<div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">Hi all,<br><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">I am getting the following error when trying to <span style="font-family:monospace,monospace">make</span> an executable for the <b>LaserSlab</b> example found in the documentation (<a href="http://flash.uchicago.edu/~jbgallag/2012/flash4_ug/node34.html#SECTION08175000000000000000">http://flash.uchicago.edu/~jbgallag/2012/flash4_ug/node34.html#SECTION08175000000000000000</a> -- I have written the exact same setup script noted in this section):<br><font size="1"><span style="font-family:monospace,monospace"><br></span></font><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote"><font size="1"><span style="font-family:monospace,monospace">io_h5file_interface.o: In function `io_h5open_file_for_read_':<br>/home/<username>/FLASH4.3/object/io_h5file_interface.c:273: undefined reference to `H5Pset_fapl_mpio'<br>/home/</span></font><font size="1"><span style="font-family:monospace,monospace"><font size="1"><span style="font-family:monospace,monospace"><username></span></font>/FLASH4.3/object/io_h5file_interface.c:271: undefined reference to `H5Pset_fapl_mpio'<br>io_h5file_interface.o: In function `io_h5init_file_':<br>/home/</span></font><font size="1"><span style="font-family:monospace,monospace"><font size="1"><span style="font-family:monospace,monospace"><username></span></font>/FLASH4.3/object/io_h5file_interface.c:165: undefined reference to `H5Pset_fapl_mpio'<br>/home/</span></font><font size="1"><span style="font-family:monospace,monospace"><font size="1"><span style="font-family:monospace,monospace"><username></span></font>/FLASH4.3/object/io_h5file_interface.c:163: undefined reference to `H5Pset_fapl_mpio'<br>io_h5read_unknowns.o: In function `io_h5read_unknowns_':<br>/home/</span></font><font size="1"><span style="font-family:monospace,monospace"><font size="1"><span style="font-family:monospace,monospace"><username></span></font>/FLASH4.3/object/io_h5read_unknowns.c:53: undefined reference to `H5Pset_dxpl_mpio'<br>io_h5write_unknowns.o: In function `io_h5write_unknowns_':<br>/home/</span></font><font size="1"><span style="font-family:monospace,monospace"><font size="1"><span style="font-family:monospace,monospace"><username></span></font>/FLASH4.3/object/io_h5write_unknowns.c:156: undefined reference to `H5Pset_dxpl_mpio'<br>io_h5write_unknowns_sp.o: In function `io_h5write_unknowns_sp_':<br>/home/</span></font><font size="1"><span style="font-family:monospace,monospace"><font size="1"><span style="font-family:monospace,monospace"><username></span></font>/FLASH4.3/object/io_h5write_unknowns_sp.c:237: undefined reference to `H5Pset_dxpl_mpio'<br>make: *** [flash4] Error 1</span></font><br></blockquote></div><br clear="all"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">​The HDF5 compiled in the<i> /opt/ </i>of the ​cluster I am on is not parallelized. So I've compiled my own PHDF5 module in my home directory. I have been able to successfully <span style="font-family:monospace,monospace">make<font face="arial,helvetica,sans-serif"> with </font>+hdf5typeio<font face="arial,helvetica,sans-serif"> with the <b>Sedov</b> problem, which yields nicely refined output.<br><br></font></span></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><span style="font-family:monospace,monospace"><font face="arial,helvetica,sans-serif">On the other hand, I've tried to make a <b>LaserSlab</b> problem with </font>+noio<font face="arial,helvetica,sans-serif">, which was successful. However when running my executable I got a segfault error, which I am not sure to be related to the problem needing parallelized HDF5.<br><br>Looking at<b><i> </i></b><i>io_h5file_interface.c</i>, there seems to be perhaps a commenting issue (?):<br><br></font></span><span style="font-family:monospace,monospace"></span><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote"><font size="1"><span style="font-family:monospace,monospace"> /* if we are splitting the output file ... */<br>  /*  if(*io_outputSplitNum == 1){                                                  <br>     ierr = H5Pset_fapl_mpio(acc_template, MPI_COMM_WORLD, MPI_INFO_NULL);          <br>  }else{                                                                            <br>  */ ierr = H5Pset_fapl_mpio(acc_template, io_comm, MPI_INFO_NULL);<br>  /*} */</span></font><br></blockquote></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><span style="font-family:monospace,monospace"><font face="arial,helvetica,sans-serif"><br></font></span></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><span style="font-family:monospace,monospace"><font face="arial,helvetica,sans-serif">(similar set up at lines 273, 271, 165, 163)<br></font></span></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><span style="font-family:monospace,monospace"><font face="arial,helvetica,sans-serif"><br></font></span></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><span style="font-family:monospace,monospace"><font face="arial,helvetica,sans-serif">Can someone help with this? Thanks for reading!<br><br>Best,<br></font></span></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><span style="font-family:monospace,monospace"><font face="arial,helvetica,sans-serif">Marissa Adams<br></font></span></div><br><br><br clear="all"><br>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><span><font size="1"><span style="color:rgb(0,0,0)"><span style="font-family:monospace,monospace"><div>Marissa Adams                         <span><font size="1"><span style="color:rgb(0,0,0)"><span style="font-family:monospace,monospace">E-mail:</span></span><span style="color:rgb(0,0,0)"><span style="font-family:monospace,monospace"><a> </a><a href="mailto:madams@pas.rochester.edu" target="_blank">madams@pas.rochester.edu</a></span></span></font></span><br>Graduate Student                      <span><font size="1"><span style="color:rgb(0,0,0)"><span style="font-family:monospace,monospace">Ph: (585) 402-5779</span></span></font></span></div><div>Department of Physics & Astronomy     <span><font size="1"><span style="color:rgb(0,0,0)"><span style="font-family:monospace,monospace">Website: <a href="http://www.pas.rochester.edu/%7Emadams/" target="_blank">http://www.pas.rochester.edu/~madams/</a></span></span></font></span></div>University of Rochester<br>478 Bausch & Lomb Hall<br>P.O. Box 270171</span></span></font></span></div></div></div></div></div></div></div></div></div>