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@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:
- *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.
- 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.
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