[MOAB-dev] Using MOAB linked to Nek5000

[Vijay S. Mahadevan]

The logs look clean. Try linking one of the NEK examples (pipe) and
verify that it runs without issues.

You should also be able to verify if the fortran examples under
moab/examples are compiled/linked with the iMesh interfaces.

Vijay

On Mon, Feb 3, 2014 at 3:56 PM, Mohsen Behzad
<m.behzad.jazi at mail.utoronto.ca> wrote:
> please find attached, config.log, make.log, make.check.log and
> make.install.log files. I think what I thought of "errors" were sort of
> error check, as I couldn't see them in log files. So it seems
> configuration/build is clean.
>
> Thanks,
> Mohsen
>
>
>
> On 3-Feb-14, at 4:31 PM, Vijay S. Mahadevan wrote:
>
>>> Vijay: As you recommended I have added explicitly hdf5-ldflags and every
>>> thing went well. However, I have got a couple of errors during "make
>>> check"
>>> regarding imesh as follows, which I think are not important at this
>>> stage.
>>
>>
>> Can you show the full error message here (make -j1 | tee make.log).
>> The itaps/imesh interface is critical for NEK to work correctly with
>> MOAB and if the configuration/build is not clean, your linkage with
>> nek examples will have problems.
>>
>> Vijay
>>
>> On Mon, Feb 3, 2014 at 3:17 PM, Mohsen Behzad
>> <m.behzad.jazi at mail.utoronto.ca> wrote:
>>>
>>> Thanks for your replies.
>>> Vijay: As you recommended I have added explicitly hdf5-ldflags and every
>>> thing went well. However, I have got a couple of errors during "make
>>> check"
>>> regarding imesh as follows, which I think are not important at this
>>> stage.
>>>
>>> make[4]: *** [ScdMeshF90] Error 1
>>> make[4]: Leaving directory
>>> `/home/a/ashgriz/mbehzad/nek5_svn/moab-4.6.2/itaps/imesh'
>>> make[3]: *** [check-am] Error 2
>>> make[3]: Leaving directory
>>> `/home/a/ashgriz/mbehzad/nek5_svn/moab-4.6.2/itaps/imesh'
>>> make[2]: *** [check] Error 2
>>> make[2]: Leaving directory
>>> `/home/a/ashgriz/mbehzad/nek5_svn/moab-4.6.2/itaps/imesh'
>>> make[1]: *** [check-recursive] Error 1
>>> make[1]: Leaving directory
>>> `/home/a/ashgriz/mbehzad/nek5_svn/moab-4.6.2/itaps'
>>> make: *** [check-recursive] Error 1
>>>
>>> tim: You mentioned that the code should check for the parallel support of
>>> HDF5. I couldn't find such thing in the log file, thought, the HDF5 that
>>> is
>>> linked to MOAB is a parallel one. I uploaded the log file for you.
>>>
>>>
>>> Thanks
>>> Mohsen
>>>
>>> On 3-Feb-14, at 2:20 PM, Vijay S. Mahadevan wrote:
>>>
>>> Mohsen,
>>>
>>> Please attach the config.log file so that we can find out the exact cause
>>> of
>>> errors. On first look the configure options do look right but it is
>>> possible
>>> that you may need to provide the library list explicitly with
>>> hdf5-ldflags.
>>> But we cant suggest any other helpful pointers at the moment without more
>>> information on why the configuration failed.
>>>
>>> Vijay
>>>
>>> Dear MOAB team,
>>>
>>> I am writing to let you know that I intend to use MOAB with "Nek5000" for
>>> my
>>> simulations which will be performed on the SciNet cluster
>>> (http://wiki.scinethpc.ca/wiki/) in collaboration with the University of
>>> Toronto, in which I am a post-doc fellow.
>>> Right now, I tried to build MOAB with previously built packages on this
>>> system including "hdf5" (v. 1.8.7 compiled with openmpi) and "netcdf"
>>> (parallel version: 1.2.0 compiled with openmpi). As it is stated both of
>>> these packages were compiled with "openmpi" (v. 1.4.4 compiled with intel
>>> v.
>>> 12.1) and therefore there should be no issue of compilers compatibility.
>>> However, when I attempted to build MOAB on this system with the following
>>> configuration options and flags:
>>>
>>> ./configure FC=mpif90 F77=mpif77 CC=mpicc CXX=mpicxx \
>>> --prefix=`pwd` \
>>> --with-mpi=${SCINET_MPI_BASE} \
>>> --with-netcdf=${SCINET_PNETCDF_BASE} \
>>> --with-hdf5=${SCINET_HDF5_BASE} \
>>> --with-zlib="/scinet/gpc/Libraries/HDF5-1.8.7/zlib-intel/" \
>>> --with-szip=${SCINET_SZIP_BASE} \
>>> --enable-mbzoltan \
>>> --with-zoltan="/home/a/ashgriz/mbehzad/nek5_svn/Zoltan_v3.8/BUILD_DIR/"
>>>
>>> I have encountered an error in the configuration as:
>>> "configure:  error: HDF5 library not found or not usable."
>>> It should be noted that "zlib" and "szip" libraries were compiled with
>>> intel
>>> too.
>>>
>>> I am wondering if you can help me on this issue.
>>>
>>> Regards,
>>>
>>> Mohsen Behzad, Ph.D.
>>> Department of Civil Eng.
>>> University of Toronto
>>> Room 117, 170 College st. M5S 3E3
>>> Toronto, Ontario, Canada
>>> m.behzad.jazi at mail.utoronto.ca
>>> http://mussl.mie.utoronto.ca/
>>>
>>>
>
>