[FLASH-USERS] Error when using flag "+hdf5typeio"

[Reem Alraddadi]

>
> Hi Chris,
>
>
>
> Thanks for your reply. I fixed that and now I can see in the
> libhdf5.settings that "Parallel HDF5: Yes" and this error is no longer
> exist. However, it's still when I add this flag "+hdf5typeio " I have an
> error message in mpirun step. The message is:
>
>
>
> “”””””””
>
> 4 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics
>
> Set MCA parameter "orte_base_help_aggregate" to 0 to see all help /error
> messages
>
> “””””””””””””””””””
>
> This is only happens with this flag. Any ideas?
>
>
>
    Regards,
     Reem



> Hi Reem,
>
> This is because your HDF5 library is not actually built with parallel
> support.
>
> An easy way to check is to look for the 'Parallel HDF5' string inside
> the libhdf5.settings file, e.g. on my laptop:
>
> $ ldd ./flash4 | grep hdf5
>      libhdf5.so.7 =>
> /opt/hdf5/1.8.10/mpich-3.0.1-gnu-4.7.2/lib/libhdf5.so.7
> (0x00007f627f243000)
>
> $ grep 'Parallel HDF5'
> /opt/hdf5/1.8.10/mpich-3.0.1-gnu-4.7.2/lib/libhdf5.settings
>                    Parallel HDF5: yes
>
>
> I expect your libhdf5.settings shows "Parallel HDF5: no".
>
>
> Note that Visit can be used with FLASH HDF5 files produced with both
> serial and parallel HDF5 I/O implementations.
>
> Regards,
> Chris
>
>
> On 04/16/2013 09:10 AM, Reem Alraddadi wrote:
> > Hi,
> > I installed install parallel HDF5 (version 1.8.9) in order to use
> > flag  "+hdf5typeio " but I got the following error message:
> > """"
> > /hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5file_interface.c:273:
> > undefined reference to `H5Pset_fapl_mpio'
> > io_h5file_interface.o: In function `io_h5init_file_':
> > /hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5file_interface.c:165:
> > undefined reference to `H5Pset_fapl_mpio'
> > io_h5read_unknowns.o: In function `io_h5read_unknowns_':
> > /hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5read_unknowns.c:53:
> > undefined reference to `H5Pset_dxpl_mpio'
> > io_h5write_bflags.o: In function `io_h5write_bflags_':
> > /hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5write_bflags.c:83:
> > undefined reference to `H5Pset_dxpl_mpio'
> > io_h5write_blksize.o: In function `io_h5write_blksize_':
> > /hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5write_blksize.c:100:
> undefined
> > reference to `H5Pset_dxpl_mpio'
> > io_h5write_bndbox.o: In function `io_h5write_bndbox_':
> > /hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5write_bndbox.c:116:
> > undefined reference to `H5Pset_dxpl_mpio'
> > io_h5write_coords.o: In function `io_h5write_coords_':
> > /hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5write_coords.c:118:
> > undefined reference to `H5Pset_dxpl_mpio'
> >
> io_h5write_gid.o:/hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5write_gid.c:86:
> > more undefined references to `H5Pset_dxpl_mpio' follow
> > collect2: ld returned 1 exit status
> > make: *** [flash4] Error 1
> > """""
> > the FLASH works without this flag and I can see the figures via IDL
> > but I need to use visit. Could anyone can help me with this error?
> > Thanks,
> > Reem
>
>
>
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>
> End of flash-users Digest, Vol 66, Issue 6
> ******************************************
>



-- 
Reem  A. Alraddadi

York Plasma Institute
Department of Physics
University of York
YO10 5DQ
United Kingdom
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