Re: [moose-generic] MOOSE_installation_problem

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

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
>>
>>
>>
>