The gmsh file does have all vertices for the higher order elements.<div><br></div><div>I am now trying to compile with moab. I am doing everything in serial for now. I compiled moab succesfully and can convert from gmsh to h5m.</div>
<div><br></div><div>But when compiling nek with moab I get this type of errors. This is the first one.</div><div><br></div><div><div><font class="Apple-style-span" color="#990000">gcc -c -O2 -DMOAB -DPTRSIZE8 -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG /Users/praveen/Applications/nek5_svn/trunk/nek/3rd_party/imeshcutil.c -o obj/imeshcutil.o</font></div>
<div><font class="Apple-style-span" color="#990000">SIZE:5.21:</font></div><div><font class="Apple-style-span" color="#990000"> Included at /Users/praveen/Applications/nek5_svn/trunk/nek/3rd_party/MOABCORE:17:</font></div>
<div><font class="Apple-style-span" color="#990000"> Included at /Users/praveen/Applications/nek5_svn/trunk/nek/3rd_party/NEKMOAB:51:</font></div><div><font class="Apple-style-span" color="#990000"> Included at /Users/praveen/Applications/nek5_svn/trunk/nek/3rd_party/moab.f:79:</font></div>
<div><font class="Apple-style-span" color="#990000"><br></font></div><div><font class="Apple-style-span" color="#990000"> parameter (ldim=2) </font></div><div><font class="Apple-style-span" color="#990000"> 1</font></div>
<div><font class="Apple-style-span" color="#990000">Error: Symbol 'ldim' at (1) has no IMPLICIT type</font></div><div><br></div><div>My makenek looks like this</div><div><br></div><div><div><font class="Apple-style-span" color="#3333ff"># Fortran compiler</font></div>
<div><font class="Apple-style-span" color="#3333ff">F77="gfortran"</font></div><div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff"># C compiler</font></div>
<div><font class="Apple-style-span" color="#3333ff">CC="gcc"</font></div><div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff"># pre-processor symbol list </font></div>
<div><font class="Apple-style-span" color="#3333ff"># (set PPLIST=? to get a list of available symbols)</font></div><div><font class="Apple-style-span" color="#3333ff">PPLIST="MOAB"</font></div><div><font class="Apple-style-span" color="#3333ff"><br>
</font></div><div><font class="Apple-style-span" color="#3333ff"># plug-in list</font></div><div><font class="Apple-style-span" color="#3333ff">PLUGIN_LIST=""</font></div><div><font class="Apple-style-span" color="#3333ff"><br>
</font></div><div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff"># OPTIONAL SETTINGS</font></div><div><font class="Apple-style-span" color="#3333ff"># -----------------</font></div>
<div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff"># enable MPI (default true)</font></div><div><font class="Apple-style-span" color="#3333ff">IFMPI="false"</font></div>
<div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff"># auxilliary files to compile</font></div><div><font class="Apple-style-span" color="#3333ff"># NOTE: source files have to located in the same directory as makenek</font></div>
<div><font class="Apple-style-span" color="#3333ff"># a makefile_usr.inc has to be provided containing the build rules </font></div><div><font class="Apple-style-span" color="#3333ff">#USR="foo.o"</font></div>
<div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff"># linking flags</font></div><div><font class="Apple-style-span" color="#3333ff">#USR_LFLAGS="-L/usr/lib -lfoo"</font></div>
<div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff"># generic compiler flags</font></div>
<div><font class="Apple-style-span" color="#3333ff">#G="-g"</font></div><div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff"># optimization flags</font></div>
<div><font class="Apple-style-span" color="#3333ff">#OPT_FLAGS_STD=""</font></div><div><font class="Apple-style-span" color="#3333ff">#OPT_FLAGS_MAG=""</font></div><div><font class="Apple-style-span" color="#3333ff"><br>
</font></div><div><font class="Apple-style-span" color="#3333ff"># enable AMG coarse grid solver (default XXT)</font></div><div><font class="Apple-style-span" color="#3333ff">#IFAMG="true"</font></div><div><font class="Apple-style-span" color="#3333ff">#IFAMG_DUMP="true"</font></div>
</div><div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><div><font class="Apple-style-span" color="#3333ff"># CVODE path</font></div><div><font class="Apple-style-span" color="#3333ff">#CVODE_DIR=$HOME/cvode/lib</font></div>
<div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff"># MOAB/iMESH path</font></div><div><font class="Apple-style-span" color="#3333ff">MOAB_DIR="/opt/moab"</font></div>
<div><font class="Apple-style-span" color="#3333ff"><br></font></div><div><font class="Apple-style-span" color="#3333ff"># For linking to MOAB, the following might be needed:</font></div><div><font class="Apple-style-span" color="#3333ff"># NOTE: compiler specific, use the appropriate one depending on your compiler</font></div>
<div><font class="Apple-style-span" color="#3333ff"># GNU:</font></div><div><font class="Apple-style-span" color="#3333ff">USR_LFLAGS="-lmpi_cxx -lstdc++"</font></div><div><font class="Apple-style-span" color="#3333ff"># Intel:</font></div>
<div><font class="Apple-style-span" color="#3333ff"># USR_LFLAGS="-cxxlib"</font></div><div><font class="Apple-style-span" color="#3333ff"># PGI:</font></div><div><font class="Apple-style-span" color="#3333ff"># USR_LFLAGS="-pgcpplibs"</font></div>
<div><font class="Apple-style-span" color="#3333ff"># USR_LFLAGS=" -lmpi_cxx -lstdc++"</font></div></div><div><br></div><div>What am I doing wrong ?</div><div><br></div><div>Thanks</div><div>praveen</div><br><div class="gmail_quote">
On Wed, Nov 28, 2012 at 8:46 PM, <span dir="ltr"><<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div id=":31">Try running 'mbsize' on the gmsh file, and check the number of vertices to make sure it's getting all of them. Or, run mbsize -ll, piping the output to a file, and check one of the hexes to make sure it's 27-noded. If that's the case, we're all set (modulo how to handle the BC's).<br>
<br>
- tim</div></blockquote></div><br></div>