[Users] segfault on ubuntu 14.10
Jonah Miller
jonah.maxwell.miller at gmail.com
Sat Jan 24 15:41:09 CST 2015
Hello everyone,
I recently switched from using Debian stable to Ubuntu 14.10 on my
development laptop, and I'm now having trouble getting the Einstein
Toolkit to run. It compiles fine, but even the simplest simulations
segfault consistently. Does anyone have any advice on how to approach
debugging this? I've attached the error output from my attempt to run
the example static tov star in the simplified tutorial for new users
(https://docs.einsteintoolkit.org/et-docs/Simplified_Tutorial_for_New_Users)
as well as the two sets of build options that I've tried using (the
first, ubuntu.cfg, is the default, the second, yugoth.cfg, is a set of
options that I've used successfully in the past).
I know your time is precious and I appreciate any that you can spare.
Thanks in advance!
Best,
Jonah Miller
-------------- next part --------------
+ set -e
+ cd /home/jmiller/simulations/static_tov/output-0000-active
+ echo Checking:
+ pwd
+ hostname
+ date
+ echo Environment:
+ export GMON_OUT_PREFIX=gmon.out
+ GMON_OUT_PREFIX=gmon.out
+ export OMP_NUM_THREADS=2
+ OMP_NUM_THREADS=2
+ env
+ echo Starting:
++ date +%s
+ export CACTUS_STARTTIME=1422134550
+ CACTUS_STARTTIME=1422134550
+ mpirun -np 1 /home/jmiller/simulations/static_tov/SIMFACTORY/exe/cactus_sim -L 3 /home/jmiller/simulations/static_tov/output-0000/static_tov.par
[yugoth:18209] *** Process received signal ***
[yugoth:18209] Signal: Segmentation fault (11)
[yugoth:18209] Signal code: Address not mapped (1)
[yugoth:18209] Failing at address: 0x44000098
[yugoth:18209] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7f767f7ee340]
[yugoth:18209] [ 1] /usr/lib/libmpich.so.10(PMPI_Comm_rank+0x4b) [0x7f767db8b63b]
[yugoth:18209] [ 2] /home/jmiller/simulations/static_tov/SIMFACTORY/exe/cactus_sim(CactusDefaultMyProc+0x6f) [0xcfa38f]
[yugoth:18209] [ 3] /home/jmiller/simulations/static_tov/SIMFACTORY/exe/cactus_sim(CCTKi_CommandLineFinished+0x42) [0xce71e2]
[yugoth:18209] [ 4] /home/jmiller/simulations/static_tov/SIMFACTORY/exe/cactus_sim(CCTKi_ProcessCommandLine+0x20c) [0xcd2a9c]
[yugoth:18209] [ 5] /home/jmiller/simulations/static_tov/SIMFACTORY/exe/cactus_sim(CCTKi_InitialiseCactus+0x3c) [0xccfc3c]
[yugoth:18209] [ 6] /home/jmiller/simulations/static_tov/SIMFACTORY/exe/cactus_sim(main+0x1e) [0xcc76be]
[yugoth:18209] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f767c8fdec5]
[yugoth:18209] [ 8] /home/jmiller/simulations/static_tov/SIMFACTORY/exe/cactus_sim() [0xccf98c]
[yugoth:18209] *** End of error message ***
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# Configuration for an Ubuntu installation, assuming the following
# list of packages is installed:
#
# build-essential perl gfortran g++ libmpich2-dev
#
# In addition, installing the following list of packaed will prevent
# Cactus from compiling its own versions of these libraries:
#
# libfftw3-dev libgsl0-dev libatlas-base-dev libjpeg-dev libssl-dev libhdf5-serial-dev hdf5-tools
#
# Tools like GetComponents and Simfactory like to have the following list
# installed too
#
# python subversion git
# Whenever this version string changes, the application is configured
# and rebuilt from scratch
VERSION = 2012-09-28
CPP = cpp
FPP = cpp
CC = gcc
CXX = g++
F77 = gfortran
F90 = gfortran
CPPFLAGS = -DMPICH_IGNORE_CXX_SEEK
FPPFLAGS = -traditional
CFLAGS = -g3 -march=native -std=gnu99
CXXFLAGS = -g3 -march=native -std=gnu++0x
F77FLAGS = -g3 -march=native -fcray-pointer -m128bit-long-double -ffixed-line-length-none
F90FLAGS = -g3 -march=native -fcray-pointer -m128bit-long-double -ffixed-line-length-none
LDFLAGS = -rdynamic
LIBDIRS =
C_LINE_DIRECTIVES = yes
F_LINE_DIRECTIVES = yes
DEBUG = no
CPP_DEBUG_FLAGS = -DCARPET_DEBUG
FPP_DEBUG_FLAGS = -DCARPET_DEBUG
C_DEBUG_FLAGS = -O0
CXX_DEBUG_FLAGS = -O0
F77_DEBUG_FLAGS = -O0
F90_DEBUG_FLAGS = -O0
OPTIMISE = yes
CPP_OPTIMISE_FLAGS = -DKRANC_VECTORS # -DCARPET_OPTIMISE -DNDEBUG
FPP_OPTIMISE_FLAGS = # -DCARPET_OPTIMISE -DNDEBUG
C_OPTIMISE_FLAGS = -O2 -ffast-math
CXX_OPTIMISE_FLAGS = -O2 -ffast-math
F77_OPTIMISE_FLAGS = -O2 -ffast-math
F90_OPTIMISE_FLAGS = -O2 -ffast-math
PROFILE = no
CPP_PROFILE_FLAGS =
FPP_PROFILE_FLAGS =
C_PROFILE_FLAGS = -pg
CXX_PROFILE_FLAGS = -pg
F77_PROFILE_FLAGS = -pg
F90_PROFILE_FLAGS = -pg
OPENMP = yes
CPP_OPENMP_FLAGS = -fopenmp
FPP_OPENMP_FLAGS = -fopenmp
C_OPENMP_FLAGS = -fopenmp
CXX_OPENMP_FLAGS = -fopenmp
F77_OPENMP_FLAGS = -fopenmp
F90_OPENMP_FLAGS = -fopenmp
WARN = yes
CPP_WARN_FLAGS = -Wall
FPP_WARN_FLAGS = -Wall
C_WARN_FLAGS = -Wall
CXX_WARN_FLAGS = -Wall
F77_WARN_FLAGS = -Wall
F90_WARN_FLAGS = -Wall
# Ubuntu's libhwloc-dev is broken; see
# <https://trac.einsteintoolkit.org/ticket/1717>
HWLOC_DIR = BUILD
MPI_DIR = /usr
# Ubuntu < 14.04 uses mpich2, >= 14.04 uses mpich
MPI_INC_DIRS = /usr/include/mpich #/usr/include/mpich2 /usr/include/mpich
MPI_LIB_DIRS = /usr/lib
MPI_LIBS = mpich fmpich mpl
PTHREADS = no
-------------- next part --------------
# Whenever this version string changes, the application is configured
# and rebuilt from scratch
VERSION = yugoth-2014-01-24
CPP = cpp
FPP = cpp
CC = gcc
CXX = g++
F77 = gfortran
F90 = gfortran
CPPFLAGS = -DOMPI_SKIP_MPICXX
FPPFLAGS = -traditional
CFLAGS = -g3 -m128bit-long-double -march=native -std=gnu99
CXXFLAGS = -g3 -m128bit-long-double -march=native -std=gnu++0x
F77FLAGS = -g3 -m128bit-long-double -march=native -fcray-pointer -ffixed-line-length-none
F90FLAGS = -g3 -m128bit-long-double -march=native -fcray-pointer -ffixed-line-length-none
LDFLAGS = -rdynamic -lgfortran
C_LINE_DIRECTIVES = yes
F_LINE_DIRECTIVES = yes
VECTORISE = yes
VECTORISE_ALIGNED_ARRAYS = no
VECTORISE_INLINE = no
DEBUG = no
CPP_DEBUG_FLAGS = -DCARPET_DEBUG
FPP_DEBUG_FLAGS = -DCARPET_DEBUG
C_DEBUG_FLAGS = -fbounds-check -fstack-protector-all -ftrapv
CXX_DEBUG_FLAGS = -fbounds-check -fstack-protector-all -ftrapv
F77_DEBUG_FLAGS = -fcheck=bounds,do,mem,pointer,recursion -finit-character=65 -finit-integer=42424242 -finit-real=nan -fstack-protector-all -ftrapv -fwhole-file
F90_DEBUG_FLAGS = -fcheck=bounds,do,mem,pointer,recursion -finit-character=65 -finit-integer=42424242 -finit-real=nan -fstack-protector-all -ftrapv -fwhole-file
OPTIMISE = yes
CPP_OPTIMISE_FLAGS = # -DCARPET_OPTIMISE -DNDEBUG
FPP_OPTIMISE_FLAGS = # -DCARPET_OPTIMISE -DNDEBUG
C_OPTIMISE_FLAGS = -Ofast -funsafe-loop-optimizations
CXX_OPTIMISE_FLAGS = -Ofast -funsafe-loop-optimizations
F77_OPTIMISE_FLAGS = -Ofast -funsafe-loop-optimizations
F90_OPTIMISE_FLAGS = -Ofast -funsafe-loop-optimizations
PROFILE = no
CPP_PROFILE_FLAGS =
FPP_PROFILE_FLAGS =
C_PROFILE_FLAGS = -pg
CXX_PROFILE_FLAGS = -pg
F77_PROFILE_FLAGS = -pg
F90_PROFILE_FLAGS = -pg
OPENMP = yes
CPP_OPENMP_FLAGS = -fopenmp
FPP_OPENMP_FLAGS = -fopenmp
C_OPENMP_FLAGS = -fopenmp
CXX_OPENMP_FLAGS = -fopenmp
F77_OPENMP_FLAGS = -fopenmp
F90_OPENMP_FLAGS = -fopenmp
# -Wuninitialized is not supported without -O
WARN = yes
CPP_WARN_FLAGS = -Wall
FPP_WARN_FLAGS = -Wall
C_WARN_FLAGS = -Wall -Wunsafe-loop-optimizations -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wstrict-prototypes -Wmissing-declarations -Wbad-function-cast -Wsign-compare
CXX_WARN_FLAGS = -Wall -Wunsafe-loop-optimizations -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Woverloaded-virtual
F77_WARN_FLAGS = -Wall -Wunsafe-loop-optimizations -Wshadow -Wsurprising
F90_WARN_FLAGS = -Wall -Wunsafe-loop-optimizations -Wshadow -Wsurprising
HDF5_DIR = BUILD
HWLOC_DIR = BUILD
## AMD (not a very good optimiser)
#OPENCL_INC_DIRS = /usr/local/AMD-APP-SDK-v2.4-lnx64/include
#OPENCL_LIB_DIRS = /usr/local/AMD-APP-SDK-v2.4-lnx64/lib/x86_64
#OPENCL_LIBS = OpenCL
# Intel
OPENCL_DIR = /usr/local/intel_ocl_sdk_2012_x64/usr
OPENCL_INC_DIRS = /usr/local/intel_ocl_sdk_2012_x64/usr/include
OPENCL_LIB_DIRS = /usr/local/intel_ocl_sdk_2012_x64/usr/lib64
OPENCL_LIBS = OpenCL
## NVidia (not properly installed):
#OPENCL_INC_DIRS = /usr/local/cuda/include
#OPENCL_LIB_DIRS =
#OPENCL_LIBS = OpenCL
#PETSC_ARCH = linux-gnu-c-opt
#PETSC_ARCH_LIBS = mpi
PETSC_DIR = BUILD
PTHREADS = yes
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