New CMF Version throws error on install on skylla.
[sf1962@skylla1 ~]$ pip install cmf --upgrade --user
Collecting cmf
Using cached cmf-1.0.4.tar.gz
Building wheels for collected packages: cmf
Running setup.py bdist_wheel for cmf ... error
Complete output from command /cm/shared/apps/python/3.5.0/bin/python3 -u -c "i mport setuptools, tokenize;file='/tmp/pip-build-1huce24n/cmf/setup.py';f=get attr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.clo se();exec(compile(code, file, 'exec'))" bdist_wheel -d /tmp/tmpl3rfuglopip-w heel- --python-tag cp35:
/cm/shared/apps/python/3.5.0/lib/python3.5/distutils/dist.py:261: UserWarning: Unknown distribution option: 'python_requires'
warnings.warn(msg)
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.5
creating build/lib.linux-x86_64-3.5/cmf
copying cmf/maps.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/fit_retention_curve.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/init.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/describe.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/jacobian.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/extend_project.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/geos_shapereader.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/soil.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/stopwatch.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/cell_factory.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/cmf_core.py -> build/lib.linux-x86_64-3.5/cmf
creating build/lib.linux-x86_64-3.5/cmf/draw
copying cmf/draw/hillplot.py -> build/lib.linux-x86_64-3.5/cmf/draw
copying cmf/draw/init.py -> build/lib.linux-x86_64-3.5/cmf/draw
copying cmf/draw/draw_misc.py -> build/lib.linux-x86_64-3.5/cmf/draw
copying cmf/draw/shapemap.py -> build/lib.linux-x86_64-3.5/cmf/draw
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
building 'cmf._cmf_core' extension
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/cmf
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/reach
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/atmosphere
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/geometry
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/math
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/math/integrators
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/math/integrators/sundial s_cvode
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/math/integrators/sundial s_cvode/src
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/water
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/upslope
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/upslope/vegetation
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/upslope/Soil
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/upslope/connections
gcc -pthread -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall - Wstrict-prototypes -fPIC -Icmf/cmf_core_src/math/integrators/sundials_cvode/incl ude -I/home/sf1962/.local/lib/python3.5/site-packages/numpy/core/include -I/cm/s hared/apps/python/3.5.0/include/python3.5m -c cmf/cmf_core_src/cmf.cpp -o build/ temp.linux-x86_64-3.5/cmf/cmf_core_src/cmf.o -Wno-comment -Wno-reorder -Wno-unus ed -Wno-sign-compare -ggdb -std=c++11 -fopenmp
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/Obj C but not for C++ [enabled by default]
gcc -pthread -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall - Wstrict-prototypes -fPIC -Icmf/cmf_core_src/math/integrators/sundials_cvode/incl ude -I/home/sf1962/.local/lib/python3.5/site-packages/numpy/core/include -I/cm/s hared/apps/python/3.5.0/include/python3.5m -c cmf/cmf_core_src/project.cpp -o bu ild/temp.linux-x86_64-3.5/cmf/cmf_core_src/project.o -Wno-comment -Wno-reorder - Wno-unused -Wno-sign-compare -ggdb -std=c++11 -fopenmp
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/Obj C but not for C++ [enabled by default]
In file included from cmf/cmf_core_src/atmosphere/meteorology.h:26:0,
from cmf/cmf_core_src/project.h:24,
from cmf/cmf_core_src/project.cpp:19:
cmf/cmf_core_src/atmosphere/../water/WaterStorage.h:22:35: fatal error: ../mat h/statevariable.h: No such file or directory
#include "../math/statevariable.h"
^
compilation terminated.
error: command 'gcc' failed with exit status 1
Failed building wheel for cmf
Running setup.py clean for cmf
Failed to build cmf
Installing collected packages: cmf
Found existing installation: cmf 1.0.3
Uninstalling cmf-1.0.3:
Successfully uninstalled cmf-1.0.3
Running setup.py install for cmf ... error
Complete output from command /cm/shared/apps/python/3.5.0/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-1huce24n/cmf/setup.py';f=g etattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.c lose();exec(compile(code, file, 'exec'))" install --record /tmp/pip-g1dnkoy7 -record/install-record.txt --single-version-externally-managed --compile --user --prefix=:
/cm/shared/apps/python/3.5.0/lib/python3.5/distutils/dist.py:261: UserWarnin g: Unknown distribution option: 'python_requires'
warnings.warn(msg)
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.5
creating build/lib.linux-x86_64-3.5/cmf
copying cmf/maps.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/fit_retention_curve.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/init.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/describe.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/jacobian.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/extend_project.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/geos_shapereader.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/soil.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/stopwatch.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/cell_factory.py -> build/lib.linux-x86_64-3.5/cmf
copying cmf/cmf_core.py -> build/lib.linux-x86_64-3.5/cmf
creating build/lib.linux-x86_64-3.5/cmf/draw
copying cmf/draw/hillplot.py -> build/lib.linux-x86_64-3.5/cmf/draw
copying cmf/draw/init.py -> build/lib.linux-x86_64-3.5/cmf/draw
copying cmf/draw/draw_misc.py -> build/lib.linux-x86_64-3.5/cmf/draw
copying cmf/draw/shapemap.py -> build/lib.linux-x86_64-3.5/cmf/draw
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
building 'cmf._cmf_core' extension
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/cmf
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/reach
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/atmosphere
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/geometry
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/math
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/math/integrators
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/math/integrators/sundi als_cvode
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/math/integrators/sundi als_cvode/src
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/water
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/upslope
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/upslope/vegetation
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/upslope/Soil
creating build/temp.linux-x86_64-3.5/cmf/cmf_core_src/upslope/connections
gcc -pthread -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Icmf/cmf_core_src/math/integrators/sundials_cvode/in clude -I/home/sf1962/.local/lib/python3.5/site-packages/numpy/core/include -I/cm /shared/apps/python/3.5.0/include/python3.5m -c cmf/cmf_core_src/cmf.cpp -o buil d/temp.linux-x86_64-3.5/cmf/cmf_core_src/cmf.o -Wno-comment -Wno-reorder -Wno-un used -Wno-sign-compare -ggdb -std=c++11 -fopenmp
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/O bjC but not for C++ [enabled by default]
gcc -pthread -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Icmf/cmf_core_src/math/integrators/sundials_cvode/in clude -I/home/sf1962/.local/lib/python3.5/site-packages/numpy/core/include -I/cm /shared/apps/python/3.5.0/include/python3.5m -c cmf/cmf_core_src/project.cpp -o build/temp.linux-x86_64-3.5/cmf/cmf_core_src/project.o -Wno-comment -Wno-reorder -Wno-unused -Wno-sign-compare -ggdb -std=c++11 -fopenmp
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/O bjC but not for C++ [enabled by default]
In file included from cmf/cmf_core_src/atmosphere/meteorology.h:26:0,
from cmf/cmf_core_src/project.h:24,
from cmf/cmf_core_src/project.cpp:19:
cmf/cmf_core_src/atmosphere/../water/WaterStorage.h:22:35: fatal error: ../m ath/statevariable.h: No such file or directory
#include "../math/statevariable.h"
^
compilation terminated.
error: command 'gcc' failed with exit status 1
----------------------------------------
Rolling back uninstall of cmf
Command "/cm/shared/apps/python/3.5.0/bin/python3 -u -c "import setuptools, toke nize;file='/tmp/pip-build-1huce24n/cmf/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code , file, 'exec'))" install --record /tmp/pip-g1dnkoy7-record/install-record.t xt --single-version-externally-managed --compile --user --prefix=" failed with e rror code 1 in /tmp/pip-build-1huce24n/cmf/