<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr"><div dir="ltr">Hi Simon!<div><br></div><div>As the error notes: "<i>executable file is not an executable</i>" so something is off with your <i>flash4</i>, perhaps<i>.</i> Can you<i> </i><font face="monospace">ls -ltr </font>in your <i>object/</i> directory where you've performed the command <font face="monospace">./flash4</font><font face="arial, sans-serif">? Do you see the permissions as being executable?</font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">When you set-up did it set-up "</font>SUCCESS"fully<font face="arial, sans-serif">? I am a fan of making my own shell scripts for set-ups and then making my own object directory (e.g. </font><font face="monospace">emacs LaserSlab-TestProblem.sh -nw</font><i style="font-family:arial,sans-serif"> </i><font face="arial, sans-serif">contains the c&p below; then I make it an executable </font><font face="monospace">chmod a+x LaserSlab-TestProblem.sh;</font><font face="arial, sans-serif"> then I just do </font><font face="monospace">./LaserSlab-TestProblem.sh</font><font face="arial, sans-serif">; this way everything is saved). Here is my example set-up command for the LaserSlab problem:</font></div><div><font face="arial, sans-serif"><br></font></div><div><p style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Andale Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures">./setup -auto LaserSlab -2d +cylindrical -nxb=16 -nyb=16 +hdf5typeio </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(157,32,111)">\</span></p>
<p style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Andale Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span></span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(193,101,28)">species</span><span style="font-variant-ligatures:no-common-ligatures">=cham,targ +mtmmmt +laser +uhd3t +mgd </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(193,101,28)">mgd_meshgroups</span><span style="font-variant-ligatures:no-common-ligatures">=6 </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(157,32,111)">\</span></p>
<p style="margin:0px;font-stretch:normal;line-height:normal;font-family:"Andale Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>-parfile=example.par -site=mbpadams -objdir=LaserSlab</span></p></div>
<br class="gmail-Apple-interchange-newline">
<div>Try simplifying your HDF5 shortcuts in the set-up command and make sure that there is no space in "<i>+uhd3t</i>". Is there a reason you're forcing the use of serial HDF5? You can also try setting this up with no HDF5 related flags; it should (1) set-up (2) make and (3) run successfully. If the same thing happens, can you <font face="monospace">make</font> the <i>Sedov/</i> problem?</div><div><br></div><div>If that doesn't work then maybe there is an issue with the <i>Makefile.h</i> you're using (flags probably) or something off with the installation of the libraries you're using. </div><div><br></div><div>These are just my initial thoughts and I hope they are helpful in your debugging.</div><div><br></div><div>Have a lovely day,</div><div>Marissa</div><div><br></div><div><br></div></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Aug 11, 2021 at 12:55 PM BolañOs, Simon <<a href="mailto:sbolanos@ucsd.edu">sbolanos@ucsd.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Hello everyone,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
When executing the Laser Slab example of Section 34.7.5, I got a Segmentation Fault, displayed below. Is someone got such a similar error during execution? How can I fix such an error? </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
By the way here are the module that I turn on: <i><b>./setup -auto LaserSlab -2d -nxb=16 -nyb=16 +hdf5 +io +serialIO species=cham,targ +mtmmmt +laser +u hd3t +mgd mgd_meshgroups=6 -parfile=example.par </b></i></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<i><b><br>
</b></i></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<b><i>Error message :</i></b></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<b><i><br>
</i></b></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<b><i>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures">Finished with Grid_initDomain, no restart</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures"><span> </span>Ready to call Hydro_init</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures"><span> </span>[Hydro_init]: Using non-Cartesian Geometry!</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures"><span> </span>Hydro initialized</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures"><span> </span>Gravity initialized</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures"><span> </span>Initial dt verified</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures"><span> </span>*** Wrote checkpoint file to lasslab_hdf5_chk_0000 ****</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures"><span> </span>*** Wrote plotfile to lasslab_hdf5_plt_cnt_0000 ****</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures"><span> </span>Initial plotfile written</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures"><span> </span>Driver init all done</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85);min-height:20px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures">Program received signal SIGSEGV: Segmentation fault - invalid memory reference.</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85);min-height:20px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures">Backtrace for this error:</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85);min-height:20px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures">Could not print backtrace: executable file is not an executable</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures">#0<span>
</span>0x104270b17</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures">#1<span>
</span>0x10426fbab</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures">#2<span>
</span>0x193edec43</span></p>
<p style="margin:0px;font-style:normal;font-variant-caps:normal;font-weight:normal;font-stretch:normal;font-size:18px;line-height:normal;font-family:"Courier New";color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)">
<span style="font-variant-ligatures:no-common-ligatures">zsh: segmentation fault<span>
</span>./flash4</span></p>
<br>
</i></b></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Thank you in advance for your help, </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Simon. </div>
</div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><font face="monospace" size="1" color="#000000">%---------------------------------------------%</font><div><font face="monospace" size="1" color="#000000">Marissa B. P. Adams</font></div><div><font face="monospace" size="1" color="#000000">(she/her/hers)</font></div><div><font face="monospace" size="1" color="#000000">Phd Candidate, University of Rochester</font></div><div><b style="color:rgb(0,0,0);font-family:monospace;font-size:x-small">E-mail:</b><span style="color:rgb(0,0,0);font-family:monospace;font-size:x-small"> <a href="mailto:madams@pas.rochester.edu" target="_blank">madams@pas.rochester.edu</a></span><br></div><div><font face="monospace" size="1" color="#000000"><b>Website:</b> <a href="http://www.pas.rochester.edu/~madams#" target="_blank">https://www.pas.rochester.edu/~madams</a></font></div><div><font color="#000000" face="monospace" size="1"><b>^^ Just updated! Please send me feedback :)</b></font></div><div><font color="#000000" face="monospace" size="1"><b>Current Location:</b></font></div><div><font color="#000000" face="monospace" size="1">Occupied Seneca Land</font></div><div><font color="#000000" face="monospace" size="1">471 Bausch and Lomb Hall</font></div><div><font color="#000000" face="monospace" size="1">University of Rochester</font></div><div><font color="#000000" face="monospace" size="1">Rochester, NY 14627</font></div></div></div></div></div></div></div>