Re: [moose-generic] MOOSE_installation_problem

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

Dear Vadim,
  You can change the following with the corresponding values for your
system:

~ Line # 339 and 340 ...

PYTHON_INCLUDES := $(shell python-config --includes)
PYTHON_LDFLAGS := $(shell python-config --ldflags)

And as I suspected, your system does not seems have python-config installed
(standard locations are /usr/bin or /usr/local/bin) because that is the
command we are using in the Makefile to get the flags. It is supposed to
come with Python development library, which is also a prerequisite for
building moose. So please make sure you have that installed (does locate
Python.h show something like: /usr/include/python2.7/Python.h? ).

Best,
 Subha


On Thu, Mar 7, 2013 at 6:16 AM, Vadim A <ast...@nc...> wrote:

> Also this example is not clear where you've mentioned
>
>
> "...and add the following to LIBS (output of python-config --ldflags)
> updated according to local system paths:
>
> -L/usr/lib/python2.7/config -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker
> -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
>
> "
>
>
> I do not see  "python2.7/config" in our system
>
>
> Vadim.
>
> On Mar 6, 2013, at 4:31 PM, Vadim A wrote:
>
> Hi Subha.
>
> Just wan to clarify one think. We decided to concentrate on simples
> installation for now and do the following steps:
>
> make clean
> make BUILD=release USE_HDF5=0
>
>
> And it still give me the error
>
> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
> -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DPYMOOSE
> -I/home/diag/opt/python2.7/include/python2.7
> -I/home/diag/opt/python2.7/include/python2.7 moosemodule.cpp -c
>
> moosemodule.cpp:80:31: error: numpy/arrayobject.h: No such file or
> directory
>
>
>
> But we loaded that module and it is located in our system here :
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h
>
>
> You've suggested to add it to CXXFLAGS flags. But where in the Makefile
> should we do that ?
>
>
> Best regards,
>
> Vadim.
>
>
>
> On Mar 5, 2013, at 7:43 PM, Subhasis Ray wrote:
>
> Dear Vadim,
>  Did you run "make clean" before rebuilding each time? If you specify
> USE_HDF5=0, then the entire content of HDF5 related files get excluded from
> the compilation process. But from the build log for the first case it seems
> the object files were compiled with HDF5 support but the linking is being
> done without.
>  In the second case, is it possible that your version of HDF5 library is
> linked to a different MPI library than what you set in MOOSE Makefile?
> Otherwise, it is also possible that HDF5 lib is dynamically linked to MPI
> and when you are building MOOSE without MPI support the MPI-lib location is
> not passed to compiler. In that case you may want to use mpicxx as the
> compiler at line 250:
>
> # Here we automagically change compilers to deal with MPI.
> ifdef USE_MPI
>     CXX = mpicxx
> #    CXX = /usr/local/mvapich2/bin/mpicxx
> #    PARALLEL_DIR = parallel
> #    PARALLEL_LIB = parallel/parallel.o
> else
>     CXX = g++ # <-- replace with mpicxx
> #    CXX = CC    # Choose between Solaris CC and g++ on a Solaris machine
> endif
>
>
>  For the third case, we use the command:
>
> python-config --includes
>
> in the Makefile in order to get the location of header files for numpy and
> python. Looks like that does not work on your system. So you need to
> explicitly add
> -I/usr/include/python2.7 -I/usr/include/python2.7
>
> and
>
> -I{location of numpy/arrayobject.h}
>
> to CXXFLAGS
>
> and add the following to LIBS (output of python-config --ldflags) updated
> according to local system paths:
>
> -L/usr/lib/python2.7/config -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker
> -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
>
>
> hth,
>   Subha
>
>
> On Wed, Mar 6, 2013 at 1:43 AM, Vadim A <ast...@nc...> wrote:
>
>> Dear Subha.
>>
>> I was trying three different ways to install MOOSE: without HDF5, with
>> HDF5 and with MPI
>>
>> Unfortunatelly, I did fail in all. Here the list of problems which we
>> have. We would very appreciate you comments or suggestions what we might
>> missing here.
>>
>>
>>
>> (1) First I did
>>
>> make BUILD=release USE_HDF5=0
>>
>>
>>
>> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
>> -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    basecode/_basecode.o
>> msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o
>> randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o
>> device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o
>> regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o
>> manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib
>> -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib
>> -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -o moose
>>
>>
>>
>> And getting a lot of error like this:
>>
>>
>> builtins/_builtins.o: In function `HDF5WriterBase::setMode(unsigned int)':
>> (.text+0x11f40): undefined reference to `H5check_version'
>> ……………….
>>
>> builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for
>> MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
>> collect2: ld returned 1 exit status
>>
>>
>>
>>
>>
>>
>> (2) Then
>>
>> We have installed  HDF5 1.8.9 and I was trying to do build release:
>>
>>
>> make BUILD=release
>>
>>
>> It seems that all libs get compiled and it can find HDF5 1.8.9
>>
>>
>> All Libs compiled
>> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>> /home/diag/opt/openmpi/1.4.3/gnu/include  -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/hdf5/1.8.9/gnu/openmpi/include* basecode/_basecode.o
>> msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o
>> randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o
>> device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o
>> regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o
>> manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib
>> -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib
>> -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5
>> -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose
>>
>>
>>
>> but it complain about a lot of "undefined references like this:
>>
>>
>> builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for
>> MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
>> collect2: ld returned 1 exit status
>> make: *** [moose] Error 1
>>
>> Looks like we still missing something. Should we have exactly same HDF5
>> library as you are using -> *libhdf5-serial   ?*
>>
>>
>>
>>
>> (3)
>>
>> Also I did try to compile with MPI:
>>
>>
>> make BUILD=release USE_MPI=1
>>
>> All Libs compiled
>> mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
>> -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I
>> /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5
>>  -DH5_NO_DEPRECATED_SYMBOLS -I
>>  /home/diag/opt/hdf5/1.8.9/gnu/openmpi/include basecode/_basecode.o
>> msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o
>> randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o
>> device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o
>> regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o
>> manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib
>> -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib
>> -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5
>> -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose
>>
>>
>>
>> But getting error:
>>
>>
>> moosemodule.cpp:80:31: error: numpy/arrayobject.h: No such file or
>> directory
>>
>>
>>
>> But We have "numpy 1.6" loaded.  Should we set some other flag or should
>> we have different version of "numpy" ?
>>
>>
>>
>> Thanks a lot in advance for any advice.
>>
>> Vadim.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Mar 2, 2013, at 10:58 PM, Subhasis Ray wrote:
>>
>> Hi,
>> In the serial version, HDF5 1.8.9 should work fine. It is used in
>> HDF5DataWriter class to incrementally dump data into an HDF5 file. It was
>> implemented to reduce memory usage for long running simulations generating
>> gigabytes of data.
>> Best,
>>   Subha
>>
>>
>> On Sun, Mar 3, 2013 at 1:22 AM, Majumdar, Amitava <maj...@sd...>wrote:
>>
>>>  If HDF5 version is the only issue, we can make HDF51.8.0 or higher
>>> available (actually we have HDF5 1.8.9 available
>>> on another parallel computer at SDSC).
>>>
>>> -Amitvai
>>>  ------------------------------
>>> *From:* Subhasis Ray [ray...@gm...]
>>> *Sent:* Saturday, March 02, 2013 1:35 AM
>>> *To:* Vadim A
>>>
>>> *Cc:* Niraj Dudani; Yoshimoto, Kenneth; Majumdar, Amitava;
>>> moo...@li...
>>> *Subject:* Re: [moose-generic] MOOSE_installation_problem
>>>
>>>    Dear Vadim,
>>>    I would recommend that you avoid the MPI build at this point. The
>>> errors again are due to a minor issue with HDF5 library that can vary from
>>> package to package. These functions were introduced in HDF5 1.8.0. Either
>>> you need the same or a newer version installed. Otherwise, you can skip
>>> HDF5 support (which is somewhat experimental anyways) altogether by passing
>>> USE_HDF5=0 to "make" command.
>>>    Hope this helps,
>>>      Subha
>>>
>>>
>>> On Sat, Mar 2, 2013 at 5:35 AM, Vadim A <ast...@nc...> wrote:
>>>
>>>> Dear Subha.
>>>>
>>>>  I set CXXFLAG to include mpi.h in "ifeq ($(BUILD),release)"
>>>>
>>>>
>>>>  like you've suggested  and it seems that it can find all libraries
>>>> now but unfortunately
>>>>
>>>>
>>>>  make BUILD=release USE_MPI=1
>>>>
>>>>
>>>>  produce another error
>>>>
>>>>
>>>>  mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>>>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>>>> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
>>>> -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -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 HDF5DataWriter.cpp -c
>>>>
>>>>
>>>>
>>>>
>>>>  ../basecode/Conv.h:1009: warning: converting to 'unsigned int' from
>>>> 'const double'
>>>> HDF5DataWriter.cpp: In member function 'hid_t
>>>> HDF5DataWriter::get_dataset(std::string)':
>>>> HDF5DataWriter.cpp:222: error: 'H5Gcreate2' was not declared in this
>>>> scope
>>>> HDF5DataWriter.cpp:225: error: 'H5Gopen2' was not declared in this scope
>>>> HDF5DataWriter.cpp:258: error: 'H5Dopen2' was not declared in this scope
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>  HDF5  and openmpi  libraries included. Do I still missing something ?
>>>>
>>>>  Thanks a lot in advance for any comments.
>>>>
>>>>  Vadim.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>  On Feb 28, 2013, at 7:37 PM, Subhasis Ray wrote:
>>>>
>>>>
>>>>
>>>>
>>>> Do not enable MPI unless you want to try the parallel version. To
>>>> enable MPI, you have to pass the argument "USE_MPI=1" to make command.
>>>>
>>>>
>>>>>
>>>>>
>>>>>  # 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
>>>>>
>>>>>
>>>>>
>>>>  In the above, the PARALLEL_DIR and PARALLEL_LIB are MOOSE source
>>>> directory and object file for the parallel version. They are not to be
>>>> modified.
>>>>
>>>>>
>>>>>
>>>>>
>>>>>  We are using "openmpi" which does not have "parallel.o"
>>>>>
>>>>
>>>>  As mentioned above, parallel.o will be generated by the build
>>>> process. It looks like your version of hdf5 includes mpi.h and the compiler
>>>> cannot find it. So you have to add -I{location of mpi.h} to the CXXFLAGS
>>>> variable somewhere.Depending on your build type, you can append this to the
>>>> CXXFLAG assignment under :
>>>>
>>>> ifeq ($(BUILD),debug)
>>>>
>>>>  and/or under
>>>>
>>>> ifeq ($(BUILD),release)
>>>>
>>>>
>>>>  Best,
>>>>    Subha
>>>>
>>>>
>>>>
>>>
>>
>>
>
>
>