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
(<[email protected]>) 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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