<div dir="ltr"><div>Hello, </div><div><br></div><div>This is a followup for retaking my questions about my failing to submit and run simulations in a remote cluster. </div><div><br></div><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">Can you show us what the error message(s) are?</blockquote><div dir="ltr"><br></div><div>Yes, the tail of my err file reads:</div><div><br></div><div><font face="monospace">+ set -<br>ERROR: ld.so: object '/lib64/libpapi.so.5.2.0.0' from LD_PRELOAD cannot be preloaded: ignored.<br>ERROR: ld.so: object '/lib64/libpapi.so.5.2.0.0' from LD_PRELOAD cannot be preloaded: ignored.</font></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</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="monospace"><br></font></div><div dir="ltr"><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Maybe. I'm not 100% sure what you are doing. Can you be clearer about how you are running the ET?</blockquote><div><br></div><div>Sure, as I mentioned in a previous email, my intention is to run and submit the ET in a queue of a remote machine using Simfactory using either PBS or SLURM, as I work in different remote machines from time to time. The key point is that, I notice that while the sim and cactus_sim build is being done, it seems that some lines printed on the shell indicate that when a module is not found in the machine, the ET compiler "builds a bundle" for those modules that weren't found in the compilation from some thorns (examples below showing creation of bundles for GSL and HDF5):</div><div><br></div><div><div><font face="monospace"><br class="gmail-Apple-interchange-newline">********************************************************************************<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></div><div><br></div></div><div>First, these messages about GSL and HDF5 not being found surprise me because both modules are located in the /usr directory and I pointed to them in the configurations file.</div><div><br></div><div>Second. If this build was completed succesfully in the home or login shell of that machine, then I assume I can run and submit simulations with the configuration and runscript files of my machine in PBS or SLURM queues, am I right? If yes then, why I still haven't been capable of doing so? My simulations die within some seconds after being started.</div><div><br></div><div>I include here the optionlist and runscript that I use for a machine that uses PBS as an example.</div><div><br></div><div>Optionlist:</div><div><br></div><div><font face="monospace">VERSION = 2025 #For Einstein Toolkit 2022_11<br><br>CPP = cpp<br>#CC = gcc<br>#CXX = g++<br>CC = mpicc<br>CXX = mpic++<br><br>FPP = cpp<br>#F90 = gfortran<br>F90 = mpif90<br><br>CPPFLAGS = -I/usr/include<br>CPPFLAGS += -DCCTK_VECTOR_DISABLE_TESTS<br>CPPFLAGS = -D__USE_ISOC99<br>PPFLAGS = -D_GLIBCXX_USE_C99_MATH<br><br>LDFLAGS = -L/usr/lib64 -lssl -lcrypto -rdynamic<br><br><br>FPPFLAGS = -traditional<br><br>CFLAGS = -g -std=gnu99<br>CXXFLAGS = -g -std=gnu++11 -fpermissive<br>F90FLAGS = -g -fcray-pointer -ffixed-line-length-none <br><br>DEBUG = no<br>CPP_DEBUG_FLAGS =<br>C_DEBUG_FLAGS =<br>CXX_DEBUG_FLAGS =<br><br>OPTIMISE = yes<br>CPP_OPTIMISE_FLAGS =<br>C_OPTIMISE_FLAGS = -O2<br>CXX_OPTIMISE_FLAGS = -O2<br>F90_OPTIMISE_FLAGS = -O2<br><br>PROFILE = no<br>CPP_PROFILE_FLAGS =<br>C_PROFILE_FLAGS = -pg<br>CXX_PROFILE_FLAGS = -pg<br>F90_PROFILE_FLAGS = -pg<br><br>WARN = yes<br>CPP_WARN_FLAGS = -Wall<br>C_WARN_FLAGS = -Wall<br>CXX_WARN_FLAGS = -Wall<br>F90_WARN_FLAGS = -Wall<br><br>OPENMP = yes<br>CPP_OPENMP_FLAGS = -fopenmp<br>FPP_OPENMP_FLAGS = -D_OPENMP<br>C_OPENMP_FLAGS = -fopenmp<br>CXX_OPENMP_FLAGS = -fopenmp<br>F90_OPENMP_FLAGS = -fopenmp<br><br>VECTORISE = no<br>VECTORISE_ALIGNED_ARRAYS = no<br>VECTORISE_INLINE = yes<br><br>PTHREADS_DIR = NO_BUILD<br><br># Para hallar todas estas opciones, hacemos: ldconfig -p | grep nombredelpaquete<br>MPI_DIR = /software/TEST/local<br># <br><br>LAPACK_DIR = /usr<br>#/usr/lib64/liblapack.so.3<br># lapack-3.4.2-8.el7.x86_64<br><br>BLAS_DIR = /usr<br>#/usr/lib64/libblas.so.3<br># blas-3.4.2-8.el7.x86_64<br><br>HDF5_DIR = /usr<br>#/usr/lib64/libhdf5.so.8<br># hdf5-1.8.12-13.el7.x86_64<br><br>HWLOC_DIR = /usr<br>#/usr/lib64/libhwloc.so.5<br># hwloc-1.11.8-4.el7.x86_64<br><br>JPEG_DIR = /usr<br>#/usr/lib64/libjpeg.so.62<br># <br><br>YAML_DIR = /usr<br>#/usr/lib64/libyaml-0.so.2<br># /usr/lib64/libyaml-0.so.2.0.<br><br>ZLIB_DIR = /usr<br>#/usr/lib64/imlib2/loaders/zlib.so<br># zlib-1.2.7-21.el7_9.x86_64<br><br>GSL_DIR = /usr<br>#/usr/lib64/libgsl.so<br># gsl-1.15-13.el7.x86_64<br><br>FFTW3_DIR = /usr<br>#/usr/lib64/libfftw3.so<br># fftw-3.3.3-8.el7.x86_64<br><br>PAPI_DIR = /usr<br>#/usr/lib64/libpapi.so.5.2.0.0<br># papi-5.2.0-26.el7.x86_64<br><br>XML2_DIR = /usr<br>#/usr/lib64/libxml2.so.2<br># xml2-0.5-7.el7.x86_64<br><br>NUMA_DIR = /usr<br>#/usr/lib64/libnuma.so.1<br><br>OPENSSL_DIR = /usr<br>#/usr/lib64/libssl3.so<br># openssl-1.0.2k-26.el7_9.x86_64</font></div><div><font face="monospace"><br></font></div><div><br></div><div>Runscript:</div><div><br></div><div><font face="monospace">#!/bin/bash<br><br>set -x<br>set -e<br><br>cd @SIMULATION_DIR@<br><br># Environment setup<br>source /opt/rh/devtoolset-8/enable<br><br>module purge<br>module load lamod/cmake/3.17<br>module load lamod/fftw/gnu/3.3.8<br>module load lamod/openmpi/gnu/4.1.0<br>module load libraries/gsl/2.6_gnu<br>module load libraries/hdf5/1.10.5_gnu<br><br>echo "Environment diagnostics:"<br>date<br>hostname<br>env<br>ldd @EXECUTABLE@ | grep -E "lapack|blas|openssl|stdc++|gfortran"<br><br># Set runtime parameters<br>export CACTUS_NUM_PROCS=64<br>export CACTUS_NUM_THREADS=1<br>export OMP_NUM_THREADS=1<br>export GMON_OUT_PREFIX=gmon.out<br>env | sort > SIMFACTORY/ENVIRONMENT<br><br>echo "Starting simulation at $(date)"<br>export CACTUS_STARTTIME=$(date +%s)<br><br>mpirun -np $CACTUS_NUM_PROCS -x LD_LIBRARY_PATH @EXECUTABLE@ -L 3 @PARFILE@<br><br>echo "Simulation finished at $(date)"<br>touch segment.done</font></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><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">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"><u></u>
<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">
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<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">
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<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>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
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