Hello, Today I installed firedrake on an ubuntu machine and that seemed to go well but then, when I tried to do an update, it had a core dump. I am including the output below. Any idea what is going wrong? Francis ------------------ Francis Poulin Professor Department of Applied Mathematics University of Waterloo email: fpoulin@uwaterloo.ca Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637 [X] (firedrake) mmstastn@boogaloo:~/software$ firedrake-update Running /home/mmstastn/software/firedrake/bin/firedrake-update Updating the git repository for firedrake Creating firedrake-update script. Running ../bin/firedrake-update --no-update-script Checking for presence of package build-essential... installed. Checking for presence of package autoconf... installed. Checking for presence of package automake... installed. Checking for presence of package cmake... installed. Checking for presence of package gfortran... installed. Checking for presence of package git... installed. Checking for presence of package libblas-dev... installed. Checking for presence of package liblapack-dev... installed. Checking for presence of package libmpich-dev... installed. Checking for presence of package libtool... installed. Checking for presence of package mercurial... installed. Checking for presence of package mpich... installed. Checking for presence of package python3-dev... installed. Checking for presence of package python3-pip... installed. Checking for presence of package python3-tk... installed. Checking for presence of package python3-venv... installed. Checking for presence of package zlib1g-dev... installed. Checking for presence of package libboost-dev... installed. Finding dependencies of PyOP2 Finding dependencies of firedrake Finding dependencies of gusto Updating the git repository for petsc Updating the git repository for petsc4py Updating the git repository for COFFEE Updating the git repository for loopy Updating the git repository for ufl Updating the git repository for fiat Updating the git repository for FInAT Updating the git repository for tsfc Updating the git repository for PyOP2 Updating the git repository for gusto Updating the git repository for firedrake Installing pip dependencies for COFFEE Installing pip dependencies for loopy Installing pip dependencies for ufl No dependencies found. Skipping. Installing pip dependencies for fiat No dependencies found. Skipping. Installing pip dependencies for FInAT Installing pip dependencies for tsfc Installing pip dependencies for PyOP2 Installing pip dependencies for gusto Installing pip dependencies for firedrake Installing h5py Updating the git repository for h5py No need to rebuild h5py Installing libspatialindex Updating the git repository for libspatialindex No need to rebuild libspatialindex Installing libsupermesh Updating the git repository for libsupermesh No need to rebuild libsupermesh Cleaning loopy Installing loopy/ Cleaning COFFEE Installing COFFEE/ Cleaning ufl Installing ufl/ Cleaning fiat Installing fiat/ Cleaning FInAT Installing FInAT/ Cleaning tsfc Installing tsfc/ Cleaning gusto Installing gusto/ Cleaning PyOP2 Installing PyOP2/ Cleaning firedrake Installing firedrake/ Configuration saved to configuration.json Clearing just in time compilation caches. Warning! ***HDF5 library version mismatched error*** The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this application is linked. Data corruption or segmentation faults may occur if the application continues. This can happen when an application was compiled by one version of HDF5 but linked with a different version of static or shared HDF5 library. You should recompile the application or check your shared library related settings such as 'LD_LIBRARY_PATH'. You can, at your own risk, disable this warning by setting the environment variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. Setting it to 2 or higher will suppress the warning messages totally. Headers are 1.8.18, library is 1.8.17 SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ------------------- HDF5 Version: 1.8.17 Configured on: Wed Sep 7 15:12:54 EDT 2016 Configured by: root@boogaloo Configure mode: production Host system: x86_64-unknown-linux-gnu Uname information: Linux boogaloo 3.13.0-95-generic #142-Ubuntu SMP Fri Aug 12 17:00:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Byte sex: little-endian Libraries: static, shared Installation point: /opt/hdf5-1.8.17/hdf5 Compiling Options: ------------------ Compilation Mode: production C Compiler: /usr/bin/mpicc ( Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.4-2ubuntu1~14.04.3' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-libmudflap --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu built with gcc version 4.8.4 (Ubuntu 4.8.4-2ubuntu1~14.04.3)) CFLAGS: H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -O3 AM_CFLAGS: CPPFLAGS: H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: -I/opt/zlib-1.2.8/zlib//include Shared C Library: yes Static C Library: yes Statically Linked Executables: no LDFLAGS: H5_LDFLAGS: AM_LDFLAGS: -L/opt/zlib-1.2.8/zlib//lib Extra libraries: -lz -ldl -lm Archiver: ar Ranlib: ranlib Debugged Packages: API Tracing: no Languages: ---------- Fortran: no C++: no Features: --------- Parallel HDF5: yes High Level library: yes Threadsafety: no Default API Mapping: v18 With Deprecated Public Symbols: yes I/O filters (external): deflate(zlib) MPE: Direct VFD: no dmalloc: no Clear file buffers before write: yes Using memory checker: no Function Stack Tracing: no Strict File Format Checks: no Optimization Instrumentation: no Bye... [boogaloo:04465] *** Process received signal *** [boogaloo:04465] Signal: Aborted (6) [boogaloo:04465] Signal code: (-6) [boogaloo:04465] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x7f35a1a35390] [boogaloo:04465] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x38)[0x7f35a168f428] [boogaloo:04465] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x16a)[0x7f35a169102a] [boogaloo:04465] [ 3] /opt/hdf5-1.8.17/hdf5/lib/libhdf5.so.10(H5check_version+0x280)[0x7f359c97b180] [boogaloo:04465] [ 4] /home/mmstastn/software/firedrake/src/h5py/h5py/h5f.cpython-35m-x86_64-linux-gnu.so(+0x84a5)[0x7f358dc6b4a5] [boogaloo:04465] [ 5] /home/mmstastn/software/firedrake/bin/python3(PyModule_ExecDef+0x85)[0x62a305] [boogaloo:04465] [ 6] /home/mmstastn/software/firedrake/bin/python3[0x523d91] [boogaloo:04465] [ 7] /home/mmstastn/software/firedrake/bin/python3(PyCFunction_Call+0xa4)[0x4e9bd4] [boogaloo:04465] [ 8] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalFrameEx+0x6edb)[0x53dbbb] [boogaloo:04465] [ 9] /home/mmstastn/software/firedrake/bin/python3[0x540199] [boogaloo:04465] [10] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalFrameEx+0x54f0)[0x53c1d0] [boogaloo:04465] [11] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalFrameEx+0x4b04)[0x53b7e4] [boogaloo:04465] [12] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalFrameEx+0x4b04)[0x53b7e4] [boogaloo:04465] [13] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalFrameEx+0x4b04)[0x53b7e4] [boogaloo:04465] [14] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalCodeEx+0x13b)[0x540f9b] [boogaloo:04465] [15] /home/mmstastn/software/firedrake/bin/python3[0x4ebd23] [boogaloo:04465] [16] /home/mmstastn/software/firedrake/bin/python3(PyObject_Call+0x47)[0x5c1797] [boogaloo:04465] [17] /home/mmstastn/software/firedrake/bin/python3(_PyObject_CallMethodIdObjArgs+0x17a)[0x5c257a] [boogaloo:04465] [18] /home/mmstastn/software/firedrake/bin/python3(PyImport_ImportModuleLevelObject+0x778)[0x5260c8] [boogaloo:04465] [19] /home/mmstastn/software/firedrake/bin/python3[0x549e78] [boogaloo:04465] [20] /home/mmstastn/software/firedrake/bin/python3(PyCFunction_Call+0x77)[0x4e9ba7] [boogaloo:04465] [21] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalFrameEx+0x6edb)[0x53dbbb] [boogaloo:04465] [22] /home/mmstastn/software/firedrake/bin/python3[0x540199] [boogaloo:04465] [23] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalFrameEx+0x54f0)[0x53c1d0] [boogaloo:04465] [24] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalCodeEx+0x13b)[0x540f9b] [boogaloo:04465] [25] /home/mmstastn/software/firedrake/bin/python3[0x4ebd23] [boogaloo:04465] [26] /home/mmstastn/software/firedrake/bin/python3(PyObject_Call+0x47)[0x5c1797] [boogaloo:04465] [27] /home/mmstastn/software/firedrake/bin/python3(_PyObject_CallMethodIdObjArgs+0x17a)[0x5c257a] [boogaloo:04465] [28] /home/mmstastn/software/firedrake/bin/python3(PyImport_ImportModuleLevelObject+0x746)[0x526096] [boogaloo:04465] [29] /home/mmstastn/software/firedrake/bin/python3[0x549e78] [boogaloo:04465] *** End of error message *** Aborted (core dumped) ------------------ Francis Poulin Professor Department of Applied Mathematics University of Waterloo email: fpoulin@uwaterloo.ca Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637 [X]