Re: [moose-generic] MOOSE_installation_problem

[Subhasis R. <ray...@gm...>]

Hi,
 Just expanding on what Niraj mentioned briefly: The errors indicate that
the compiler could not find the gsl/gsl_errno.h and hdf5.h in its include
path. We put the common locations of HDF and GSL libraries on Debian based
systems in the Makefile, but it seems you need to update that with your
local settings.

For hdf5, search for "DUSE_HDF5" in the Makefile and replace the line:

CXXFLAGS+= -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I/usr/local/hdf5/include

with
CXXFLAGS+= -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I{path of directory
containing hdf5.h on your system}

and in the next line:

    LIBS+= -lhdf5 -L/usr/local/hdf5/lib

with

    LIBS+= -lhdf5 -L{path directory containing libhdf5.so on your system}

Similarly for GSL, search for "ifdef USE_GSL" in the Makefile and in that
section replace:

LIBS+= -L/usr/lib -lgsl -lgslcblas -lm

with

LIBS+= -L/usr/lib -L{path to directory containing libgsl.so on your system}
-lgsl -lgslcblas -lm

and replace

CXXFLAGS+= -DUSE_GSL

with

CXXFLAGS+= -DUSE_GSL -I{path to directory containing gsl/gsl_cblas.h}

Note that in the above the directory should be "/usr/include" when
gsl_cblas.h located in /usr/include/gsl. If you have the 'locate' utility
installed you can use that to find the location of the above mentioned
files.

Hope this helps,

   Subha


On Thu, Feb 28, 2013 at 11:03 AM, Niraj Dudani <ni...@nc...> wrote:

> Hi Vadim,
>
> Thanks for your mail: it appears that your mails were stuck in the spam
> filter, because
> you're not subscribed to the mailing list. To avoid this the next time,
> you could
> subscribe to the mailing list here:
> https://lists.sourceforge.net/lists/listinfo/moose-generic.
>
> The errors you reported seem to be due to path issues. Can you check where
> the GSL and
> HDF5 libraries have been installed? You may have to edit the Makefile to
> get it to work.
> The library path has to be appended to the LIBS variable, and the include
> path to the
> CXXFLAGS variable. In the current revision (r4433), the GSL section of the
> Makefile is
> on line numbers 208-209, and the HDF5 section is at line numbers 262-263.
>
> Best,
> Niraj
>
> >
> > Hi
> > I have python-2.7 with GSL and HDF5 libraries installed    but I am
> getting  a lot of
> > errors every time I try to do "make BUILD=release" on CentOS 5.5  x86_64
> x86_64 x86_64
> > GNU/Linux
> > We are trying to have it installed on the cluster and using "module"
> commands to load
> > all libraries.
> >
> > Can somebody advice what might be missing ?  Thanks a lot in advance.
> > Vadim.
> >
> > Here the error:
> >
> >
> > MarkovChannel.cpp:16:27: error: gsl/gsl_errno.h: No such file or
> directory***
> > [MarkovChannel.o] Error 1
> >
> > HDF5WriterBase.cpp:33:18: error: hdf5.h: No such file or
> directorymake[1]: ***
> > [HDF5WriterBase.o] Error 1
> >
> > Stoich.cpp:42:27: error: gsl/gsl_errno.h: No such file or
> directorymake[1]: ***
> > [Stoich.o] Error 1
> >
> > rtMultiCompartment.cpp:11:27: error: gsl/gsl_errno.h: No such file or
> > directoryrtMultiCompartment.cpp:12:28: error: gsl/gsl_matrix.h: No such
> file or
> > directoryrtMultiCompartment.cpp:13:27: error: gsl/gsl_odeiv.h: No such
> file or directory
> > ../ksolve/OdeSystem.h:51: warning: ISO C++ forbids declaration of
> 'gsl_odeiv_step_type'
> > with no type../ksolve/OdeSystem.h:51: error: expected ';' before '*'
> > token../ksolve/OdeSystem.h:52: warning: ISO C++ forbids declaration of
> 'gsl_odeiv_step'
> > with no type../ksolve/OdeSystem.h:52: error: expected ';' before '*'
> > token../ksolve/OdeSystem.h:53: warning: ISO C++ forbids declaration of
> > 'gsl_odeiv_control' with no type../ksolve/OdeSystem.h:53: error:
> expected ';' before '*'
> > token../ksolve/OdeSystem.h:54: warning: ISO C++ forbids declaration of
> > 'gsl_odeiv_evolve' with no type../ksolve/OdeSystem.h:54: error: expected
> ';' before '*'
> > token../ksolve/OdeSystem.h:55: error: 'gsl_odeiv_system' does not name a
> type
> > [rtMultiCompartment.o] Error 1No rule to make target
> `biophysics/_biophysics.o', needed
> > by `moose'.  Stop.
> >
> ------------------------------------------------------------------------------
> > Everyone hates slow websites. So do we.
> > Make your web apps faster with AppDynamics
> > Download AppDynamics Lite for free today:
> >
> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
> > moose-generic mailing list
> > moo...@li...
> > https://lists.sourceforge.net/lists/listinfo/moose-generic
> >
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> _______________________________________________
> moose-generic mailing list
> moo...@li...
> https://lists.sourceforge.net/lists/listinfo/moose-generic
>