSC_DIR_set=set
ac_cv_env_PETSC_DIR_value=/home/buildbot/install/pylith_centos_x86_64_binbot
ac_cv_env_PYTHONPATH_set=set
ac_cv_env_PYTHONPATH_value=/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages:/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages:/home/buildbot/install/pylith_centos_x86_64_binbot/lib64/python2.6/site-packages:/home/buildbot/pylith_deps/lib/python2.6/site-packages:/home/buildbot/buildbot/lib/python2.4/site-packages:/home/buildbot/buildbot/lib64/python2.4/site-packages
ac_cv_env_PYTHON_set=set
ac_cv_env_PYTHON_value=python2.6
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_exeext=
ac_cv_f77_compiler_gnu=yes
ac_cv_header_cppunit_TestRunner_h=yes
ac_cv_header_dlfcn_h=yes
ac_cv_header_hdf5_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_netcdfcpp_h=yes
ac_cv_header_proj_api_h=yes
ac_cv_header_spatialdata_spatialdb_SpatialDB_hh=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_host=x86_64-redhat-linux-gnu
ac_cv_host_alias=x86_64-redhat-linux-gnu
ac_cv_lib_proj_pj_init_plus=yes
ac_cv_objext=o
ac_cv_path_PYTHON=/home/buildbot/install/pylith_centos_x86_64_binbot/bin/nemesis
ac_cv_path_SWIG=/home/buildbot/pylith_deps/bin/swig
ac_cv_path_install='/usr/bin/install -c'
ac_cv_prog_AWK=gawk
ac_cv_prog_CPP='mpicc -E'
ac_cv_prog_CXXCPP='mpicxx -E'
ac_cv_prog_ac_ct_AR=ar
ac_cv_prog_ac_ct_CC=mpicc
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_ac_ct_STRIP=strip
ac_cv_prog_cc_g=yes
ac_cv_prog_cc_stdc=
ac_cv_prog_cxx_g=yes
ac_cv_prog_egrep='grep -E'
ac_cv_prog_f77_g=yes
ac_cv_prog_make_make_set=yes
ac_cv_search_H5Pset_dxpl_mpio=-lhdf5
ac_cv_sys_file_offset_bits=no
ac_cv_sys_large_files=no
ac_cv_sys_largefile_CC=no
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=gcc3
am_cv_python_platform=linux2
am_cv_python_pyexecdir='${exec_prefix}/lib/python2.6/site-packages'
am_cv_python_pythondir='${prefix}/lib/python2.6/site-packages'
am_cv_python_version=2.6
lt_cv_deplibs_check_method=pass_all
lt_cv_file_magic_cmd='$MAGIC_CMD'
lt_cv_file_magic_test_file=
lt_cv_ld_reload_flag=-r
lt_cv_objdir=.libs
lt_cv_path_LD=/usr/bin/ld
lt_cv_path_LDCXX='/usr/bin/ld -m elf_x86_64'
lt_cv_path_NM='/usr/bin/nm -B'
lt_cv_path_SED=/bin/sed
lt_cv_prog_compiler_c_o=yes
lt_cv_prog_compiler_c_o_CXX=yes
lt_cv_prog_compiler_c_o_F77=yes
lt_cv_prog_compiler_rtti_exceptions=no
lt_cv_prog_gnu_ld=yes
lt_cv_prog_gnu_ldcxx=yes
lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\'''
lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (lt_ptr) 0},/p'\'' -e '\''s/^[BCDEGRST] \([^ ]*\) \([^ ]*\)$/ {"\2", (lt_ptr) \&\2},/p'\'''
lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^. .* \(.*\)$/extern int \1;/p'\'''
lt_cv_sys_max_cmd_len=32768
lt_lt_cv_prog_compiler_c_o='"yes"'
lt_lt_cv_prog_compiler_c_o_CXX='"yes"'
lt_lt_cv_prog_compiler_c_o_F77='"yes"'
lt_lt_cv_sys_global_symbol_pipe='"sed -n -e '\''s/^.*[ ]\\([ABCDGIRSTW][ABCDGIRSTW]*\\)[ ][ ]*\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1 \\2 \\2/p'\''"'
lt_lt_cv_sys_global_symbol_to_c_name_address='"sed -n -e '\''s/^: \\([^ ]*\\) \$/ {\\\"\\1\\\", (lt_ptr) 0},/p'\'' -e '\''s/^[BCDEGRST] \\([^ ]*\\) \\([^ ]*\\)\$/ {\"\\2\", (lt_ptr) \\&\\2},/p'\''"'
lt_lt_cv_sys_global_symbol_to_cdecl='"sed -n -e '\''s/^. .* \\(.*\\)\$/extern int \\1;/p'\''"'
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL} /home/buildbot/slave/build/pylith_centos_x86_64_binbot/PyLith/trunk/binaries/aux-config/missing --run aclocal-1.9'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL} /home/buildbot/slave/build/pylith_centos_x86_64_binbot/PyLith/trunk/binaries/aux-config/missing --run tar'
AM_LDFLAGS=''
AR='ar'
AUTOCONF='${SHELL} /home/buildbot/slave/build/pylith_centos_x86_64_binbot/PyLith/trunk/binaries/aux-config/missing --run autoconf'
AUTOHEADER='${SHELL} /home/buildbot/slave/build/pylith_centos_x86_64_binbot/PyLith/trunk/binaries/aux-config/missing --run autoheader'
AUTOMAKE='${SHELL} /home/buildbot/slave/build/pylith_centos_x86_64_binbot/PyLith/trunk/binaries/aux-config/missing --run automake-1.9'
AWK='gawk'
CC='mpicc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CPP='mpicc -E'
CPPFLAGS='-DENABLE_HDF5 -DENABLE_CUBIT -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/pylith_deps/include'
CXX='mpicxx'
CXXCPP='mpicxx -E'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS='-g -O2'
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
ECHO='echo'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='grep -E'
ENABLE_CUBIT_FALSE='#'
ENABLE_CUBIT_TRUE=''
ENABLE_CUDA_FALSE=''
ENABLE_CUDA_TRUE='#'
ENABLE_DOCUMENTATION_FALSE=''
ENABLE_DOCUMENTATION_TRUE='#'
ENABLE_FULL_TESTING_FALSE='#'
ENABLE_FULL_TESTING_TRUE=''
ENABLE_HDF5_FALSE='#'
ENABLE_HDF5_TRUE=''
ENABLE_MEMORY_LOGGING_FALSE=''
ENABLE_MEMORY_LOGGING_TRUE='#'
ENABLE_SWIG_FALSE='#'
ENABLE_SWIG_TRUE=''
ENABLE_TESTING_FALSE='#'
ENABLE_TESTING_TRUE=''
ENABLE_TETGEN_FALSE=''
ENABLE_TETGEN_TRUE='#'
EXEEXT=''
F77='mpif77'
FFLAGS='-g -O2'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s'
LDFLAGS='-L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/pylith_deps/lib'
LIBOBJS=''
LIBS='-lproj -lhdf5 '
LIBTOOL='$(SHELL) $(top_builddir)/libtool'
LN_S='ln -s'
LTLIBOBJS=''
MAKEINFO='${SHELL} /home/buildbot/slave/build/pylith_centos_x86_64_binbot/PyLith/trunk/binaries/aux-config/missing --run makeinfo'
NO_UNDEFINED_FALSE=''
NO_UNDEFINED_TRUE='#'
NUMPY_INCDIR='/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/numpy/core/include'
NVCC=''
OBJEXT='o'
PACKAGE='pylith'
PACKAGE_BUGREPORT='cig-short@geodynamics.org'
PACKAGE_NAME='PyLith'
PACKAGE_STRING='PyLith 1.7.0'
PACKAGE_TARNAME='pylith'
PACKAGE_VERSION='1.7.0'
PATH_SEPARATOR=':'
PETSC_ARCH='pylith-linux-gnu-cxx-opt'
PETSC_CC='mpicc'
PETSC_CC_INCLUDES='-I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/install/pylith_centos_x86_64_binbot/include/sieve -I/home/buildbot/install/pylith_centos_x86_64_binbot/include'
PETSC_CXX='mpicxx'
PETSC_CXX_INCLUDE=' '
PETSC_CXX_LIB=''
PETSC_DIR='/home/buildbot/install/pylith_centos_x86_64_binbot'
PETSC_FC='mpif90'
PETSC_FC_INCLUDES='-I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/install/pylith_centos_x86_64_binbot/include -I/home/buildbot/install/pylith_centos_x86_64_binbot/include/sieve -I/home/buildbot/install/pylith_centos_x86_64_binbot/include'
PETSC_FORTRAN_LIB=''
PETSC_LIB='-L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lpetsc -lpthread -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lml -lchaco -lflapack -lfblas -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -lhdf5_fortran -lhdf5 -lz -lm -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib/gcc/x86_64-unknown-linux-gnu/4.5.2 -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib/gcc/x86_64-unknown-linux-gnu/4.5.2 -Wl,-rpath,/home/buildbot/install/pylith_centos_x86_64_binbot/lib64 -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib64 -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -lmpichf90 -lgfortran -lm -lm -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -ldl'
PETSC_MPI_INCLUDE='-I/home/buildbot/install/pylith_centos_x86_64_binbot/include'
PETSC_MPI_LIB=''
PETSC_SIEVE_FLAGS=''
PETSC_VERSION_MAJOR='3'
PETSC_VERSION_MINOR='2'
PETSC_VERSION_SUBMINOR='0'
PYLITH_SWIG_CPPFLAGS='-DENABLE_HDF5 -DENABLE_CUBIT '
PYTHON='/home/buildbot/install/pylith_centos_x86_64_binbot/bin/nemesis'
PYTHONPATH='${prefix}/lib/python2.6/site-packages:${exec_prefix}/lib/python2.6/site-packages:/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages:/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages:/home/buildbot/install/pylith_centos_x86_64_binbot/lib64/python2.6/site-packages:/home/buildbot/pylith_deps/lib/python2.6/site-packages:/home/buildbot/buildbot/lib/python2.4/site-packages:/home/buildbot/buildbot/lib64/python2.4/site-packages'
PYTHON_BLDLIBRARY='-L/home/buildbot/install/pylith_centos_x86_64_binbot/lib -L/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/config -lpython2.6'
PYTHON_EGG_CFLAGS=''
PYTHON_EGG_CPPFLAGS='-I/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/pythia-0.8.1.13-py2.6.egg'
PYTHON_EGG_LDFLAGS=''
PYTHON_EGG_LIBS=''
PYTHON_EGG_PYXFLAGS='-I/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/site-packages/pythia-0.8.1.13-py2.6.egg/mpi'
PYTHON_EXEC_PREFIX='${exec_prefix}'
PYTHON_INCDIR='/home/buildbot/install/pylith_centos_x86_64_binbot/include/python2.6'
PYTHON_LA_LDFLAGS=''
PYTHON_LDFLAGS=''
PYTHON_LDLAST=''
PYTHON_LDLIBRARY='libpython2.6.so'
PYTHON_LIBDIR='/home/buildbot/install/pylith_centos_x86_64_binbot/lib'
PYTHON_LIBP='/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6'
PYTHON_LIBPL='/home/buildbot/install/pylith_centos_x86_64_binbot/lib/python2.6/config'
PYTHON_LIBS='-lpthread -ldl -lutil'
PYTHON_LINKFORSHARED='-Xlinker -export-dynamic'
PYTHON_MODLIBS=''
PYTHON_PLATFORM='linux2'
PYTHON_PREFIX='${prefix}'
PYTHON_SYSLIBS='-lm'
PYTHON_VERSION='2.6'
RANLIB='ranlib'
SED='/bin/sed'
SET_MAKE=''
SHELL='/bin/sh'
STRIP='strip'
SWIG='/home/buildbot/pylith_deps/bin/swig'
SWIG_LIB='/home/buildbot/pylith_deps/share/swig/2.0.2'
VERSION='1.7.0'
ac_ct_AR='ar'
ac_ct_CC='mpicc'
ac_ct_CXX=''
ac_ct_F77=''
ac_ct_RANLIB='ranlib'
ac_ct_STRIP='strip'
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE='#'
am__fastdepCXX_TRUE=''
am__include='include'
am__leading_dot='.'
am__quote=''
am__tar='${AMTAR} chof - "$$tardir"'
am__untar='${AMTAR} xf -'
bindir='${exec_prefix}/bin'
build='x86_64-redhat-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='redhat'
datadir='${prefix}/share'
exec_prefix='${prefix}'
have_doxygen=''
host='x86_64-redhat-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='redhat'
includedir='${prefix}/include'
infodir='${prefix}/info'
install_sh='/home/buildbot/slave/build/pylith_centos_x86_64_binbot/PyLith/trunk/binaries/aux-config/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localstatedir='${prefix}/var'
mandir='${prefix}/man'
mkdir_p='mkdir -p --'
oldincludedir='/usr/include'
pkgpyexecdir='${pyexecdir}/pylith'
pkgpythondir='${pythondir}/pylith'
prefix='/home/buildbot/install/pylith_centos_x86_64_binbot'
program_transform_name='s,x,x,'
pyexecdir='${exec_prefix}/lib/python2.6/site-packages'
pythondir='${prefix}/lib/python2.6/site-packages'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
#define HAVE_DLFCN_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_LIBPROJ 1
#define HAVE_MEMORY_H 1
#define HAVE_STDINT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRINGS_H 1
#define HAVE_STRING_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_UNISTD_H 1
#define PACKAGE "pylith"
#define PACKAGE_BUGREPORT "cig-short@geodynamics.org"
#define PACKAGE_NAME "PyLith"
#define PACKAGE_STRING "PyLith 1.7.0"
#define PACKAGE_TARNAME "pylith"
#define PACKAGE_VERSION "1.7.0"
#define STDC_HEADERS 1
#define VERSION "1.7.0"
#define __FUNCTION_NAME__ __PRETTY_FUNCTION__
#endif
#ifdef __cplusplus
extern "C" void exit (int) throw ();
configure: exit 0