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

[Christopher Daley]

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