[MOAB-dev] Using MOAB linked to Nek5000

[Mohsen Behzad]

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
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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/
>>
>>