Graph tool installation issues on SGI machine

shankha · January 6, 2011, 9:23pm

Hi,
I am trying to install graph-tool on a SGI system.
uname -a : Linux 2.6.16.60-0.69.1-default #1 SMP Fri Sep 17 17:07:54
UTC 2010 ia64 ia64 ia64 GNU/Linux

Command line used :
/home/arcadm/SGI/Software/graph-tool/graph-tool-2.2.9/configure
--with-boost=/apps/packages/boost_1_45_0
--with-boost-libdir=/apps/packages/boost_1_45_0/lib
--with-boost-python=/apps/packages/boost_1_45_0/lib/libboost_python.so
--prefix=/apps/packages/graph-tool

ENVIORNMENT VARIABLES:
LDFLAGS=-L/apps/packages/boost_1_45_0/lib -L/apps/packages/cgal-3.6.1/lib

CPPFLAGS=-I/apps/packages/boost_1_45_0/include
-I/apps/packages/cgal-3.6.1/include
-I/apps/packages/Python-2.6.6/include/python2.6

LD_LIBRARY_PATH=/apps/packages/cgal-3.6.1/lib:/apps/packages/RS:/apps/packages/taucs:/apps/packages/metis-4.0:/apps/packages/atlas-3.9.32/lib:/apps/packages/boost_1_45_0/lib:/apps/packages/gcc-4.4.4/lib:/apps/packages/mpfr-3.0.0/lib:/apps/packages/gmp-5.0.1/lib:/apps/packages/Python-2.6.6/lib

I have made sure all the dependent libraries for graph-tool are taken
care by the LD_LIBRARY_PATH.

ERROR MESSAGE:
checking for python2.6/Python.h... (cached) no
  results of the Python check:
    Binary: python2.6
    Library: python2.6
    Include Dir: no
checking whether the Boost::Python library is available... no
configure: error: No usable boost::python found

config.log error message:
configure:17155: checking for python2.6/Python.h
configure:17155: result: no
configure:17180: result: results of the Python check:
configure:17182: result: Binary: python2.6
configure:17184: result: Library: python2.6
configure:17186: result: Include Dir: no
configure:17198: checking whether the Boost::Python library is available
configure:17228: g++ -c -Wall -ftemplate-depth-150 -Wno-deprecated
-O99 -fvisibility=default -fvisibility-inlines-hidden
-Wno-unknown-pragmas -I/apps/packages/Python-2.6.6/include/python2.6
conftest.cpp >&5
conftest.cpp:35:36: error: boost/python/module.hpp: No such file or directory
conftest.cpp:36: error: 'boost' has not been declared
conftest.cpp:36: error: 'python' is not a namespace-name
conftest.cpp:36: error: expected namespace-name before ';' token
conftest.cpp:37: error: expected constructor, destructor, or type
conversion before '(' token
configure:17228: $? = 1

I have attached config.log for your reference.

python.h is installed in Python2.6/include/python2.6 and not
Python2.6. I am not sure why it is searching for python.h in
Python2.6. I can create a soft link inside Python2.6 to the actual
file in
Python2.6/include/python2.6 but I am not sure if that is the right way
to go about it.

Could you please help me out on this issue.

config.log (82.1 KB)

tiago · January 7, 2011, 10:34am

Hi,

Hi,
I am trying to install graph-tool on a SGI system.
uname -a : Linux 2.6.16.60-0.69.1-default #1 SMP Fri Sep 17 17:07:54
UTC 2010 ia64 ia64 ia64 GNU/Linux

Command line used :
/home/arcadm/SGI/Software/graph-tool/graph-tool-2.2.9/configure
--with-boost=/apps/packages/boost_1_45_0
--with-boost-libdir=/apps/packages/boost_1_45_0/lib
--with-boost-python=/apps/packages/boost_1_45_0/lib/libboost_python.so
--prefix=/apps/packages/graph-tool

ENVIORNMENT VARIABLES:
LDFLAGS=-L/apps/packages/boost_1_45_0/lib -L/apps/packages/cgal-3.6.1/lib

CPPFLAGS=-I/apps/packages/boost_1_45_0/include
-I/apps/packages/cgal-3.6.1/include
-I/apps/packages/Python-2.6.6/include/python2.6

LD_LIBRARY_PATH=/apps/packages/cgal-3.6.1/lib:/apps/packages/RS:/apps/packages/taucs:/apps/packages/metis-4.0:/apps/packages/atlas-3.9.32/lib:/apps/packages/boost_1_45_0/lib:/apps/packages/gcc-4.4.4/lib:/apps/packages/mpfr-3.0.0/lib:/apps/packages/gmp-5.0.1/lib:/apps/packages/Python-2.6.6/lib

I have made sure all the dependent libraries for graph-tool are taken
care by the LD_LIBRARY_PATH.

ERROR MESSAGE:
checking for python2.6/Python.h... (cached) no
  results of the Python check:
    Binary: python2.6
    Library: python2.6
    Include Dir: no
checking whether the Boost::Python library is available... no
configure: error: No usable boost::python found

It seems that your include flags are not being used. If we look in the
config.log, we see that the compile command is:

    g++ -c -Wall -ftemplate-depth-150 -Wno-deprecated -O99
    -fvisibility=default -fvisibility-inlines-hidden
    -Wno-unknown-pragmas -I/apps/packages/Python-2.6.6/include/python2.6
    conftest.cpp >&5

Which doesn't have any of your include paths. This is because you
defined them in "CPPFLAGS" which is for the C _preprocessor_ not for the
C++ compiler. You should use CXXFLAGS instead.

Cheers,
Tiago

shankha · January 7, 2011, 11:57am

Hi Tiago,
Thanks for your help. Setting up of CXXFLAGS did help.
The configure script still can't figure out the Python.h file's location.

LOG MESSAGE :
checking for python2.6/Python.h... (cached) no
  results of the Python check:
    Binary: python2.6
    Library: python2.6
    Include Dir: no

I am attaching the config.log for your reference.
http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n2211349/config.log
config.log

Hi,

Hi,
I am trying to install graph-tool on a SGI system.
uname -a : Linux 2.6.16.60-0.69.1-default #1 SMP Fri Sep 17 17:07:54
UTC 2010 ia64 ia64 ia64 GNU/Linux

Command line used :
/home/arcadm/SGI/Software/graph-tool/graph-tool-2.2.9/configure
--with-boost=/apps/packages/boost_1_45_0
--with-boost-libdir=/apps/packages/boost_1_45_0/lib
--with-boost-python=/apps/packages/boost_1_45_0/lib/libboost_python.so
--prefix=/apps/packages/graph-tool

ENVIORNMENT VARIABLES:
LDFLAGS=-L/apps/packages/boost_1_45_0/lib -L/apps/packages/cgal-3.6.1/lib

CPPFLAGS=-I/apps/packages/boost_1_45_0/include
-I/apps/packages/cgal-3.6.1/include
-I/apps/packages/Python-2.6.6/include/python2.6

LD_LIBRARY_PATH=/apps/packages/cgal-3.6.1/lib:/apps/packages/RS:/apps/packages/taucs:/apps/packages/metis-4.0:/apps/packages/atlas-3.9.32/lib:/apps/packages/boost_1_45_0/lib:/apps/packages/gcc-4.4.4/lib:/apps/packages/mpfr-3.0.0/lib:/apps/packages/gmp-5.0.1/lib:/apps/packages/Python-2.6.6/lib

I have made sure all the dependent libraries for graph-tool are taken
care by the LD_LIBRARY_PATH.

ERROR MESSAGE:
checking for python2.6/Python.h... (cached) no
  results of the Python check:
    Binary: python2.6
    Library: python2.6
    Include Dir: no
checking whether the Boost::Python library is available... no
configure: error: No usable boost::python found

It seems that your include flags are not being used. If we look in the
config.log, we see that the compile command is:

    g++ -c -Wall -ftemplate-depth-150 -Wno-deprecated -O99
    -fvisibility=default -fvisibility-inlines-hidden
    -Wno-unknown-pragmas -I/apps/packages/Python-2.6.6/include/python2.6
    conftest.cpp >&5

Which doesn't have any of your include paths. This is because you
defined them in "CPPFLAGS" which is for the C _preprocessor_ not for the
C++ compiler. You should use CXXFLAGS instead.

Thanks
Shankha

shankha · January 7, 2011, 11:58am

Hi Tiago,
Thanks for your help. Setting up of CXXFLAGS did help.
The configure script still can't figure out the Python.h file's location.

LOG MESSAGE :
checking for python2.6/Python.h... (cached) no
  results of the Python check:
    Binary: python2.6
    Library: python2.6
    Include Dir: no

I am attaching the config.log for your reference.

Thanks

shankha · January 7, 2011, 12:06pm

Hi,
The configure did went fine except one issue which I have mentioned in my
previous post.
make didn't go through.

ERROR MESSAGE:
/apps/packages/cgal-3.6.1/include/CGAL/Gmpq.h: In member function
'std::pair<double, double>
CGAL::Real_embeddable_traits<CGAL::Gmpq>::To_interval::operator()(const
CGAL::Gmpq&) const':
/apps/packages/cgal-3.6.1/include/CGAL/Gmpq.h:91: error: 'mpfr_t' was not
declared in this scope
/apps/packages/cgal-3.6.1/include/CGAL/Gmpq.h:91: error: expected ';' before
'y'
/apps/packages/cgal-3.6.1/include/CGAL/Gmpq.h:92: error: 'y' was not
declared in this scope
/apps/packages/cgal-3.6.1/include/CGAL/Gmpq.h:92: error: 'mpfr_init2' was
not declared in this scope
/apps/packages/cgal-3.6.1/include/CGAL/Gmpq.h:93: error: 'GMP_RNDD' was not
declared in this scope
/apps/packages/cgal-3.6.1/include/CGAL/Gmpq.h:93: error: 'mpfr_set_q' was
not declared in this scope
/apps/packages/cgal-3.6.1/include/CGAL/Gmpq.h:94: error: 'mpfr_get_d' was
not declared in this scope
/apps/packages/cgal-3.6.1/include/CGAL/Gmpq.h:95: error: 'GMP_RNDU' was not
declared in this scope
/apps/packages/cgal-3.6.1/include/CGAL/Gmpq.h:97: error: 'mpfr_clear' was
not declared in this scope
make[4]: *** [graph_triangulation.lo] Error 1
make[4]: Leaving directory
`/home/arcadm/SGI/Software/graph-tool/build/src/graph/generation'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/home/arcadm/SGI/Software/graph-tool/build/src/graph'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/arcadm/SGI/Software/graph-tool/build/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/arcadm/SGI/Software/graph-tool/build'

I have attached the LOG file for your reference.

Thanks
Shankha
http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n2211387/LOG_MAKE
LOG_MAKE

tiago · January 7, 2011, 12:11pm

The only errors I'm seeing in the log are that the include files for
Python and CGAL are not being found. Are you sure the include paths you
provided are correct?

Cheers,
Tiago

tiago · January 7, 2011, 12:14pm

This seems like a problem with the CGAL installation (mprf_t belongs to
the the GNU MPRF library http://www.mpfr.org/, which you should
have). Are you sure CGAL is installed properly?

Cheers,
Tiago

shankha · January 7, 2011, 9:47pm

Hi,
I fixed the path issues and configure went on fine. The build is going on
forever(5 hrs). Usually how much time it takes to build graph tool.

attachment.html (3.96 KB)

tiago · January 7, 2011, 11:22pm

On my laptop, a full compile takes about an hour or two... But this
depends of course on how fast the machine is.

Cheers,
Tiago