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Re: [moose-generic] MOOSE_installation_problem
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From: Vadim A <ast...@nc...> - 2013-02-28 23:35:28
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Actually , we found the problem with GSL lib (it was mis-typed letter)
But we still straggling with configuring MPI.
I am getting this error:
g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/ -DUSE_HDF5 -DH5_NO_DEPRECATED_SYMBOLS -I /home/diag/opt/hdf5/1.6/gnu/include -I. -I../basecode -I../msg HDF5WriterBase.cpp -c
In file included from /home/diag/opt/hdf5/1.6/gnu/include/hdf5.h:23,
from HDF5WriterBase.cpp:33:
/home/diag/opt/hdf5/1.6/gnu/include/H5public.h:54:20: error: mpi.h: No such file or directory
Even, I set flags for MPI in the Makefile. Could you please advise what might be missing ?
# Here we automagically change compilers to deal with MPI.
ifdef USE_MPI
CXX = mpicxx
# CXX = /usr/local/mvapich2/bin/mpicxx
PARALLEL_DIR = /home/diag/opt/openmpi/1.4.3/gnu/ #parallel
PARALLEL_LIB = /home/diag/opt/openmpi/1.4.3/gnu/lib/ #parallel/parallel.o
else
CXX = g++
# CXX = CC # Choose between Solaris CC and g++ on a Solaris machine
endif
We are using "openmpi" which does not have "parallel.o"
Thanks a lot in advance for any suggestions,
Vadim.
>
>
>
> Also,
>
> I having error about MPI
>
> /home/diag/opt/hdf5/1.6/gnu/include/H5public.h:54:20: error: mpi.h: No such file or directory
>
> , should I set some more flags ? I see one for mpicxx - but it is commented.
>
>
>
>
> Here the error log:
>
> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -l/home/diag/opt/gsl/1.15/gnu/include/ -DUSE_HDF5 -DH5_NO_DEPRECATED_SYMBOLS -I /home/diag/opt/hdf5/1.6/gnu/include -I. -I../basecode -I../msg HDF5WriterBase.cpp -c
> In file included from /home/diag/opt/hdf5/1.6/gnu/include/hdf5.h:23,
> from HDF5WriterBase.cpp:33:
> /home/diag/opt/hdf5/1.6/gnu/include/H5public.h:54:20: error: mpi.h: No such file or directory
> /home/diag/opt/hdf5/1.6/gnu/include/H5public.h:56:21: error: mpio.h: No such file or directory
>
>
>
>
>>
>> Subhasis Ray <ray...@gm...> wrote:
>>
>> 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.
>> > ------------------------------------------------------------------------------
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>>
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>> ------------------------------------------------------------------------------
>> 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
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>> 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
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