[CIG-MC] Cookbook 9 exchanger problems - ExchangerLib not compiled/linked?
Lonn Brown
lbrown at phys.ualberta.ca
Thu May 20 13:16:36 PDT 2010
Hey CIG,
I've run into a problem trying to execute the example "Cookbook 9" included in
the 3.1.1 distribution. A similar problem was addressed here;
http://www.geodynamics.org/pipermail/cig-mc/2009-March/000119.html
However the solution presented there does not fix my problem.
I installed as:
$ ./configure --with-exchanger
$ make
And after typing
$ citcoms --coupled cookbook9.cfg
The following is output to my terminal window.
Problem has 17 x 25 x 17 nodes per cap, 7225 nodes and 6144 elements in total
Problem has 21 x 49 x 21 nodes per cap, 21609 nodes and 19200 elements in total
memory allocation done
parallel setup done
memory allocation done
node locations done
parallel setup done
velocity vars done
boundary conditions done
id/lm done
13 0.795000 0.205000 1.000000e+00 4
14 0.815000 0.185000 1.000000e+00 4
15 0.835000 0.165000 1.000000e+00 4
16 0.855000 0.145000 1.000000e+00 4
v communications done
17 0.875000 0.125000 1.000000e+00 4
18 0.895000 0.105000 1.000000e+00 4
19 0.915000 0.085000 1.000000e+00 3
20 0.935000 0.065000 1.000000e+00 3
21 0.955000 0.045000 1.000000e+00 2
22 0.966250 0.033750 1.000000e+00 2
23 0.977500 0.022500 1.000000e+00 2
24 0.988750 0.011250 1.000000e+00 1
25 1.000000 0.000000 1.000000e+00 1
nz radius depth rho layer
1 0.550000 0.450000 1.000000e+00 4
2 0.572500 0.427500 1.000000e+00 4
3 0.595000 0.405000 1.000000e+00 4
4 0.615000 0.385000 1.000000e+00 4
5 0.635000 0.365000 1.000000e+00 4
6 0.655000 0.345000 1.000000e+00 4
7 0.675000 0.325000 1.000000e+00 4
8 0.695000 0.305000 1.000000e+00 4
9 0.715000 0.285000 1.000000e+00 4
10 0.735000 0.265000 1.000000e+00 4
11 0.755000 0.245000 1.000000e+00 4
12 0.775000 0.225000 1.000000e+00 4
13 0.795000 0.205000 1.000000e+00 4
node locations done
velocity vars done
boundary conditions done
id/lm done
v communications done
nz radius depth rho layer
1 0.551000 0.449000 1.000000e+00 4
2 0.560333 0.439667 1.000000e+00 4
3 0.569667 0.430333 1.000000e+00 4
4 0.579000 0.421000 1.000000e+00 4
5 0.588333 0.411667 1.000000e+00 4
6 0.597667 0.402333 1.000000e+00 4
7 0.607000 0.393000 1.000000e+00 4
8 0.616333 0.383667 1.000000e+00 4
9 0.625667 0.374333 1.000000e+00 4
10 0.635000 0.365000 1.000000e+00 4
11 0.644333 0.355667 1.000000e+00 4
12 0.653667 0.346333 1.000000e+00 4
13 0.663000 0.337000 1.000000e+00 4
14 0.672333 0.327667 1.000000e+00 4
15 0.681667 0.318333 1.000000e+00 4
16 0.691000 0.309000 1.000000e+00 4
17 0.700333 0.299667 1.000000e+00 4
18 0.709667 0.290333 1.000000e+00 4
19 0.719000 0.281000 1.000000e+00 4
20 0.728333 0.271667 1.000000e+00 4
21 0.737667 0.262333 1.000000e+00 4
22 0.747000 0.253000 1.000000e+00 4
23 0.756333 0.243667 1.000000e+00 4
24 0.765667 0.234333 1.000000e+00 4
25 0.775000 0.225000 1.000000e+00 4
25 0.775000 0.225000 1.000000e+00 4
26 0.784333 0.215667 1.000000e+00 4
27 0.793667 0.206333 1.000000e+00 4
28 0.803000 0.197000 1.000000e+00 4
29 0.812333 0.187667 1.000000e+00 4
30 0.821667 0.178333 1.000000e+00 4
31 0.831000 0.169000 1.000000e+00 4
32 0.840333 0.159667 1.000000e+00 4
33 0.849667 0.150333 1.000000e+00 4
34 0.859000 0.141000 1.000000e+00 4
35 0.868333 0.131667 1.000000e+00 4
36 0.877667 0.122333 1.000000e+00 4
37 0.887000 0.113000 1.000000e+00 4
38 0.896333 0.103667 1.000000e+00 3
39 0.905667 0.094333 1.000000e+00 3
40 0.915000 0.085000 1.000000e+00 3
41 0.924333 0.075667 1.000000e+00 3
42 0.933667 0.066333 1.000000e+00 3
43 0.943000 0.057000 1.000000e+00 2
44 0.952333 0.047667 1.000000e+00 2
45 0.961667 0.038333 1.000000e+00 2
46 0.971000 0.029000 1.000000e+00 2
47 0.980333 0.019667 1.000000e+00 2
48 0.989667 0.010333 1.000000e+00 1
49 0.999000 0.001000 1.000000e+00 1
mass matrix, dets done
initial_mesh_solver_setup done
initialization time = 0.077650
Traceback (most recent call last):
File "<string>", line 1, in ?
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/mpi/__init__.py",
line 42, in mpistart
kwds = kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/__init__.py",
line 41, in start
shell.run(**kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/Shell.py",
line 143, in run
method(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/SuperScript.py",
line 49, in execute
self.main(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/SuperScript.py",
line 58, in main
self.runSubscript(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/SuperScript.py",
line 62, in runSubscript
self.subscript.run(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/Application.py",
line 42, in run
shell.run(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/Shell.py",
line 143, in run
method(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/mpi/Application.py",
line 118, in _onComputeNodes
self.onComputeNodes(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/mpi/Application.py",
line 124, in onComputeNodes
self.main(*args, **kwds)
File "/usr/local/lib/python2.4/site-packages/CitcomS/BaseApplication.py",
line 67, in main
self.initialize()
File "/usr/local/lib/python2.4/site-packages/CitcomS/CoupledApp.py", line
71, in initialize
self.controller.initialize(self)
File "/usr/local/lib/python2.4/site-packages/CitcomS/Controller.py", line
57, in initialize
self.solver.initialize(app)
File
"/usr/local/lib/python2.4/site-packages/CitcomS/Solver/CoupledSolver.py", line
53, in initialize
self.coupler.initialize(self)
File
"/usr/local/lib/python2.4/site-packages/CitcomS/Coupler/ContainingCoupler.py",
line 40, in initialize
Coupler.initialize(self, solver)
File "/usr/local/lib/python2.4/site-packages/CitcomS/Coupler/Coupler.py",
line 76, in initialize
from ExchangerLib import initConvertor
ImportError: No module named ExchangerLib
Traceback (most recent call last):
File "<string>", line 1, in ?
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/mpi/__init__.py",
line 42, in mpistart
kwds = kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/__init__.py",
line 41, in start
shell.run(**kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/Shell.py",
line 143, in run
method(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/SuperScript.py",
line 49, in execute
self.main(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/SuperScript.py",
line 58, in main
self.runSubscript(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/SuperScript.py",
line 62, in runSubscript
self.subscript.run(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/Application.py",
line 42, in run
shell.run(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/Shell.py",
line 143, in run
method(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/mpi/Application.py",
line 118, in _onComputeNodes
self.onComputeNodes(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/mpi/Application.py",
line 124, in onComputeNodes
self.main(*args, **kwds)
File "/usr/local/lib/python2.4/site-packages/CitcomS/BaseApplication.py",
line 67, in main
self.initialize()
File "/usr/local/lib/python2.4/site-packages/CitcomS/CoupledApp.py", line
71, in initialize
self.controller.initialize(self)
File "/usr/local/lib/python2.4/site-packages/CitcomS/Controller.py", line
57, in initialize
self.solver.initialize(app)
File
"/usr/local/lib/python2.4/site-packages/CitcomS/Solver/CoupledSolver.py", line
53, in initialize
self.coupler.initialize(self)
File
"/usr/local/lib/python2.4/site-packages/CitcomS/Coupler/ContainingCoupler.py",
line 40, in initialize
Coupler.initialize(self, solver)
File "/usr/local/lib/python2.4/site-packages/CitcomS/Coupler/Coupler.py",
line 76, in initialize
from ExchangerLib import initConvertor
ImportError: No module named ExchangerLib
mass matrix, dets done
initial_mesh_solver_setup done
Traceback (most recent call last):
File "<string>", line 1, in ?
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/mpi/__init__.py",
line 42, in mpistart
kwds = kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/__init__.py",
line 41, in start
shell.run(**kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/Shell.py",
line 143, in run
method(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/SuperScript.py",
line 49, in execute
self.main(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/SuperScript.py",
line 58, in main
self.runSubscript(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/SuperScript.py",
line 62, in runSubscript
self.subscript.run(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/Application.py",
line 42, in run
shell.run(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/Shell.py",
line 143, in run
method(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/mpi/Application.py",
line 118, in _onComputeNodes
self.onComputeNodes(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/mpi/Application.py",
line 124, in onComputeNodes
self.main(*args, **kwds)
File "/usr/local/lib/python2.4/site-packages/CitcomS/BaseApplication.py",
line 67, in main
self.initialize()
File "/usr/local/lib/python2.4/site-packages/CitcomS/CoupledApp.py", line
71, in initialize
self.controller.initialize(self)
File "/usr/local/lib/python2.4/site-packages/CitcomS/Controller.py", line
57, in initialize
self.solver.initialize(app)
Traceback (most recent call last):
File
"/usr/local/lib/python2.4/site-packages/CitcomS/Solver/CoupledSolver.py", line
53, in initialize
self.coupler.initialize(self)
File
"/usr/local/lib/python2.4/site-packages/CitcomS/Coupler/EmbeddedCoupler.py",
line 49, in initialize
Coupler.initialize(self, solver)
File "/usr/local/lib/python2.4/site-packages/CitcomS/Coupler/Coupler.py",
line 76, in initialize
from ExchangerLib import initConvertor
ImportError: No module named ExchangerLib
File "<string>", line 1, in ?
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/mpi/__init__.py",
line 42, in mpistart
kwds = kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/__init__.py",
line 41, in start
shell.run(**kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/Shell.py",
line 143, in run
method(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/SuperScript.py",
line 49, in execute
self.main(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/SuperScript.py",
line 58, in main
self.runSubscript(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/SuperScript.py",
line 62, in runSubscript
self.subscript.run(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/Application.py",
line 42, in run
shell.run(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/pyre/applications/Shell.py",
line 143, in run
method(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/mpi/Application.py",
line 118, in _onComputeNodes
self.onComputeNodes(*args, **kwds)
File
"/local/sys/usr/local/lib/python2.4/site-packages/pythia-0.8.1.10-py2.4.egg/mpi/Application.py",
line 124, in onComputeNodes
self.main(*args, **kwds)
File "/usr/local/lib/python2.4/site-packages/CitcomS/BaseApplication.py",
line 67, in main
self.initialize()
File "/usr/local/lib/python2.4/site-packages/CitcomS/CoupledApp.py", line
71, in initialize
self.controller.initialize(self)
File "/usr/local/lib/python2.4/site-packages/CitcomS/Controller.py", line
57, in initialize
self.solver.initialize(app)
File
"/usr/local/lib/python2.4/site-packages/CitcomS/Solver/CoupledSolver.py", line
53, in initialize
self.coupler.initialize(self)
File
"/usr/local/lib/python2.4/site-packages/CitcomS/Coupler/EmbeddedCoupler.py",
line 49, in initialize
Coupler.initialize(self, solver)
File "/usr/local/lib/python2.4/site-packages/CitcomS/Coupler/Coupler.py",
line 76, in initialize
from ExchangerLib import initConvertor
ImportError: No module named ExchangerLib
/usr/local/bin/pycitcoms: mpirun: exit 1
/usr/local/bin/citcoms: /usr/local/bin/pycitcoms: exit 1
My config.log file is also appended.
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by CitcomS configure 3.1.1, which was
generated by GNU Autoconf 2.61. Invocation command line was
$ ./configure --with-exchanger
## --------- ##
## Platform. ##
## --------- ##
hostname = marmot
uname -m = x86_64
uname -r = 2.6.20-1.3002.fc6xen
uname -s = Linux
uname -v = #1 SMP Mon Aug 13 14:21:21 EDT 2007
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = x86_64
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /usr/local/PROGRAMS.330/bin
PATH: /usr/local/paraview/bin
PATH: /opt/intel_cc_80/bin
PATH: /opt/intel_fc_80/bin
PATH: /opt/java/jdk1.5/bin
PATH: /opt/java/jre1.5/bin
PATH: /usr/local/PROGRAMS.330/bin
PATH: /usr/local/paraview/bin
PATH: /opt/intel_cc_80/bin
PATH: /opt/intel_fc_80/bin
PATH: /opt/java/jdk1.5/bin
PATH: /opt/java/jre1.5/bin
PATH: /usr/local/PROGRAMS.330/bin
PATH: /usr/local/paraview/bin
PATH: /opt/intel_cc_80/bin
PATH: /opt/intel_fc_80/bin
PATH: /opt/java/jdk1.5/bin
PATH: /opt/java/jre1.5/bin
PATH: /usr/local/PROGRAMS.330/bin
PATH: /usr/local/paraview/bin
PATH: /opt/intel_cc_80/bin
PATH: /opt/intel_fc_80/bin
PATH: /opt/java/jdk1.5/bin
PATH: /opt/java/jre1.5/bin
PATH: /usr/local/PROGRAMS.330/bin
PATH: /usr/local/paraview/bin
PATH: /opt/intel_cc_80/bin
PATH: /opt/intel_fc_80/bin
PATH: /opt/java/jdk1.5/bin
PATH: /opt/java/jre1.5/bin
PATH: /usr/lib64/qt-3.3/bin
PATH: /usr/kerberos/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/X11R6/bin
PATH: /usr/X11R6/bin
PATH: /usr/local/su/bin
PATH: /users/lbrown/bin
PATH: .
PATH: /usr/X11R6/bin
PATH: /usr/local/su/bin
PATH: /users/lbrown/bin
PATH: .
PATH: /usr/X11R6/bin
PATH: /usr/local/su/bin
PATH: /users/lbrown/bin
PATH: .
PATH: /usr/X11R6/bin
PATH: /usr/local/su/bin
PATH: /users/lbrown/bin
PATH: .
PATH: /usr/X11R6/bin
PATH: /usr/local/su/bin
PATH: /users/lbrown/bin
PATH: .
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2035: checking for a BSD-compatible install
configure:2091: result: /usr/bin/install -c
configure:2102: checking whether build environment is sane
configure:2145: result: yes
configure:2210: checking for gawk
configure:2226: found /usr/bin/gawk
configure:2237: result: gawk
configure:2248: checking whether make sets $(MAKE)
configure:2269: result: yes
configure:2605: checking for mpicc
configure:2621: found /usr/bin/mpicc
configure:2632: result: mpicc
configure:2668: checking for C compiler version
configure:2675: mpicc --version >&5
gcc (GCC) 4.1.2 20070626 (Red Hat 4.1.2-13)
Copyright (C) 2006 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:2678: $? = 0
configure:2685: mpicc -v >&5
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--enable-checking=release --with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-libgcj-multifile
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk
--disable-dssi --enable-plugin
--with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic
--host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.2 20070626 (Red Hat 4.1.2-13)
configure:2688: $? = 0
configure:2695: mpicc -V >&5
gcc: '-V' option must have argument
configure:2698: $? = 1
configure:2721: checking for C compiler default output file name
configure:2748: mpicc conftest.c >&5
configure:2751: $? = 0
configure:2789: result: a.out
configure:2806: checking whether the C compiler works
configure:2816: ./a.out
configure:2819: $? = 0
configure:2836: result: yes
configure:2843: checking whether we are cross compiling
configure:2845: result: no
configure:2848: checking for suffix of executables
configure:2855: mpicc -o conftest conftest.c >&5
configure:2858: $? = 0
configure:2882: result:
configure:2888: checking for suffix of object files
configure:2914: mpicc -c conftest.c >&5
configure:2917: $? = 0
configure:2940: result: o
configure:2944: checking whether we are using the GNU C compiler
configure:2973: mpicc -c conftest.c >&5
configure:2979: $? = 0
configure:2996: result: yes
configure:3001: checking whether mpicc accepts -g
configure:3031: mpicc -c -g conftest.c >&5
configure:3037: $? = 0
configure:3136: result: yes
configure:3153: checking for mpicc option to accept ISO C89
configure:3227: mpicc -c -g -O2 conftest.c >&5
configure:3233: $? = 0
configure:3256: result: none needed
configure:3285: checking for style of include used by make
configure:3313: result: GNU
configure:3341: checking dependency style of mpicc
configure:3431: result: gcc3
configure:3506: checking for mpicxx
configure:3522: found /usr/bin/mpicxx
configure:3533: result: mpicxx
configure:3564: checking for C++ compiler version
configure:3571: mpicxx --version >&5
g++ (GCC) 4.1.2 20070626 (Red Hat 4.1.2-13)
Copyright (C) 2006 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:3574: $? = 0
configure:3581: mpicxx -v >&5
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--enable-checking=release --with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-libgcj-multifile
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk
--disable-dssi --enable-plugin
--with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic
--host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.2 20070626 (Red Hat 4.1.2-13)
configure:3584: $? = 0
configure:3591: mpicxx -V >&5
g++: '-V' option must have argument
configure:3594: $? = 1
configure:3597: checking whether we are using the GNU C++ compiler
configure:3626: mpicxx -c conftest.cpp >&5
configure:3632: $? = 0
configure:3649: result: yes
configure:3654: checking whether mpicxx accepts -g
configure:3684: mpicxx -c -g conftest.cpp >&5
configure:3690: $? = 0
configure:3789: result: yes
configure:3814: checking dependency style of mpicxx
configure:3904: result: gcc3
configure:3929: checking how to run the C preprocessor
configure:3969: mpicc -E conftest.c
configure:3975: $? = 0
configure:4006: mpicc -E conftest.c
conftest.c:10:28: error: ac_nonexistent.h: No such file or directory
configure:4012: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "CitcomS"
| #define PACKAGE_TARNAME "CitcomS"
| #define PACKAGE_VERSION "3.1.1"
| #define PACKAGE_STRING "CitcomS 3.1.1"
| #define PACKAGE_BUGREPORT "cig-mc at geodynamics.org"
| #define PACKAGE "CitcomS"
| #define VERSION "3.1.1"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4045: result: mpicc -E
configure:4074: mpicc -E conftest.c
configure:4080: $? = 0
configure:4111: mpicc -E conftest.c
conftest.c:10:28: error: ac_nonexistent.h: No such file or directory
configure:4117: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "CitcomS"
| #define PACKAGE_TARNAME "CitcomS"
| #define PACKAGE_VERSION "3.1.1"
| #define PACKAGE_STRING "CitcomS 3.1.1"
| #define PACKAGE_BUGREPORT "cig-mc at geodynamics.org"
| #define PACKAGE "CitcomS"
| #define VERSION "3.1.1"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4155: checking for grep that handles long lines and -e
configure:4229: result: /bin/grep
configure:4234: checking for egrep
configure:4312: result: /bin/grep -E
configure:4317: checking for ANSI C header files
configure:4347: mpicc -c -g -O2 conftest.c >&5
configure:4353: $? = 0
configure:4452: mpicc -o conftest -g -O2 conftest.c >&5
configure:4455: $? = 0
configure:4461: ./conftest
configure:4464: $? = 0
configure:4481: result: yes
configure:4505: checking for sys/types.h
configure:4526: mpicc -c -g -O2 conftest.c >&5
configure:4532: $? = 0
configure:4548: result: yes
configure:4505: checking for sys/stat.h
configure:4526: mpicc -c -g -O2 conftest.c >&5
configure:4532: $? = 0
configure:4548: result: yes
configure:4505: checking for stdlib.h
configure:4526: mpicc -c -g -O2 conftest.c >&5
configure:4532: $? = 0
configure:4548: result: yes
configure:4505: checking for string.h
configure:4526: mpicc -c -g -O2 conftest.c >&5
configure:4532: $? = 0
configure:4548: result: yes
configure:4505: checking for memory.h
configure:4526: mpicc -c -g -O2 conftest.c >&5
configure:4532: $? = 0
configure:4548: result: yes
configure:4505: checking for strings.h
configure:4526: mpicc -c -g -O2 conftest.c >&5
configure:4532: $? = 0
configure:4548: result: yes
configure:4505: checking for inttypes.h
configure:4526: mpicc -c -g -O2 conftest.c >&5
configure:4532: $? = 0
configure:4548: result: yes
configure:4505: checking for stdint.h
configure:4526: mpicc -c -g -O2 conftest.c >&5
configure:4532: $? = 0
configure:4548: result: yes
configure:4505: checking for unistd.h
configure:4526: mpicc -c -g -O2 conftest.c >&5
configure:4532: $? = 0
configure:4548: result: yes
configure:4575: checking malloc.h usability
configure:4592: mpicc -c -g -O2 conftest.c >&5
configure:4598: $? = 0
configure:4612: result: yes
configure:4616: checking malloc.h presence
configure:4631: mpicc -E conftest.c
configure:4637: $? = 0
configure:4651: result: yes
configure:4684: checking for malloc.h
configure:4692: result: yes
configure:4740: checking for a Python interpreter with version >= 2.3
configure:4755: python -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('2.3', '.')) + [0, 0, 0]
minverhex = 0 for i in xrange(0, 4): minverhex = (minverhex << 8) + minver[i]
sys.exit(sys.hexversion < minverhex)
configure:4758: $? = 0
configure:4765: result: python
configure:4773: checking for python
configure:4791: found /usr/bin/python
configure:4803: result: /usr/bin/python
configure:4823: checking for python version
configure:4830: result: 2.4
configure:4842: checking for python platform
configure:4849: result: linux2
configure:4856: checking for python script directory
configure:4864: result: ${prefix}/lib/python2.4/site-packages
configure:4873: checking for python extension module directory
configure:4881: result: ${exec_prefix}/lib64/python2.4/site-packages
configure:4897: checking python sysconfig
configure:4978: result: ok
configure:5023: checking for python include directory
configure:5031: result: /usr/include/python2.4
configure:5051: checking Python.h usability
configure:5068: mpicc -c -g -O2 -I/usr/include/python2.4 conftest.c >&5
configure:5074: $? = 0
configure:5088: result: yes
configure:5092: checking Python.h presence
configure:5107: mpicc -E -I/usr/include/python2.4 conftest.c
configure:5113: $? = 0
configure:5127: result: yes
configure:5160: checking for Python.h
configure:5167: result: yes
configure:5196: downloading missing Python dependencies
configure:5199: /usr/bin/python setup.py install_deps -f
/users/lbrown/cig/CitcomS-3.1.1/deps -zmxd
/users/lbrown/cig/CitcomS-3.1.1/deps >&5 2>&5
running install_deps
Checking .pth file support in /users/lbrown/cig/CitcomS-3.1.1/deps
/usr/bin/python -E -c pass
running egg_info
writing requirements to CitcomS.egg-info/requires.txt
writing CitcomS.egg-info/PKG-INFO
writing top-level names to CitcomS.egg-info/top_level.txt
writing dependency_links to CitcomS.egg-info/dependency_links.txt
reading manifest file 'CitcomS.egg-info/SOURCES.txt'
writing manifest file 'CitcomS.egg-info/SOURCES.txt'
Installed /local/users/lbrown/cig/CitcomS-3.1.1
Because this distribution was installed --multi-version, before you can
import modules from this package in an application, you will need to
'import merlin' and then use a 'require()' call similar to one of
these examples, in order to select the desired version:
merlin.require("CitcomS") # latest installed version
merlin.require("CitcomS==3.1") # this exact version
merlin.require("CitcomS>=3.1") # this version or higher
Note also that the installation directory must be on sys.path at runtime for
this to work. (e.g. by being the application's script directory, by being on
PYTHONPATH, or by being added to sys.path by your code.)
Processing dependencies for CitcomS==3.1
configure:5202: $? = 0
configure:5214: building Python dependencies
configure:5217: /usr/bin/python setup.py develop -H None -f
/users/lbrown/cig/CitcomS-3.1.1/deps -x -d
/users/lbrown/cig/CitcomS-3.1.1/python >&5 2>&5
running develop
Checking .pth file support in /users/lbrown/cig/CitcomS-3.1.1/python
/usr/bin/python -E -c pass
running egg_info
writing requirements to CitcomS.egg-info/requires.txt
writing CitcomS.egg-info/PKG-INFO
writing top-level names to CitcomS.egg-info/top_level.txt
writing dependency_links to CitcomS.egg-info/dependency_links.txt
reading manifest file 'CitcomS.egg-info/SOURCES.txt'
writing manifest file 'CitcomS.egg-info/SOURCES.txt'
running build_ext
Creating /local/users/lbrown/cig/CitcomS-3.1.1/python/CitcomS.egg-link (link to .)
CitcomS 3.1 is already the active version in merlin-install.pth
Installed /local/users/lbrown/cig/CitcomS-3.1.1
Processing dependencies for CitcomS==3.1
configure:5220: $? = 0
configure:5232: checking for egg-related flags
configure:5235: /usr/bin/python setup.py egg_flags >&5 2>&5
running egg_flags
configure:5238: $? = 0
configure:5240: result: ok
configure:5277: creating pyconfig
configure:5428: checking build system type
configure:5446: result: x86_64-unknown-linux-gnu
configure:5468: checking host system type
configure:5483: result: x86_64-unknown-linux-gnu
configure:5505: checking for a sed that does not truncate output
configure:5561: result: /bin/sed
configure:5575: checking for ld used by mpicc
configure:5642: result: /usr/bin/ld
configure:5651: checking if the linker (/usr/bin/ld) is GNU ld
configure:5666: result: yes
configure:5671: checking for /usr/bin/ld option to reload object files
configure:5678: result: -r
configure:5696: checking for BSD-compatible nm
configure:5745: result: /usr/bin/nm -B
configure:5749: checking whether ln -s works
configure:5753: result: yes
configure:5760: checking how to recognize dependent libraries
configure:5946: result: pass_all
configure:6034: mpicc -c -g -O2 conftest.c >&5
configure:6037: $? = 0
configure:6200: checking dlfcn.h usability
configure:6217: mpicc -c -g -O2 conftest.c >&5
configure:6223: $? = 0
configure:6237: result: yes
configure:6241: checking dlfcn.h presence
configure:6256: mpicc -E conftest.c
configure:6262: $? = 0
configure:6276: result: yes
configure:6309: checking for dlfcn.h
configure:6317: result: yes
configure:6340: checking how to run the C++ preprocessor
configure:6376: mpicxx -E conftest.cpp
configure:6382: $? = 0
configure:6413: mpicxx -E conftest.cpp
conftest.cpp:22:28: error: ac_nonexistent.h: No such file or directory
configure:6419: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "CitcomS"
| #define PACKAGE_TARNAME "CitcomS"
| #define PACKAGE_VERSION "3.1.1"
| #define PACKAGE_STRING "CitcomS 3.1.1"
| #define PACKAGE_BUGREPORT "cig-mc at geodynamics.org"
| #define PACKAGE "CitcomS"
| #define VERSION "3.1.1"
| #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_MALLOC_H 1
| #define HAVE_DLFCN_H 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:6452: result: mpicxx -E
configure:6481: mpicxx -E conftest.cpp
configure:6487: $? = 0
configure:6518: mpicxx -E conftest.cpp
conftest.cpp:22:28: error: ac_nonexistent.h: No such file or directory
configure:6524: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "CitcomS"
| #define PACKAGE_TARNAME "CitcomS"
| #define PACKAGE_VERSION "3.1.1"
| #define PACKAGE_STRING "CitcomS 3.1.1"
| #define PACKAGE_BUGREPORT "cig-mc at geodynamics.org"
| #define PACKAGE "CitcomS"
| #define VERSION "3.1.1"
| #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_MALLOC_H 1
| #define HAVE_DLFCN_H 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:6568: checking the maximum length of command line arguments
configure:6680: result: 98304
configure:6692: checking command to parse /usr/bin/nm -B output from mpicc object
configure:6797: mpicxx -c -g -O2 conftest.cpp >&5
configure:6800: $? = 0
configure:6804: /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:6807: $? = 0
configure:6859: mpicxx -o conftest -g -O2 conftest.cpp conftstm.o >&5
configure:6862: $? = 0
configure:6900: result: ok
configure:6904: checking for objdir
configure:6919: result: .libs
configure:7011: checking for ar
configure:7027: found /usr/bin/ar
configure:7038: result: ar
configure:7107: checking for ranlib
configure:7123: found /usr/bin/ranlib
configure:7134: result: ranlib
configure:7203: checking for strip
configure:7219: found /usr/bin/strip
configure:7230: result: strip
configure:7828: checking if mpicc supports -fno-rtti -fno-exceptions
configure:7846: mpicc -c -g -O2 -fno-rtti -fno-exceptions conftest.c >&5
cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not
for C
configure:7850: $? = 0
configure:7863: result: no
configure:7878: checking for mpicc option to produce PIC
configure:8110: result: -fPIC
configure:8118: checking if mpicc PIC flag -fPIC works
configure:8136: mpicc -c -g -O2 -fPIC -DPIC conftest.c >&5
configure:8140: $? = 0
configure:8153: result: yes
configure:8181: checking if mpicc static flag -static works
configure:8209: result: no
configure:8219: checking if mpicc supports -c -o file.o
configure:8240: mpicc -c -g -O2 -o out/conftest2.o conftest.c >&5
configure:8244: $? = 0
configure:8266: result: yes
configure:8292: checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64)
supports shared libraries
configure:9273: result: yes
configure:9294: checking whether -lc should be explicitly linked in
configure:9299: mpicc -c -g -O2 conftest.c >&5
configure:9302: $? = 0
configure:9317: mpicc -shared conftest.o -v -Wl,-soname -Wl,conftest -o
conftest 2\>\&1 \| grep -lc \>/dev/null 2\>\&1
configure:9320: $? = 0
configure:9332: result: no
configure:9340: checking dynamic linker characteristics
configure:9954: result: GNU/Linux ld.so
configure:9978: checking how to hardcode library paths into programs
configure:10003: result: immediate
configure:10017: checking whether stripping libraries is possible
configure:10022: result: yes
configure:10824: checking if libtool supports shared libraries
configure:10826: result: yes
configure:10829: checking whether to build shared libraries
configure:10850: result: yes
configure:10853: checking whether to build static libraries
configure:10857: result: yes
configure:10951: creating libtool
configure:11544: checking for ld used by mpicxx
configure:11611: result: /usr/bin/ld -m elf_x86_64
configure:11620: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld
configure:11635: result: yes
configure:11686: checking whether the mpicxx linker (/usr/bin/ld -m
elf_x86_64) supports shared libraries
configure:12632: result: yes
configure:12649: mpicxx -c -g -O2 conftest.cpp >&5
configure:12652: $? = 0
configure:12808: checking for mpicxx option to produce PIC
configure:13092: result: -fPIC
configure:13100: checking if mpicxx PIC flag -fPIC works
configure:13118: mpicxx -c -g -O2 -fPIC -DPIC conftest.cpp >&5
configure:13122: $? = 0
configure:13135: result: yes
configure:13163: checking if mpicxx static flag -static works
configure:13191: result: no
configure:13201: checking if mpicxx supports -c -o file.o
configure:13222: mpicxx -c -g -O2 -o out/conftest2.o conftest.cpp >&5
configure:13226: $? = 0
configure:13248: result: yes
configure:13274: checking whether the mpicxx linker (/usr/bin/ld -m
elf_x86_64) supports shared libraries
configure:13303: result: yes
configure:13370: checking dynamic linker characteristics
configure:13932: result: GNU/Linux ld.so
configure:13956: checking how to hardcode library paths into programs
configure:13981: result: immediate
configure:20230: checking for library containing MPI_Init
configure:20271: mpicc -o conftest -g -O2 conftest.c >&5
configure:20277: $? = 0
configure:20305: result: none required
configure:20317: checking for library containing sqrt
configure:20358: mpicc -o conftest -g -O2 conftest.c >&5
conftest.c:29: warning: conflicting types for built-in function 'sqrt'
configure:20364: $? = 0
configure:20392: result: none required
configure:20408: checking for library containing H5Fopen
configure:20449: mpicc -o conftest -g -O2 conftest.c >&5
/tmp/cc8UvPbA.o: In function `main':
/users/lbrown/cig/CitcomS-3.1.1/conftest.c:33: undefined reference to `H5Fopen'
collect2: ld returned 1 exit status
configure:20455: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "CitcomS"
| #define PACKAGE_TARNAME "CitcomS"
| #define PACKAGE_VERSION "3.1.1"
| #define PACKAGE_STRING "CitcomS 3.1.1"
| #define PACKAGE_BUGREPORT "cig-mc at geodynamics.org"
| #define PACKAGE "CitcomS"
| #define VERSION "3.1.1"
| #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_MALLOC_H 1
| #define HAVE_DLFCN_H 1
| /* end confdefs.h. */
|
| /* Override any GCC internal prototype to avoid an error.
| Use char because int might match the return type of a GCC
| builtin and then its argument prototype would still apply. */
| #ifdef __cplusplus
| extern "C"
| #endif
| char H5Fopen ();
| int
| main ()
| {
| return H5Fopen ();
| ;
| return 0;
| }
configure:20449: mpicc -o conftest -g -O2 conftest.c -lhdf5 >&5
/usr/bin/ld: cannot find -lhdf5
collect2: ld returned 1 exit status
configure:20455: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "CitcomS"
| #define PACKAGE_TARNAME "CitcomS"
| #define PACKAGE_VERSION "3.1.1"
| #define PACKAGE_STRING "CitcomS 3.1.1"
| #define PACKAGE_BUGREPORT "cig-mc at geodynamics.org"
| #define PACKAGE "CitcomS"
| #define VERSION "3.1.1"
| #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_MALLOC_H 1
| #define HAVE_DLFCN_H 1
| /* end confdefs.h. */
|
| /* Override any GCC internal prototype to avoid an error.
| Use char because int might match the return type of a GCC
| builtin and then its argument prototype would still apply. */
| #ifdef __cplusplus
| extern "C"
| #endif
| char H5Fopen ();
| int
| main ()
| {
| return H5Fopen ();
| ;
| return 0;
| }
configure:20483: result: no
configure:20493: WARNING: HDF5 library not found; disabling HDF5 support
configure:20614: checking for PyExchanger_exchangeBoundedBox
configure:20670: mpicxx -o conftest -g -O2 conftest.c
-L/users/lbrown/cig/lib -lExchanger -L/usr/lib64 -L/usr/lib64/python2.4/config
-lpython2.4 -lpthread -ldl -lutil -lm >&5
configure:20676: $? = 0
configure:20693: result: yes
configure:20727: checking mpi.h usability
configure:20744: mpicc -c -g -O2 conftest.c >&5
configure:20750: $? = 0
configure:20764: result: yes
configure:20768: checking mpi.h presence
configure:20783: mpicc -E conftest.c
configure:20789: $? = 0
configure:20803: result: yes
configure:20836: checking for mpi.h
configure:20843: result: yes
configure:21038: checking whether we can link a trivial C++ MPI program
configure:21076: mpicxx -o conftest -g -O2 conftest.cpp >&5
configure:21082: $? = 0
configure:21090: result: yes
configure:21212: checking Exchanger/DIM.h usability
configure:21229: mpicxx -c -g -O2 -I/users/lbrown/cig/include
-I/local/users/lbrown/cig/CitcomS-3.1.1/python/pythia-0.8.1.10-py2.4.egg
conftest.cpp >&5
configure:21235: $? = 0
configure:21249: result: yes
configure:21253: checking Exchanger/DIM.h presence
configure:21268: mpicxx -E -I/users/lbrown/cig/include
-I/local/users/lbrown/cig/CitcomS-3.1.1/python/pythia-0.8.1.10-py2.4.egg
conftest.cpp
configure:21274: $? = 0
configure:21288: result: yes
configure:21321: checking for Exchanger/DIM.h
configure:21329: result: yes
configure:21393: checking for library containing gzopen
configure:21434: mpicc -o conftest -g -O2 conftest.c >&5
/tmp/ccSbaCU5.o: In function `main':
/users/lbrown/cig/CitcomS-3.1.1/conftest.c:34: undefined reference to `gzopen'
collect2: ld returned 1 exit status
configure:21440: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "CitcomS"
| #define PACKAGE_TARNAME "CitcomS"
| #define PACKAGE_VERSION "3.1.1"
| #define PACKAGE_STRING "CitcomS 3.1.1"
| #define PACKAGE_BUGREPORT "cig-mc at geodynamics.org"
| #define PACKAGE "CitcomS"
| #define VERSION "3.1.1"
| #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_MALLOC_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_EXCHANGER_DIM_H 1
| /* end confdefs.h. */
|
| /* Override any GCC internal prototype to avoid an error.
| Use char because int might match the return type of a GCC
| builtin and then its argument prototype would still apply. */
| #ifdef __cplusplus
| extern "C"
| #endif
| char gzopen ();
| int
| main ()
| {
| return gzopen ();
| ;
| return 0;
| }
configure:21434: mpicc -o conftest -g -O2 conftest.c -lz >&5
configure:21440: $? = 0
configure:21468: result: -lz
configure:22283: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by CitcomS config.status 3.1.1, which was
generated by GNU Autoconf 2.61. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on marmot
config.status:713: creating Makefile
config.status:713: creating bin/Makefile
config.status:713: creating CitcomS/Makefile
config.status:713: creating etc/Makefile
config.status:713: creating examples/Makefile
config.status:713: creating lib/Makefile
config.status:713: creating module/Makefile
config.status:713: creating module/Exchanger/Makefile
config.status:713: creating tests/Makefile
config.status:713: creating visual/Makefile
config.status:713: creating visual/OpenDXMacro/Makefile
config.status:713: creating config.h
config.status:936: config.h is unchanged
config.status:982: executing depfiles commands
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_build=x86_64-unknown-linux-gnu
ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
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=
ac_cv_env_CXX_value=
ac_cv_env_HC_HOME_set=
ac_cv_env_HC_HOME_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_PHDF5_HOME_set=
ac_cv_env_PHDF5_HOME_value=
ac_cv_env_PYTHONPATH_set=set
ac_cv_env_PYTHONPATH_value=/users/lbrown/cig/lib/python2.4/site-packages:
ac_cv_env_PYTHON_set=
ac_cv_env_PYTHON_value=
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_func_PyExchanger_exchangeBoundedBox=yes
ac_cv_header_Exchanger_DIM_h=yes
ac_cv_header_Python_h=yes
ac_cv_header_dlfcn_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_malloc_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_mpi_h=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-unknown-linux-gnu
ac_cv_objext=o
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_GREP=/bin/grep
ac_cv_path_PYTHON=/usr/bin/python
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_CXX=mpicxx
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_ac_ct_STRIP=strip
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_make_make_set=yes
ac_cv_search_H5Fopen=no
ac_cv_search_MPI_Init='none required'
ac_cv_search_gzopen=-lz
ac_cv_search_sqrt='none required'
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=gcc3
am_cv_pathless_PYTHON=python
am_cv_python_platform=linux2
am_cv_python_pyexecdir='${exec_prefix}/lib64/python2.4/site-packages'
am_cv_python_pythondir='${prefix}/lib/python2.4/site-packages'
am_cv_python_version=2.4
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_pic_works=yes
lt_cv_prog_compiler_pic_works_CXX=yes
lt_cv_prog_compiler_rtti_exceptions=no
lt_cv_prog_compiler_static_works=no
lt_cv_prog_compiler_static_works_CXX=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/^. .* \(.*\)$/extern int
\1;/p'\'''
lt_cv_sys_lib_dlsearch_path_spec='/lib /usr/lib /usr/lib64/atlas
/usr/local/lib/ /usr/lib/openmpi /usr/lib64/openmpi /usr/lib/mysql
/usr/lib64/mysql /usr/lib/qt-3.3/lib /usr/lib64/qt-3.3/lib '
lt_cv_sys_lib_search_path_spec='/usr/lib/gcc/x86_64-redhat-linux/4.1.2
/usr/lib64 /lib64'
lt_cv_sys_max_cmd_len=98304
lt_lt_cv_prog_compiler_c_o='"yes"'
lt_lt_cv_prog_compiler_c_o_CXX='"yes"'
lt_lt_cv_sys_global_symbol_pipe='"sed -n -e '\''s/^.*[
]\\([ABCDGIRSTW][ABCDGIRSTW]*\\)[ ][ ]*\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1
\\2 \\2/p'\''"'
lt_lt_cv_sys_global_symbol_to_c_name_address='"sed -n -e '\''s/^: \\([^ ]*\\)
\$/ {\\\"\\1\\\", (lt_ptr) 0},/p'\'' -e '\''s/^[BCDEGRST] \\([^ ]*\\) \\([^
]*\\)\$/ {\"\\2\", (lt_ptr) \\&\\2},/p'\''"'
lt_lt_cv_sys_global_symbol_to_cdecl='"sed -n -e '\''s/^. .* \\(.*\\)\$/extern
int \\1;/p'\''"'
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL} /users/lbrown/cig/CitcomS-3.1.1/aux-config/missing --run
aclocal-1.9'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL} /users/lbrown/cig/CitcomS-3.1.1/aux-config/missing --run tar'
AR='ar'
AUTOCONF='${SHELL} /users/lbrown/cig/CitcomS-3.1.1/aux-config/missing --run
autoconf'
AUTOHEADER='${SHELL} /users/lbrown/cig/CitcomS-3.1.1/aux-config/missing --run
autoheader'
AUTOMAKE='${SHELL} /users/lbrown/cig/CitcomS-3.1.1/aux-config/missing --run
automake-1.9'
AWK='gawk'
CC='mpicc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
COND_CUDA_FALSE=''
COND_CUDA_TRUE='#'
COND_EMBEDDING_FALSE='#'
COND_EMBEDDING_TRUE=''
COND_EXCHANGER_FALSE='#'
COND_EXCHANGER_TRUE=''
COND_GGRD_FALSE=''
COND_GGRD_TRUE='#'
COND_HDF5_FALSE=''
COND_HDF5_TRUE='#'
COND_PYRE_FALSE='#'
COND_PYRE_TRUE=''
CPP='mpicc -E'
CPPFLAGS='-DUSE_GZDIR '
CXX='mpicxx'
CXXCPP='mpicxx -E'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS='-g -O2'
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
DSYMUTIL=''
ECHO='echo'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
GREP='/bin/grep'
HC_HOME=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s'
LDFLAGS=''
LIBOBJS=''
LIBS='-lz '
LIBTOOL='$(SHELL) $(top_builddir)/libtool'
LN_S='ln -s'
LTLIBOBJS=''
MAKEINFO='${SHELL} /users/lbrown/cig/CitcomS-3.1.1/aux-config/missing --run
makeinfo'
NMEDIT=''
OBJEXT='o'
PACKAGE='CitcomS'
PACKAGE_BUGREPORT='cig-mc at geodynamics.org'
PACKAGE_NAME='CitcomS'
PACKAGE_STRING='CitcomS 3.1.1'
PACKAGE_TARNAME='CitcomS'
PACKAGE_VERSION='3.1.1'
PATH_SEPARATOR=':'
PHDF5_HOME=''
PYCONFIG='$(top_builddir)/pyconfig'
PYTHON='/usr/bin/python'
PYTHONPATH='${prefix}/lib/python2.4/site-packages:${exec_prefix}/lib64/python2.4/site-packages:/users/lbrown/cig/lib/python2.4/site-packages:'
PYTHON_BLDLIBRARY='-L/usr/lib64 -L/usr/lib64/python2.4/config -lpython2.4'
PYTHON_EGG_CFLAGS=''
PYTHON_EGG_CPPFLAGS='-I/users/lbrown/cig/include
-I/local/users/lbrown/cig/CitcomS-3.1.1/python/pythia-0.8.1.10-py2.4.egg'
PYTHON_EGG_LDFLAGS='-L/users/lbrown/cig/lib -lExchanger'
PYTHON_EGG_LIBS=''
PYTHON_EGG_PYXFLAGS='-I/local/users/lbrown/cig/CitcomS-3.1.1/python/pythia-0.8.1.10-py2.4.egg/mpi'
PYTHON_EXEC_PREFIX='${exec_prefix}'
PYTHON_INCDIR='/usr/include/python2.4'
PYTHON_LA_LDFLAGS=''
PYTHON_LDFLAGS=''
PYTHON_LDLAST=''
PYTHON_LDLIBRARY='libpython2.4.so'
PYTHON_LIBDIR='/usr/lib64'
PYTHON_LIBP='/usr/lib64/python2.4'
PYTHON_LIBPL='/usr/lib64/python2.4/config'
PYTHON_LIBS='-lpthread -ldl -lutil'
PYTHON_LINKFORSHARED='-Xlinker -export-dynamic'
PYTHON_MODLIBS=''
PYTHON_PLATFORM='linux2'
PYTHON_PREFIX='${prefix}'
PYTHON_SYSLIBS='-lm'
PYTHON_VERSION='2.4'
RANLIB='ranlib'
SED='/bin/sed'
SET_MAKE=''
SHELL='/bin/sh'
STRIP='strip'
VERSION='3.1.1'
ac_ct_CC='mpicc'
ac_ct_CXX='mpicxx'
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE='#'
am__fastdepCXX_TRUE=''
am__include='include'
am__leading_dot='.'
am__quote=''
am__tar='${AMTAR} chof - "$$tardir"'
am__untar='${AMTAR} xf -'
bindir='${exec_prefix}/bin'
build='x86_64-unknown-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='unknown'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host='x86_64-unknown-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='unknown'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='/users/lbrown/cig/CitcomS-3.1.1/aux-config/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
mkdir_p='mkdir -p --'
oldincludedir='/usr/include'
pdfdir='${docdir}'
pkgpyexecdir='${pyexecdir}/CitcomS'
pkgpythondir='${pythondir}/CitcomS'
pkgsysconfdir='${sysconfdir}/CitcomS'
prefix='/usr/local'
program_transform_name='s,x,x,'
psdir='${docdir}'
pyexecdir='${exec_prefix}/lib64/python2.4/site-packages'
pythondir='${prefix}/lib/python2.4/site-packages'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
#define PACKAGE_NAME "CitcomS"
#define PACKAGE_TARNAME "CitcomS"
#define PACKAGE_VERSION "3.1.1"
#define PACKAGE_STRING "CitcomS 3.1.1"
#define PACKAGE_BUGREPORT "cig-mc at geodynamics.org"
#define PACKAGE "CitcomS"
#define VERSION "3.1.1"
#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_MALLOC_H 1
#define HAVE_DLFCN_H 1
#define HAVE_EXCHANGER_DIM_H 1
configure: exit 0
As suggested in the above link, the command;
$ touch bin/pycitcoms.c
$ make
produces the following output
make all-recursive
make[1]: Entering directory `/local/users/lbrown/cig/CitcomS-3.1.1'
Making all in lib
make[2]: Entering directory `/local/users/lbrown/cig/CitcomS-3.1.1/lib'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/local/users/lbrown/cig/CitcomS-3.1.1/lib'
Making all in CitcomS
make[2]: Entering directory `/local/users/lbrown/cig/CitcomS-3.1.1/CitcomS'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/local/users/lbrown/cig/CitcomS-3.1.1/CitcomS'
Making all in etc
make[2]: Entering directory `/local/users/lbrown/cig/CitcomS-3.1.1/etc'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/local/users/lbrown/cig/CitcomS-3.1.1/etc'
Making all in examples
make[2]: Entering directory `/local/users/lbrown/cig/CitcomS-3.1.1/examples'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/local/users/lbrown/cig/CitcomS-3.1.1/examples'
Making all in module
make[2]: Entering directory `/local/users/lbrown/cig/CitcomS-3.1.1/module'
Making all in Exchanger
make[3]: Entering directory
`/local/users/lbrown/cig/CitcomS-3.1.1/module/Exchanger'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory
`/local/users/lbrown/cig/CitcomS-3.1.1/module/Exchanger'
make[3]: Entering directory `/local/users/lbrown/cig/CitcomS-3.1.1/module'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/local/users/lbrown/cig/CitcomS-3.1.1/module'
make[2]: Leaving directory `/local/users/lbrown/cig/CitcomS-3.1.1/module'
Making all in tests
make[2]: Entering directory `/local/users/lbrown/cig/CitcomS-3.1.1/tests'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/local/users/lbrown/cig/CitcomS-3.1.1/tests'
Making all in visual
make[2]: Entering directory `/local/users/lbrown/cig/CitcomS-3.1.1/visual'
Making all in OpenDXMacro
make[3]: Entering directory
`/local/users/lbrown/cig/CitcomS-3.1.1/visual/OpenDXMacro'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory
`/local/users/lbrown/cig/CitcomS-3.1.1/visual/OpenDXMacro'
make[3]: Entering directory `/local/users/lbrown/cig/CitcomS-3.1.1/visual'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/local/users/lbrown/cig/CitcomS-3.1.1/visual'
make[2]: Leaving directory `/local/users/lbrown/cig/CitcomS-3.1.1/visual'
Making all in bin
make[2]: Entering directory `/local/users/lbrown/cig/CitcomS-3.1.1/bin'
if mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../lib -I../module
-I../module/Exchanger -I/users/lbrown/cig/include
-I/local/users/lbrown/cig/CitcomS-3.1.1/python/pythia-0.8.1.10-py2.4.egg
-I/usr/include/python2.4 -DUSE_GZDIR -DWITH_EXCHANGER -g -O2 -MT
pycitcoms-pycitcoms.o -MD -MP -MF ".deps/pycitcoms-pycitcoms.Tpo" -c -o
pycitcoms-pycitcoms.o `test -f 'pycitcoms.c' || echo './'`pycitcoms.c; \
then mv -f ".deps/pycitcoms-pycitcoms.Tpo" ".deps/pycitcoms-pycitcoms.Po";
else rm -f ".deps/pycitcoms-pycitcoms.Tpo"; exit 1; fi
/bin/sh ../libtool --tag=CXX --mode=link mpicxx -g -O2 -o pycitcoms
-Xlinker -export-dynamic \
pycitcoms-pycitcoms.o dummy.o ../module/libCitcomSLibmodule.a
../module/Exchanger/libExchangerLibmodule.a ../lib/libCitcomS.a \
-L/users/lbrown/cig/lib -lExchanger \
-L/usr/lib64 -L/usr/lib64/python2.4/config -lpython2.4 \
-lpthread -ldl -lutil -lm \
-lz \
mpicxx -g -O2 -o pycitcoms -Wl,-export-dynamic pycitcoms-pycitcoms.o dummy.o
../module/libCitcomSLibmodule.a ../module/Exchanger/libExchangerLibmodule.a
../lib/libCitcomS.a -L/users/lbrown/cig/lib
/users/lbrown/cig/lib/libExchanger.a /usr/lib64/openmpi/libmpi_cxx.so
/usr/lib64/openmpi/libmpi.so /usr/lib64/openmpi/liborte.so
/usr/lib64/openmpi/libopal.so -L/usr/lib64 -L/usr/lib64/python2.4/config
-lpython2.4 -lpthread -ldl -lutil -lm -lz
if mpicc -DHAVE_CONFIG_H -I. -I. -I.. -I../lib -I../module
-I../module/Exchanger -I/users/lbrown/cig/include
-I/local/users/lbrown/cig/CitcomS-3.1.1/python/pythia-0.8.1.10-py2.4.egg
-I/usr/include/python2.4 -DUSE_GZDIR -DUSE_MPI -DWITH_EXCHANGER -g -O2 -MT
mpipycitcoms-pycitcoms.o -MD -MP -MF ".deps/mpipycitcoms-pycitcoms.Tpo" -c -o
mpipycitcoms-pycitcoms.o `test -f 'pycitcoms.c' || echo './'`pycitcoms.c; \
then mv -f ".deps/mpipycitcoms-pycitcoms.Tpo"
".deps/mpipycitcoms-pycitcoms.Po"; else rm -f
".deps/mpipycitcoms-pycitcoms.Tpo"; exit 1; fi
/bin/sh ../libtool --tag=CXX --mode=link mpicxx -g -O2 -o mpipycitcoms
-Xlinker -export-dynamic \
mpipycitcoms-pycitcoms.o dummy.o ../module/libCitcomSLibmodule.a
../module/Exchanger/libExchangerLibmodule.a ../lib/libCitcomS.a \
-L/users/lbrown/cig/lib -lExchanger \
-L/usr/lib64 -L/usr/lib64/python2.4/config -lpython2.4 \
-lpthread -ldl -lutil -lm \
-lz \
mpicxx -g -O2 -o mpipycitcoms -Wl,-export-dynamic mpipycitcoms-pycitcoms.o
dummy.o ../module/libCitcomSLibmodule.a
../module/Exchanger/libExchangerLibmodule.a ../lib/libCitcomS.a
-L/users/lbrown/cig/lib /users/lbrown/cig/lib/libExchanger.a
/usr/lib64/openmpi/libmpi_cxx.so /usr/lib64/openmpi/libmpi.so
/usr/lib64/openmpi/liborte.so /usr/lib64/openmpi/libopal.so -L/usr/lib64
-L/usr/lib64/python2.4/config -lpython2.4 -lpthread -ldl -lutil -lm -lz
sed -e s%[@]INTERPRETER[@]%/users/lbrown/cig/CitcomS-3.1.1/bin/pycitcoms%g -e
s%[@]PYTHONPATH[@]%/users/lbrown/cig/CitcomS-3.1.1/python%g < ./citcoms.in >
citcoms || (rm -f citcoms && exit 1)
chmod +x citcoms
make[2]: Leaving directory `/local/users/lbrown/cig/CitcomS-3.1.1/bin'
make[2]: Entering directory `/local/users/lbrown/cig/CitcomS-3.1.1'
make[2]: Leaving directory `/local/users/lbrown/cig/CitcomS-3.1.1'
make[1]: Leaving directory `/local/users/lbrown/cig/CitcomS-3.1.1'
After the above procedure, the following command;
$ mpipycitcoms -c "import ExchangerLib"
gives the output
Traceback (most recent call last):
File "<string>", line 1, in ?
ImportError: No module named ExchangerLib
Any help, instructions, or advice would be greatly appreciated!
Thanks,
Lonn Brown
---
Lonn Brown
University of Alberta
Edmonton CANADA
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