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

[Steven Brandt]

On 9/18/2025 11:11 PM, Omar Elías Velasco Castillo wrote:
> 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.

Have you tried running without papi? Have you determined whether 
/lib64/libpapi.so.5.2.0.0 exists on the compute nodes?

>
>
>     _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,

Right, but the error was for papi, not GSL or HDF5. Is papi disabled in 
your thornlist? I.e. do you have

#DISABLED ExternalLibraries/PAPI

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.

--Steve

>
>
>
> 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.
>>
>>
>>
>>
>>
>>     _______________________________________________
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>>     Users at einsteintoolkit.org
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>
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