[Users] Errors when submitting runs in remote machine
Omar Elías Velasco Castillo
oevelasco at astro.unam.mx
Thu Oct 2 14:10:04 CDT 2025
Hello,
This is a followup for retaking my questions about my failing to submit and
run simulations in a remote cluster.
Can you show us what the error message(s) are?
Yes, the tail of my err file reads:
+ set -
ERROR: ld.so: object '/lib64/libpapi.so.5.2.0.0' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object '/lib64/libpapi.so.5.2.0.0' from LD_PRELOAD cannot be
preloaded: ignored.
--------------------------------------------------------------------------
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
Maybe. I'm not 100% sure what you are doing. Can you be clearer about how
> you are running the ET?
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):
********************************************************************************
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.
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.
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.
I include here the optionlist and runscript that I use for a machine that
uses PBS as an example.
Optionlist:
VERSION = 2025 #For Einstein Toolkit 2022_11
CPP = cpp
#CC = gcc
#CXX = g++
CC = mpicc
CXX = mpic++
FPP = cpp
#F90 = gfortran
F90 = mpif90
CPPFLAGS = -I/usr/include
CPPFLAGS += -DCCTK_VECTOR_DISABLE_TESTS
CPPFLAGS = -D__USE_ISOC99
PPFLAGS = -D_GLIBCXX_USE_C99_MATH
LDFLAGS = -L/usr/lib64 -lssl -lcrypto -rdynamic
FPPFLAGS = -traditional
CFLAGS = -g -std=gnu99
CXXFLAGS = -g -std=gnu++11 -fpermissive
F90FLAGS = -g -fcray-pointer -ffixed-line-length-none
DEBUG = no
CPP_DEBUG_FLAGS =
C_DEBUG_FLAGS =
CXX_DEBUG_FLAGS =
OPTIMISE = yes
CPP_OPTIMISE_FLAGS =
C_OPTIMISE_FLAGS = -O2
CXX_OPTIMISE_FLAGS = -O2
F90_OPTIMISE_FLAGS = -O2
PROFILE = no
CPP_PROFILE_FLAGS =
C_PROFILE_FLAGS = -pg
CXX_PROFILE_FLAGS = -pg
F90_PROFILE_FLAGS = -pg
WARN = yes
CPP_WARN_FLAGS = -Wall
C_WARN_FLAGS = -Wall
CXX_WARN_FLAGS = -Wall
F90_WARN_FLAGS = -Wall
OPENMP = yes
CPP_OPENMP_FLAGS = -fopenmp
FPP_OPENMP_FLAGS = -D_OPENMP
C_OPENMP_FLAGS = -fopenmp
CXX_OPENMP_FLAGS = -fopenmp
F90_OPENMP_FLAGS = -fopenmp
VECTORISE = no
VECTORISE_ALIGNED_ARRAYS = no
VECTORISE_INLINE = yes
PTHREADS_DIR = NO_BUILD
# Para hallar todas estas opciones, hacemos: ldconfig -p | grep
nombredelpaquete
MPI_DIR = /software/TEST/local
#
LAPACK_DIR = /usr
#/usr/lib64/liblapack.so.3
# lapack-3.4.2-8.el7.x86_64
BLAS_DIR = /usr
#/usr/lib64/libblas.so.3
# blas-3.4.2-8.el7.x86_64
HDF5_DIR = /usr
#/usr/lib64/libhdf5.so.8
# hdf5-1.8.12-13.el7.x86_64
HWLOC_DIR = /usr
#/usr/lib64/libhwloc.so.5
# hwloc-1.11.8-4.el7.x86_64
JPEG_DIR = /usr
#/usr/lib64/libjpeg.so.62
#
YAML_DIR = /usr
#/usr/lib64/libyaml-0.so.2
# /usr/lib64/libyaml-0.so.2.0.
ZLIB_DIR = /usr
#/usr/lib64/imlib2/loaders/zlib.so
# zlib-1.2.7-21.el7_9.x86_64
GSL_DIR = /usr
#/usr/lib64/libgsl.so
# gsl-1.15-13.el7.x86_64
FFTW3_DIR = /usr
#/usr/lib64/libfftw3.so
# fftw-3.3.3-8.el7.x86_64
PAPI_DIR = /usr
#/usr/lib64/libpapi.so.5.2.0.0
# papi-5.2.0-26.el7.x86_64
XML2_DIR = /usr
#/usr/lib64/libxml2.so.2
# xml2-0.5-7.el7.x86_64
NUMA_DIR = /usr
#/usr/lib64/libnuma.so.1
OPENSSL_DIR = /usr
#/usr/lib64/libssl3.so
# openssl-1.0.2k-26.el7_9.x86_64
Runscript:
#!/bin/bash
set -x
set -e
cd @SIMULATION_DIR@
# Environment setup
source /opt/rh/devtoolset-8/enable
module purge
module load lamod/cmake/3.17
module load lamod/fftw/gnu/3.3.8
module load lamod/openmpi/gnu/4.1.0
module load libraries/gsl/2.6_gnu
module load libraries/hdf5/1.10.5_gnu
echo "Environment diagnostics:"
date
hostname
env
ldd @EXECUTABLE@ | grep -E "lapack|blas|openssl|stdc++|gfortran"
# Set runtime parameters
export CACTUS_NUM_PROCS=64
export CACTUS_NUM_THREADS=1
export OMP_NUM_THREADS=1
export GMON_OUT_PREFIX=gmon.out
env | sort > SIMFACTORY/ENVIRONMENT
echo "Starting simulation at $(date)"
export CACTUS_STARTTIME=$(date +%s)
mpirun -np $CACTUS_NUM_PROCS -x LD_LIBRARY_PATH @EXECUTABLE@ -L 3 @PARFILE@
echo "Simulation finished at $(date)"
touch segment.done
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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