[Users] Questions about old ET releases and bundled libraries on clusters

Thu Sep 18 23:11:43 CDT 2025

Hi Steven, thank you very much for your attention.

*Can you show us what the error message(s) are? *

Yes, my error messages displayed in the .err file of a simulation are:
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
ERROR: ld.so: object '/lib64/libpapi.so.5.2.0.0' from LD_PRELOAD cannot be
preloaded: ignored.
/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
=>> PBS: job killed: walltime 864033 exceeded limit 864000
mpirun: abort is already in progress...hit ctrl-c again to forcibly
terminate

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.

*Maybe. I'm not 100% sure what you are doing. Can you be clearer about how
> you are running the ET?*

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:

********************************************************************************
Running configuration script for thorn GSL:
GSL selected, but GSL_DIR not set. Checking pkg-config ...
GSL not found. Checking standard paths ...
GSL not found.
Using bundled GSL...
Finished running configuration script for thorn GSL.
********************************************************************************
Running configuration script for thorn HDF5:
Additional requested language support:  Fortran
HDF5 selected, but HDF5_DIR not set. Checking pkg-config ...
HDF5 not found. Checking standard paths ...
HDF5 not found.
Using bundled HDF5...
Finished running configuration script for thorn HDF5.

I attach here too as an example a logfile, called "build.log", produced
with the prints on the terminal I refer to.

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. The bundle itself
doesn't replace the lack of recent versions of modules or the availability
of those modules in those remote machines/nodes?

Sending you my best regards,

El jue, 18 sept 2025 a las 14:04, Steven Brandt (<sbrandt at cct.lsu.edu>)
escribió:

>
> On 9/17/2025 12:11 PM, Omar Elías Velasco Castillo wrote:
>
> Dear Einstein Toolkit team,
>
> 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:
>
> 1. *Are there ET versions prior to 2022_05 (e.g. 2019–2020 releases) that
> can still be downloaded and compiled successfully?* 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.
>
> 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.
>
> Can you show us what the error message(s) are?
>
>
> *What is the role of the bundled versions in this case*?* If the build
> uses bundled GSL/HDF5, do I still need to load corresponding, compatible
> modules in the runscript?*
>
> Could this mismatch explain why jobs die right after submission?
>
> Maybe. I'm not 100% sure what you are doing. Can you be clearer about how
> you are running the ET?
>
> --Steve
>
>
> Any advice on handling these issues would be very helpful. Thank you very
> much for your time and support.
>
> Greetings,
>
> O.V.
>
>
>
>
>
> _______________________________________________
> Users mailing listUsers at einsteintoolkit.orghttp://lists.einsteintoolkit.org/mailman/listinfo/users
>
>
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