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That helped. I now read my input file correctly. I am getting an error with the line below:
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<div>DM da;</div>
<div>ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_GHOSTED,DM_BOUNDARY_GHOSTED,DM_BOUNDARY_GHOSTED,DMDA_STENCIL_STAR,21,21,21,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,19,1,PETSC_NULL,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr);</div>
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<div>The error is: </div>
<div>0]PETSC ERROR: ------------------------------------------------------------------------</div>
<div>[0]PETSC ERROR: Caught signal number 10 BUS: Bus Error, possibly illegal memory access</div>
<div>[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</div>
<div>[0]PETSC ERROR: or see <a href="https://urldefense.us/v3/__https://petsc.org/release/faq/*valgrind__;Iw!!G_uCfscf7eWS!drLsYfgMTCNAyHHkj7gJrIUzQ9gnkjwyajLeWWqLLyV3mEdA2B7X0fX4pFYTyw9FVWpCJQ7BKm4Ba2f-wE5DJLwP$">https://petsc.org/release/faq/#valgrind</a> and <a href="https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!drLsYfgMTCNAyHHkj7gJrIUzQ9gnkjwyajLeWWqLLyV3mEdA2B7X0fX4pFYTyw9FVWpCJQ7BKm4Ba2f-wJxIkrms$">https://petsc.org/release/faq/</a></div>
<div>[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run </div>
<div>[0]PETSC ERROR: to get more information on the crash.</div>
<div>[0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash.</div>
<div>--------------------------------------------------------------------------</div>
<div>MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD</div>
<div> Proc: [[44836,1],0]</div>
<div> Errorcode: 59</div>
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<div>Since the code was running with an old version of PETSc, I am wondering what I did to break it.</div>
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<b><span style="font-family: Arial, sans-serif; color: rgb(51, 51, 51);">Jeremy A. Riousset, Ph.D.<span class="apple-converted-space"> </span></span></b><i><span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(51, 51, 51);">(he, him, his)<span class="apple-converted-space"> </span></span></i><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(51, 51, 51);"><br>
<b><i>Associate Professor of Engineering Physics</i></b><span class="apple-converted-space"> </span><br>
<i>Physical Science</i><o:p></o:p></span></p>
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<span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(51, 51, 51);">1 Aerospace Boulevard<br>
Daytona Beach, FL 32114<br>
+1 (386) 226-6407<br>
<a href="mailto:jeremy.riousset@erau.edu" style="color: rgb(5, 99, 193);">jeremy.riousset@erau.edu</a><br>
<a href="https://urldefense.us/v3/__https://orcid.org/0000-0003-1516-5337__;!!G_uCfscf7eWS!drLsYfgMTCNAyHHkj7gJrIUzQ9gnkjwyajLeWWqLLyV3mEdA2B7X0fX4pFYTyw9FVWpCJQ7BKm4Ba2f-wPlXko4P$" title="https://orcid.org/0000-0003-1516-5337" style="color: rgb(5, 99, 193);">https://orcid.org/0000-0003-1516-5337</a><o:p></o:p></span></p>
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<b><span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(0, 84, 158);">Embry-Riddle Aeronautical University</span></b><span class="apple-converted-space"><span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(51, 51, 51);"> </span></span><span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(51, 51, 51);"><br>
Florida | Arizona | Worldwide</span></p>
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<blockquote type="cite">
<div>On Sep 18, 2025, at 3:59 PM, Barry Smith <bsmith@petsc.dev> wrote:</div>
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<td style="padding:5px 10px;"><span style="color:#873301;"><b>External Sender:</b></span> Use caution with links, attachments, or when sharing information.</td>
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The PETSc options all begin with a single dash, so it is -options_file input/main.in
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<div>On Sep 18, 2025, at 3:44 PM, Riousset, Jeremy via petsc-users <petsc-users@mcs.anl.gov> wrote:</div>
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Hi,
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<div>I’m updating a code from PETSc 3.4 to run with the latest PETSc. Here is my status:</div>
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<li>I read the parameters via: mpiexec -n 1 bin/./M4 --options_file input/main.in</li><li>I’m not opening main.in correctly</li><li>None of the options are retrieved by e.g., PetscOptionsGetReal</li></ul>
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<p style="margin-right: 0in; margin-bottom: 7.5pt; margin-left: 0in;">Do you have a suggestion to test what file the code is actually trying to access?</p>
<p style="margin-right: 0in; margin-bottom: 7.5pt; margin-left: 0in;">Thanks</p>
<p style="font-family: -webkit-standard; margin-right: 0in; margin-bottom: 7.5pt; margin-left: 0in;">
<b><span style="font-family: Arial, sans-serif; color: rgb(51, 51, 51);">Jeremy A. Riousset, Ph.D.<span class="apple-converted-space"> </span></span></b><i><span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(51, 51, 51);">(he, him, his)<span class="apple-converted-space"> </span></span></i><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(51, 51, 51);"><br>
<b><i>Associate Professor of Engineering Physics</i></b><span class="apple-converted-space"> </span><br>
<i>Physical Science</i><o:p></o:p></span></p>
<p style="font-family: -webkit-standard; margin-right: 0in; margin-bottom: 7.5pt; margin-left: 0in; box-sizing: border-box; caret-color: rgb(51, 51, 51);">
<span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(51, 51, 51);">1 Aerospace Boulevard<br>
Daytona Beach, FL 32114<br>
+1 (386) 226-6407<br>
<a href="mailto:jeremy.riousset@erau.edu" style="color: rgb(5, 99, 193);">jeremy.riousset@erau.edu</a><br>
<a href="https://urldefense.us/v3/__https://orcid.org/0000-0003-1516-5337__;!!G_uCfscf7eWS!YiGxTKiNGs8EnS4pzFoO1YK18z4fx-sCtisUBloRO8dd6sUuh3kfUkimanAH5cJ-jgPhYw-Qk_8q8BBxAtPO0s_6$" title="https://orcid.org/0000-0003-1516-5337" style="color: rgb(5, 99, 193);">https://orcid.org/0000-0003-1516-5337</a><o:p></o:p></span></p>
<p style="font-family: -webkit-standard; margin-right: 0in; margin-bottom: 7.5pt; margin-left: 0in;">
<b><span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(0, 84, 158);">Embry-Riddle Aeronautical University</span></b><span class="apple-converted-space"><span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(51, 51, 51);"> </span></span><span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(51, 51, 51);"><br>
Florida | Arizona | Worldwide</span></p>
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