<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><br><div><br><blockquote type="cite"><div>On 17 Apr 2023, at 6:22 PM, Matteo Semplice <matteo.semplice@uninsubria.it> wrote:</div><br class="Apple-interchange-newline"><div>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<div><p>Dear PETSc users,</p><p> I am investigating a strange error occurring when using my
code on a cluster; I managed to reproduce it on my machine as well
and it's weird:</p><p>- on petsc3.19, optimized build, the code runs fine, serial and
parallel</p><p>- on petsc 3,19, --with=debugging=1, the code crashes without
giving me a meaningful message. The output is</p><p><span style="font-family:monospace"><span style="background-color: rgb(255, 255, 255);">$ ../levelSet
-options_file ../test.opts </span><br>
Converting from ../pointClouds/2d/ptCloud_cerchio.txt in binary
format: this is slow!
<br>
Pass in the .info file instead!
<br>
Read 50 particles from ../pointClouds/2d/ptCloud_cerchio.txt
<br>
Bounding box: [-0.665297, 0.666667] x [-0.666324, 0.666324]
<br>
<span style="font-weight:bold;color:#ff5454;background-color:#ffffff;">[0]PETSC
ERROR: --------------------- Error Message
--------------------------------------------------------------</span><span style="background-color: rgb(255, 255, 255);">
</span><br>
[0]PETSC ERROR: Petsc has generated inconsistent data
<br>
[0]PETSC ERROR: Invalid stack size 0, pop convertCloudTxt
clouds.cpp:139.
<br>
<br>
[0]PETSC ERROR: WARNING! There are option(s) set that were not
used! Could be the program crashed before they were used or a
spell<br>
ing mistake, etc!
<br>
[0]PETSC ERROR: Option left: name:-delta value: 1.0 source:
file
<br>
[0]PETSC ERROR: Option left: name:-dx value: 0.1 source: file
<br>
[0]PETSC ERROR: Option left: name:-extraCells value: 5 source:
file
<br>
[0]PETSC ERROR: Option left: name:-maxIter value: 200 source:
file
<br>
[0]PETSC ERROR: Option left: name:-p value: 1.0 source: file
<br>
[0]PETSC ERROR: Option left: name:-tau value: 0.1 source: file
<br>
[0]PETSC ERROR: Option left: name:-u0tresh value: 0.3 source:
file
<br>
[0]PETSC ERROR: See <a class="moz-txt-link-freetext" href="https://petsc.org/release/faq/">https://petsc.org/release/faq/</a> for trouble
shooting.
<br>
[0]PETSC ERROR: Petsc Release Version 3.19.0, unknown <br>
[0]PETSC ERROR: ../levelSet on a named signalkuppe by matteo
Mon Apr 17 18:04:03 2023
<br>
[0]PETSC ERROR: Configure options --download-ml \ --with-metis
--with-parmetis \ --download-hdf5 \ --with-triangle --with-gmsh
\ P<br>
ETSC_DIR=/home/matteo/software/petsc --PETSC_ARCH=dbg
--with-debugging=1 --COPTFLAGS=-O --CXXOPTFLAGS=-O
--FOPTFLAGS=-O --prefix=/<br>
home/matteo/software/petsc/3.19-dbg/
<br>
[0]PETSC ERROR: #1 convertCloudTxt() at clouds.cpp:139
<br>
--------------------------------------------------------------------------
<br>
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
<br>
with errorcode 77.
<br>
<br>
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
processes.
<br>
You may or may not see output from other processes, depending on
<br>
exactly when Open MPI kills them.
<br>
--------------------------------------------------------------------------<br>
</span></p><p>Now, line 139 of clouds.cpp is
PetscFunctionReturn(PETSC_SUCCESS), so I cannot understand what is
the offending operation in that routine. (Note: this is a
convertion routine and, skipping it, just make the next routine
fail in a similar way...)</p><p>My student has also tried to compile PETSc with <code class="docutils literal notranslate"><span class="pre">--with-strict-petscerrorcode</span></code>
and fixing all the compilation errors that were raised, but it
didn't help.</p><p>Do you have any guess on what to look for?</p></div></div></blockquote><div>There may be a PetscFunctionBeginUser; missing at the beginning of the convertCloudTxt() function.</div><div>Could you double-check this?</div><div><br></div><div>Thanks,</div><div>Pierre</div><blockquote type="cite"><div><div><p>Bonus question to assess the cluster output what is the default
value for --with-debugging? I that option is not specified during
PETSc configure, does one get optimized or debug build?<br>
</p><p>Thanks</p><p> Matteo<br>
</p>
<pre class="moz-signature" cols="72">--
Professore Associato in Analisi Numerica
Dipartimento di Scienza e Alta Tecnologia
Università degli Studi dell'Insubria
Via Valleggio, 11 - Como</pre>
</div>
</div></blockquote></div><br></body></html>