(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)