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<div class="moz-cite-prefix">On 9/18/2025 11:11 PM, Omar Elías
Velasco Castillo wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAM3SPH25xBA1gZPFCJ8dLvodiWhAqu1HoRgsTiwfgxG-XbGxkw@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hi Steven, thank you very much for your attention.
<div><br>
</div>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><u>Can
you show us what the error message(s) are? </u></blockquote>
<div><br>
</div>
<div>Yes, my error messages displayed in the .err file of a
simulation are:</div>
<div><font face="monospace">--------------------------------------------------------------------------<br>
Primary job terminated normally, but 1 process returned<br>
a non-zero exit code. Per user-direction, the job has been
aborted.<br>
--------------------------------------------------------------------------<br>
ERROR: ld.so: object '/lib64/libpapi.so.5.2.0.0' from
LD_PRELOAD cannot be preloaded: ignored.<br>
/home/ia/ovelasco/simulations/tov_ET_decisiva/SIMFACTORY/exe/cactus_sim:
error while loading shared libraries: libpapi.so.5.2.0.0:
cannot open shared object file: No such file or directory<br>
</font></div>
<div><font face="monospace">=>> PBS: job killed: walltime
864033 exceeded limit 864000<br>
mpirun: abort is already in progress...hit ctrl-c again to
forcibly terminate</font></div>
<div><font face="monospace"><br>
</font></div>
<div><font face="arial, sans-serif">I attach below the
configurations file, runscript and submitscript I used for
this job, together with the .err and .out files generated
for that case.</font></div>
</div>
</blockquote>
<p><font face="arial, sans-serif">Have you tried running without
papi? Have you determined whether </font><font face="monospace">/lib64/libpapi.so.5.2.0.0
exists on the compute nodes?</font></p>
<blockquote type="cite"
cite="mid:CAM3SPH25xBA1gZPFCJ8dLvodiWhAqu1HoRgsTiwfgxG-XbGxkw@mail.gmail.com">
<div dir="ltr">
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif"><br>
</font></div>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><u>Maybe.
I'm not 100% sure what you are doing. Can you be clearer
about how you are running the ET?</u></blockquote>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif">Yes, my intention is to run
the ET in the queue of a remote machine using Simfactory and
a proper configurations file for the machine, as well as a
suitable runscript and submitscript for either PBS or SLURM
nodes, whatever I need in one node or another. The key point
is that, I notice that while the sim build is being done, it
seems that some lines printed on the shell indicate that
when a module is not found in that machine, the ET compiler
"builds a bundle" from a thorn, for those modules that
weren't found: </font></div>
<div><span style="font-family:arial,sans-serif"><br>
</span></div>
<div><font face="monospace">********************************************************************************<br>
Running configuration script for thorn GSL:<br>
GSL selected, but GSL_DIR not set. Checking pkg-config ...<br>
GSL not found. Checking standard paths ...<br>
GSL not found.<br>
Using bundled GSL...<br>
Finished running configuration script for thorn GSL.</font></div>
<div><font face="monospace">********************************************************************************<br>
Running configuration script for thorn HDF5:<br>
Additional requested language support: Fortran<br>
HDF5 selected, but HDF5_DIR not set. Checking pkg-config ...<br>
HDF5 not found. Checking standard paths ...<br>
HDF5 not found.<br>
Using bundled HDF5...<br>
Finished running configuration script for thorn HDF5.</font><span
style="font-family:arial,sans-serif"></span></div>
<div><br>
</div>
<div><br>
</div>
<div><span style="font-family:arial,sans-serif">I attach here
too as an example a logfile, called "build.log", produced
with the prints on the terminal I refer to.</span></div>
<div><span style="font-family:arial,sans-serif"><br>
</span></div>
<div><span style="font-family:arial,sans-serif">So then, my
question is, why can't I still run simulations in a queue if
the sim build instruction is completed and done
successfully? And I get errors like, for example, the one I
showed you above. </span><span
style="font-family:arial,sans-serif">The bundle itself
doesn't replace the lack of recent versions of modules or
the availability of those modules in those remote
machines/nodes?</span><span
style="font-family:arial,sans-serif"> </span></div>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif">Sending you my best regards,</font></div>
</div>
</blockquote>
<p><font face="arial, sans-serif">Right, but the error was for papi,
not GSL or HDF5. Is papi disabled in your thornlist? I.e. do you
have</font></p>
<p><font face="arial, sans-serif">#DISABLED ExternalLibraries/PAPI</font></p>
<p><font face="arial, sans-serif">in your thornlist? If not, you
need to figure out where the papi dependency is coming from. It
may be that your sysadmins can help.</font></p>
<p><font face="arial, sans-serif">--Steve</font></p>
<blockquote type="cite"
cite="mid:CAM3SPH25xBA1gZPFCJ8dLvodiWhAqu1HoRgsTiwfgxG-XbGxkw@mail.gmail.com">
<div dir="ltr">
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif"><br>
</font></div>
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<br>
<div class="gmail_quote gmail_quote_container">
<div dir="ltr" class="gmail_attr">El jue, 18 sept 2025 a las
14:04, Steven Brandt (<<a href="mailto:sbrandt@cct.lsu.edu"
moz-do-not-send="true" class="moz-txt-link-freetext">sbrandt@cct.lsu.edu</a>>)
escribió:<br>
</div>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p><br>
</p>
<div>On 9/17/2025 12:11 PM, Omar Elías Velasco Castillo
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div>Dear Einstein Toolkit team,<br>
<br>
I hope this message finds you well. I am a
beginner with the Einstein Toolkit. On personal
workstations I have been able to compile and run
tutorial simulations at low resolution, but I am
facing problems on two different clusters. I would
like to ask two questions:<br>
<br>
1. <b>Are there ET versions prior to 2022_05
(e.g. 2019–2020 releases) that can still be
downloaded and compiled successfully?</b> When I
try to fetch them from the website using
./GetComponents, the process fails
(CactusSourceJar.git is not created and some
components do not download). Since some of the
nodes I use have older GCC versions (8 or 10) and
limited modules, a stable older release might be
more practical.<br>
<br>
2. During compilation, I notice that thorns (such
as GSL and HDF5, for example) fall back to using
the bundled versions because system modules are
not found. The build completes successfully, but
jobs fail immediately after submission to PBS or
SLURM queues.<br>
</div>
</div>
</div>
</div>
</blockquote>
Can you show us what the error message(s) are?
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div><br>
<b>What is the role of the bundled versions in
this case</b>?<b> If the build uses bundled
GSL/HDF5, do I still need to load corresponding,
compatible modules in the runscript?</b><br>
<br>
Could this mismatch explain why jobs die right
after submission?<br>
</div>
</div>
</div>
</div>
</blockquote>
<p>Maybe. I'm not 100% sure what you are doing. Can you be
clearer about how you are running the ET?</p>
<p>--Steve</p>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div><br>
Any advice on handling these issues would be very
helpful. Thank you very much for your time and
support.</div>
<div><br>
</div>
<div>Greetings,</div>
<div><br>
</div>
<div>O.V.</div>
<div><br>
</div>
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