<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><blockquote style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class="gmail_quote">
<font color="#000000" size="3" face="Times New Roman">
</font><p style="margin:0cm 0cm 0pt;line-height:normal"><span style="font-family:"Arial","sans-serif";font-size:12pt"><font color="#000000">Hi Chris,</font></span></p><font color="#000000" size="3" face="Times New Roman">
</font><p style="margin:0cm 0cm 0pt;line-height:normal"><span style="font-family:"Arial","sans-serif";font-size:12pt"><font color="#000000"> </font></span></p><font color="#000000" size="3" face="Times New Roman">
</font><p style="margin:0cm 0cm 0pt;line-height:normal"><span style="font-family:"Arial","sans-serif";font-size:12pt"><font color="#000000">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:</font></span></p><font color="#000000" size="3" face="Times New Roman">
</font><p style="margin:0cm 0cm 0pt;line-height:normal"><span style="font-family:"Arial","sans-serif";font-size:12pt"><font color="#000000"> </font></span></p><font color="#000000" size="3" face="Times New Roman">
</font><p style="margin:0cm 0cm 0pt;line-height:normal"><span style="font-family:"Arial","sans-serif";font-size:12pt"><font color="#000000"></font></span></p><font color="#000000" size="3" face="Times New Roman">
</font><p style="margin:0cm 0cm 0pt;line-height:normal"><span style="font-family:"Arial","sans-serif";font-size:12pt"><font color="#000000">4 more
processes have sent help message help-mpi-btl-base.txt / btl:no-nics</font></span></p><font color="#000000" size="3" face="Times New Roman">
</font><p style="margin:0cm 0cm 0pt;line-height:normal"><span style="font-family:"Arial","sans-serif";font-size:12pt"><font color="#000000">Set MCA
parameter "orte_base_help_aggregate" to 0 to see all help /error
messages</font></span></p><font color="#000000" size="3" face="Times New Roman">
</font><p style="margin:0cm 0cm 0pt;line-height:normal"><span style="font-family:"Arial","sans-serif";font-size:12pt"><font color="#000000"></font></span></p><font color="#000000" size="3" face="Times New Roman">
</font><p style="margin:0cm 0cm 0pt;line-height:normal"><span style="font-family:"Arial","sans-serif";font-size:12pt"><font color="#000000">This is
only happens with this flag. Any ideas?</font></span></p><p style="margin:0cm 0cm 0pt;line-height:normal"><span style="font-family:"Arial","sans-serif";font-size:12pt"></span> </p></blockquote><div> Regards,</div>
<div> Reem </div><font color="#000000" size="3" face="Times New Roman">
</font><br><br><blockquote style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class="gmail_quote"><br>
Hi Reem,<br>
<br>
This is because your HDF5 library is not actually built with parallel<br>
support.<br>
<br>
An easy way to check is to look for the 'Parallel HDF5' string inside<br>
the libhdf5.settings file, e.g. on my laptop:<br>
<br>
$ ldd ./flash4 | grep hdf5<br>
libhdf5.so.7 =><br>
/opt/hdf5/1.8.10/mpich-3.0.1-gnu-4.7.2/lib/libhdf5.so.7 (0x00007f627f243000)<br>
<br>
$ grep 'Parallel HDF5'<br>
/opt/hdf5/1.8.10/mpich-3.0.1-gnu-4.7.2/lib/libhdf5.settings<br>
Parallel HDF5: yes<br>
<br>
<br>
I expect your libhdf5.settings shows "Parallel HDF5: no".<br>
<br>
<br>
Note that Visit can be used with FLASH HDF5 files produced with both<br>
serial and parallel HDF5 I/O implementations.<br>
<br>
Regards,<br>
Chris<br>
<br>
<br>
On 04/16/2013 09:10 AM, Reem Alraddadi wrote:<br>
> Hi,<br>
> I installed install parallel HDF5 (version 1.8.9) in order to use<br>
> flag "+hdf5typeio " but I got the following error message:<br>
> """"<br>
> /hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5file_interface.c:273:<br>
> undefined reference to `H5Pset_fapl_mpio'<br>
> io_h5file_interface.o: In function `io_h5init_file_':<br>
> /hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5file_interface.c:165:<br>
> undefined reference to `H5Pset_fapl_mpio'<br>
> io_h5read_unknowns.o: In function `io_h5read_unknowns_':<br>
> /hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5read_unknowns.c:53:<br>
> undefined reference to `H5Pset_dxpl_mpio'<br>
> io_h5write_bflags.o: In function `io_h5write_bflags_':<br>
> /hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5write_bflags.c:83:<br>
> undefined reference to `H5Pset_dxpl_mpio'<br>
> io_h5write_blksize.o: In function `io_h5write_blksize_':<br>
> /hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5write_blksize.c:100: undefined<br>
> reference to `H5Pset_dxpl_mpio'<br>
> io_h5write_bndbox.o: In function `io_h5write_bndbox_':<br>
> /hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5write_bndbox.c:116:<br>
> undefined reference to `H5Pset_dxpl_mpio'<br>
> io_h5write_coords.o: In function `io_h5write_coords_':<br>
> /hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5write_coords.c:118:<br>
> undefined reference to `H5Pset_dxpl_mpio'<br>
> io_h5write_gid.o:/hwdisks/home/raba500/flash/FLASH4.0.1/object/io_h5write_gid.c:86:<br>
> more undefined references to `H5Pset_dxpl_mpio' follow<br>
> collect2: ld returned 1 exit status<br>
> make: *** [flash4] Error 1<br>
> """""<br>
> the FLASH works without this flag and I can see the figures via IDL<br>
> but I need to use visit. Could anyone can help me with this error?<br>
> Thanks,<br>
> Reem<br>
<br>
<br>
<br>
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End of flash-users Digest, Vol 66, Issue 6<br>
******************************************<br>
</blockquote></div><br><br clear="all"><br>-- <br><div dir="ltr"><div>Reem A. Alraddadi</div><div> </div><div>York Plasma Institute</div><div>Department of Physics<br>University of York<br>YO10 5DQ<br>United Kingdom<br>
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