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gwenchee/gist:c234bcff5a1810f75aa096bbba1cdea2

Created October 4, 2019 20:43
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pyne install error
Raw
gistfile1.txt
(base) arfc@arfc-VirtualBox:~/github/pyne$ python setup.py install --user
atomic_data.h generated is the same as existing file, skipping.
atomic_data.cpp generated is the same as existing file, skipping.
/home/arfc/anaconda3/bin/cmake
CMake command is
cmake .. -DCMAKE_INSTALL_PREFIX=/home/arfc/.local -DPYTHON_EXECUTABLE=/home/arfc/anaconda3/bin/python
/ \
) (( )) (
(@) /|\ ))_(( /|\
|-| / | \ (/\|/\) / | \ (@)
| | -------------------/--|-voV---\`|'/--Vov-|--\---------------------|-|
|-| '^` (o o) '^` | |
| | `\Y/' |-|
|-| | |
| | /\ ___ __ __ /\ |-|
|-| /^~\ / _ \_ _ /\ \ \/__\ /^~\ | |
| | /^~\ / /_)/ | | |/ \/ /_\ /^~\ |-|
|-| /^~\ / ___/| |_| / /\ //__ /^~\ | |
| | ^||` \/ \__, \_\ \/\__/ ^||` |-|
|-| || |____/ || | |
| | ==== ==== |-|
|-| | |
| | |-|
|-|___________________________________________________________________| |
(@) l /\ / ( ( \ /\ l `\|-|
l / V \ \ V \ l (@)
l/ _) )_ \I
`\ /'
`
-- Pyne platform defined as: __LINUX__
-- Build type: Release
-- PyNE Fast Compile: TRUE
-- CMAKE_INSTALL_RPATH: /home/arfc/.local/lib:/home/arfc/anaconda3/lib
-- CMake Install Prefix: /home/arfc/.local
-- Dependency Root Dir (DEPS_ROOT_DIR): /home/arfc/anaconda3
-- Dependency Hints (DEPS_HINTS): HINTS;/home/arfc/anaconda3
-- Dependency Binary Hints (DEPS_BIN_HINTS): HINTS;/home/arfc/anaconda3;/home/arfc/anaconda3/bin
-- Dependency Library Hints (DEPS_LIB_HINTS): HINTS;/home/arfc/anaconda3;/home/arfc/anaconda3/lib
-- Dependency Include Hints (DEPS_INCLUDE_HINTS): HINTS;/home/arfc/anaconda3/include
-- HDF5 Root:
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- HDF5 Include directory: /home/arfc/anaconda3/include
-- HDF5 Library directories:
-- HDF5 Libraries: /home/arfc/anaconda3/lib/libhdf5.so;rt;pthread;/home/arfc/anaconda3/lib/libz.so;dl;m
-- PYTHON_EXECUTABLE: /home/arfc/anaconda3/bin/python
-- PYTHON_SITE_PACKAGES: /home/arfc/.local/lib/python3.6/site-packages
-- NUMPY_VERSION_STRING = 1.17.2
-- The Fortran compiler identification is GNU 7.3.0
-- Check for working Fortran compiler: /home/arfc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-gfortran
-- Check for working Fortran compiler: /home/arfc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-gfortran -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /home/arfc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-gfortran supports Fortran 90
-- Checking whether /home/arfc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-gfortran supports Fortran 90 -- yes
-- CMAKE_Fortran_IMPLICIT_LINK_DIRECTORIES: /home/arfc/anaconda3/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0;/home/arfc/anaconda3/lib/gcc;/home/arfc/anaconda3/x86_64-conda_cos6-linux-gnu/lib;/home/arfc/anaconda3/x86_64-conda_cos6-linux-gnu/sysroot/lib;/home/arfc/anaconda3/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib
-- CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES: gfortran;m;gcc_s;gcc;quadmath;m;gcc_s;gcc;c;gcc_s;gcc
-- NUMPY_VERSION_STRING = 1.17.2
-- Found F2py: /home/arfc/anaconda3/bin/f2py
-- F2PY Executable: /home/arfc/anaconda3/bin/f2py
-- F2PY Version: 2
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - not found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- Found BLAS: /home/arfc/anaconda3/lib/libmkl_gf_lp64.so;/home/arfc/anaconda3/lib/libmkl_gnu_thread.so;/home/arfc/anaconda3/lib/libmkl_core.so;/home/arfc/anaconda3/lib/libgomp.so;-lpthread;-lm;-ldl
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
-- Found LAPACK Linker Flags:
-- Found LAPACK Libraries: /home/arfc/anaconda3/lib/libmkl_gf_lp64.so;/home/arfc/anaconda3/lib/libmkl_gnu_thread.so;/home/arfc/anaconda3/lib/libmkl_core.so;/home/arfc/anaconda3/lib/libgomp.so;-lpthread;-lm;-ldl
-- Found BLAS Libraries: /home/arfc/anaconda3/lib/libmkl_gf_lp64.so;/home/arfc/anaconda3/lib/libmkl_gnu_thread.so;/home/arfc/anaconda3/lib/libmkl_core.so;/home/arfc/anaconda3/lib/libgomp.so;-lpthread;-lm;-ldl
-- Found Cython: /home/arfc/anaconda3/bin/cython
-- LIBS: /home/arfc/anaconda3/lib/libhdf5.so;rt;pthread;/home/arfc/anaconda3/lib/libz.so;dl;m;/home/arfc/anaconda3/lib/libpython3.6m.so
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-- Extracting cram-linux-gnu.tar.gz
x cram-linux-gnu.s
-- Compiling decay.cpp fast from assembly decay-linux-gnu.s
-- Compiling cram.c fast from assembly cram-linux-gnu.s
-- Include paths for /home/arfc/github/pyne/src: /home/arfc/anaconda3/include;/home/arfc/anaconda3/lib/python3.6/site-packages/numpy/core/include;/home/arfc/github/pyne/build/pyne;/home/arfc/github/pyne/src
-- Include paths for /home/arfc/github/pyne/pyne: /home/arfc/anaconda3/include;/home/arfc/anaconda3/lib/python3.6/site-packages/numpy/core/include;/home/arfc/github/pyne/build/pyne;/home/arfc/github/pyne/src
-- Modules to Cythonize: ace;bins;data;dtypes;endf;enrichment;extra_types;jsoncpp;material;nucname;particle;pyne_config;rxname;stlcontainers;tally;transmuters;_utils
-- F2PY F90 FLAGS:
-- Include paths for /home/arfc/github/pyne/pyne/xs: /home/arfc/anaconda3/include;/home/arfc/anaconda3/lib/python3.6/site-packages/numpy/core/include;/home/arfc/github/pyne/build/pyne;/home/arfc/github/pyne/src
-- Configuring done
-- Generating done
-- Build files have been written to: /home/arfc/github/pyne/build
Scanning dependencies of target ReplicatePythonSourceTree
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/home/arfc/github/pyne/src/ensdf_processing/HSICC/hsicc.for:1683:17:
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/home/arfc/github/pyne/src/ensdf_processing/HSICC/hsicc.for:1683:17:
COMMON /C2/ E1, E2, NS, L, N, ALPHA, NP, EE 07 00060
1
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/home/arfc/github/pyne/src/ensdf_processing/HSICC/hsicc.for:188:20:
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x86_64-conda_cos6-linux-gnu-gfortran.bin: warning: CMakeFiles/hsicc.dir/ensdf_processing/HSICC/hsicc.for.o: linker input file unused because linking not done
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building extension "transport_spatial_methods" sources
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creating /tmp/tmp0yuvedna/src.linux-x86_64-3.6
Reading fortran codes...
Reading file '/home/arfc/github/pyne/src/transport_spatial_methods/3d/main.f90' (format:free)
Post-processing...
Block: transport_spatial_methods
Block: main
In: :transport_spatial_methods:/home/arfc/github/pyne/src/transport_spatial_methods/3d/main.f90:main
get_useparameters: no module invar info used by main
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get_useparameters: no module precision_module info used by main
Post-processing (stage 2)...
Building modules...
Building module "transport_spatial_methods"...
Creating wrapper for Fortran subroutine "main"("main")...
Constructing wrapper function "main"...
qdfile,xsfile,srcfile,mtfile,inflow_file,phi_file,fluxout,error_code_out,tsolve_out,ttosolve_out,tend_out = main(titlein,solver_in,solver_type_in,spatial_order_in,angular_quadrature_order_in,qdtypin,nodes_x_in,nodes_y_in,nodes_z_in,num_groups_in,num_materials_in,x_cell_widths_in,y_cell_widths_in,z_cell_widths_in,x_boundry_condition_1_in,x_boundry_condition_2_in,y_boundry_condition_1_in,y_boundry_condition_2_in,z_boundry_condition_1_in,z_boundry_condition_2_in,material_id_in,quadrature_file,xs_file_in,source_input_file_in,bc_input_filein,flux_output_filein,convergence_criterion_in,itmxin,moments_converged_in,converge_tolerence_in,max_mom_printed_in,moment_sum_flag_in,mom_at_a_pt_flag_in,quad_flux_print_flag_in)
Wrote C/API module "transport_spatial_methods" to file "/tmp/tmp0yuvedna/src.linux-x86_64-3.6/transport_spatial_methodsmodule.c"
Fortran 77 wrappers are saved to "/tmp/tmp0yuvedna/src.linux-x86_64-3.6/transport_spatial_methods-f2pywrappers.f"
adding '/tmp/tmp0yuvedna/src.linux-x86_64-3.6/fortranobject.c' to sources.
adding '/tmp/tmp0yuvedna/src.linux-x86_64-3.6' to include_dirs.
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adding '/tmp/tmp0yuvedna/src.linux-x86_64-3.6/transport_spatial_methods-f2pywrappers.f' to sources.
build_src: building npy-pkg config files
running build_ext
customize UnixCCompiler
C compiler: /home/arfc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC
creating /tmp/tmp3gjbk7_y/tmp
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x86_64-conda_cos6-linux-gnu-cc: /tmp/tmp3gjbk7_y/file.c
customize UnixCCompiler using build_ext
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Found executable /home/arfc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-gfortran
Found executable /home/arfc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-ld
Found executable /home/arfc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-ar
Found executable /home/arfc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-ranlib
/home/arfc/anaconda3/lib/python3.6/site-packages/numpy/distutils/fcompiler/__init__.py:517: UserWarning: FFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
fflags = self.flag_vars.flags + dflags + oflags + aflags
/home/arfc/anaconda3/lib/python3.6/site-packages/numpy/distutils/fcompiler/__init__.py:530: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
linker_so_flags = self.flag_vars.linker_so
/home/arfc/anaconda3/lib/python3.6/site-packages/numpy/distutils/fcompiler/__init__.py:540: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
linker_exe_flags = self.flag_vars.linker_exe
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'transport_spatial_methods' extension
compiling C sources
C compiler: /home/arfc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC
creating /tmp/tmp0yuvedna/tmp
creating /tmp/tmp0yuvedna/tmp/tmp0yuvedna
creating /tmp/tmp0yuvedna/tmp/tmp0yuvedna/src.linux-x86_64-3.6
compile options: '-I/home/arfc/github/pyne/build/src -I/tmp/tmp0yuvedna/src.linux-x86_64-3.6 -I/home/arfc/anaconda3/lib/python3.6/site-packages/numpy/core/include -I/home/arfc/anaconda3/include/python3.6m -c'
x86_64-conda_cos6-linux-gnu-cc: /tmp/tmp0yuvedna/src.linux-x86_64-3.6/transport_spatial_methodsmodule.c
In file included from /home/arfc/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:0,
from /home/arfc/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/arfc/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /tmp/tmp0yuvedna/src.linux-x86_64-3.6/fortranobject.h:13,
from /tmp/tmp0yuvedna/src.linux-x86_64-3.6/transport_spatial_methodsmodule.c:16:
/home/arfc/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with " \
^~~~~~~
/tmp/tmp0yuvedna/src.linux-x86_64-3.6/transport_spatial_methodsmodule.c:170:12: warning: 'f2py_size' defined but not used [-Wunused-function]
static int f2py_size(PyArrayObject* var, ...)
^~~~~~~~~
x86_64-conda_cos6-linux-gnu-cc: /tmp/tmp0yuvedna/src.linux-x86_64-3.6/fortranobject.c
In file included from /home/arfc/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:0,
from /home/arfc/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/arfc/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /tmp/tmp0yuvedna/src.linux-x86_64-3.6/fortranobject.h:13,
from /tmp/tmp0yuvedna/src.linux-x86_64-3.6/fortranobject.c:2:
/home/arfc/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with " \
^~~~~~~
compiling Fortran sources
Fortran f77 compiler: /home/arfc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -ffixed-form -fno-second-underscore -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -O3 -funroll-loops
Fortran f90 compiler: /home/arfc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-gfortran -fdefault-real-8 -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -O3 -funroll-loops
Fortran fix compiler: /home/arfc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -ffixed-form -fno-second-underscore -fdefault-real-8 -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -O3 -funroll-loops
creating /tmp/tmp0yuvedna/home
creating /tmp/tmp0yuvedna/home/arfc
creating /tmp/tmp0yuvedna/home/arfc/github
creating /tmp/tmp0yuvedna/home/arfc/github/pyne
creating /tmp/tmp0yuvedna/home/arfc/github/pyne/src
creating /tmp/tmp0yuvedna/home/arfc/github/pyne/src/transport_spatial_methods
creating /tmp/tmp0yuvedna/home/arfc/github/pyne/src/transport_spatial_methods/3d
compile options: '-I/home/arfc/github/pyne/build/src -I/tmp/tmp0yuvedna/src.linux-x86_64-3.6 -I/home/arfc/anaconda3/lib/python3.6/site-packages/numpy/core/include -I/home/arfc/anaconda3/include/python3.6m -c'
x86_64-conda_cos6-linux-gnu-gfortran:f90: /home/arfc/github/pyne/src/transport_spatial_methods/3d/main.f90
x86_64-conda_cos6-linux-gnu-gfortran:f77: /tmp/tmp0yuvedna/src.linux-x86_64-3.6/transport_spatial_methods-f2pywrappers.f
/home/arfc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections /tmp/tmp0yuvedna/tmp/tmp0yuvedna/src.linux-x86_64-3.6/transport_spatial_methodsmodule.o /tmp/tmp0yuvedna/tmp/tmp0yuvedna/src.linux-x86_64-3.6/fortranobject.o /tmp/tmp0yuvedna/home/arfc/github/pyne/src/transport_spatial_methods/3d/main.o /tmp/tmp0yuvedna/tmp/tmp0yuvedna/src.linux-x86_64-3.6/transport_spatial_methods-f2pywrappers.o -L/home/arfc/github/pyne/build/src -L/home/arfc/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib -L/home/arfc/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib -lpyne -lgfortran -o ./transport_spatial_methods.cpython-36m-x86_64-linux-gnu.so
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libhdf5.so.103, needed by /home/arfc/github/pyne/build/src/libpyne.so, not found (try using -rpath or -rpath-link)
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libmkl_gf_lp64.so, needed by /home/arfc/github/pyne/build/src/libpyne.so, not found (try using -rpath or -rpath-link)
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libmkl_gnu_thread.so, needed by /home/arfc/github/pyne/build/src/libpyne.so, not found (try using -rpath or -rpath-link)
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libmkl_core.so, needed by /home/arfc/github/pyne/build/src/libpyne.so, not found (try using -rpath or -rpath-link)
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/Scrt1.o: in function `_start':
/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/.build/src/glibc-2.12.2/csu/../sysdeps/x86_64/elf/start.S:99: undefined reference to `main'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Dextend'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Dset_extent'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Pcreate'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Lget_name_by_idx'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Fflush'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Fopen'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5T_NATIVE_INT_g'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5check_version'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Pget_layout'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Gget_info'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Awrite'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Dget_create_plist'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Acreate2'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `dgesv_'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Dget_space'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Pget_chunk'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Sget_simple_extent_npoints'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Aopen'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Gget_objinfo'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Tinsert'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Dread'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Tarray_create2'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Tset_strpad'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Pset_fclose_degree'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Pset_deflate'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Sget_simple_extent_ndims'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5T_IEEE_F64BE_g'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Tset_size'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Fis_hdf5'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Fcreate'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Pclose'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Screate_simple'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Sselect_hyperslab'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5T_NATIVE_DOUBLE_g'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Sget_simple_extent_dims'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Dvlen_reclaim'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5T_C_S1_g'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Tvlen_create'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Dopen2'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Tcopy'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Screate'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5T_NATIVE_UINT_g'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Eset_auto2'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Aread'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Sclose'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Aget_info'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Pset_fill_value'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5open'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Pset_chunk'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Tclose'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5T_NATIVE_SCHAR_g'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Gopen2'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Dwrite'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Dclose'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Tcreate'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5P_CLS_FILE_ACCESS_ID_g'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `dgemv_'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Fclose'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Gclose'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5Dcreate2'
/home/arfc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/arfc/github/pyne/build/src/libpyne.so: undefined reference to `H5T_STD_I64BE_g'
collect2: error: ld returned 1 exit status
error: Command "/home/arfc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections /tmp/tmp0yuvedna/tmp/tmp0yuvedna/src.linux-x86_64-3.6/transport_spatial_methodsmodule.o /tmp/tmp0yuvedna/tmp/tmp0yuvedna/src.linux-x86_64-3.6/fortranobject.o /tmp/tmp0yuvedna/home/arfc/github/pyne/src/transport_spatial_methods/3d/main.o /tmp/tmp0yuvedna/tmp/tmp0yuvedna/src.linux-x86_64-3.6/transport_spatial_methods-f2pywrappers.o -L/home/arfc/github/pyne/build/src -L/home/arfc/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib -L/home/arfc/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib -lpyne -lgfortran -o ./transport_spatial_methods.cpython-36m-x86_64-linux-gnu.so" failed with exit status 1
make[2]: *** [pyne/CMakeFiles/transport_spatial_methods.dir/build.make:62: pyne/transport_spatial_methods_so] Error 1
make[1]: *** [CMakeFiles/Makefile2:555: pyne/CMakeFiles/transport_spatial_methods.dir/all] Error 2
make: *** [Makefile:130: all] Error 2
--------------------
If you are having issues building pyne, please report your problem to pyne-dev@googlegroups.com or look for help at http://pyne.io
--------------------
Traceback (most recent call last):
File "setup.py", line 425, in <module>
main()
File "setup.py", line 409, in main
main_safe(ns)
File "setup.py", line 401, in main_safe
main_body(ns)
File "setup.py", line 384, in main_body
rtn = subprocess.check_call(['make'] + ns.make_args, cwd=ns.build_dir)
File "/home/arfc/anaconda3/lib/python3.6/subprocess.py", line 291, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['make']' returned non-zero exit status 2.
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