Re: [moose-generic] MOOSE_installation_problem

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

I was suggesting that you avoid the MPI version altogether unless you want
to specifically try it. This is because it is not stable and different
approaches are still being tried out on the parallel front.

Best,
  Subha


On Sat, Mar 2, 2013 at 11:38 PM, Vadim Astakhov <ast...@nc...>wrote:

> Thank you for information. It seems that we need mpi version because we
> are installing software on cluster. Thus it make more since to have
> parallel version.
> Please let me clarify that, you do not suggest to install mpi version at
> all or we can proceed just installing appropriate hdf5.?
> Vadim
>
>
> Subhasis Ray <ray...@gm...> wrote:
>
> 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
>>
>>
>>
>