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Chris Rackauckas vs Pycall - Round 1
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julia> Pkg.test("PyDSTool") | |
INFO: Computing test dependencies for PyDSTool... | |
INFO: No packages to install, update or remove | |
INFO: Testing PyDSTool | |
Warning: matplotlib failed to import properly and so is not | |
providing a graphing interface | |
2.026891 seconds (1.63 M allocations: 72.990 MB, 5.09% gc time) | |
LP Point found | |
LP Point found | |
PyCont curve EQ1 (type EP-C) | |
Using model: Calcium channel model | |
Model Info | |
---------- | |
Variables : v, w | |
Parameters: gca, vca, c, i, vl, v1, v2, gl | |
Continuation Parameters | |
----------------------- | |
name = EQ1 | |
auxpars = [] | |
freepars = ['i'] | |
MaxNumPoints = 450 | |
MaxCorrIters = 5 | |
MaxTestIters = 10 | |
MaxStepSize = 2 | |
MinStepSize = 1e-05 | |
StepSize = 2 | |
VarTol = 1e-06 | |
FuncTol = 1e-06 | |
TestTol = 0.0001 | |
LocBifPoints = ['B', 'SP', 'BP', 'LP', 'H'] | |
verbosity = 1 | |
ClosedCurve = 50 | |
SaveJacobian = False | |
SaveEigen = True | |
Corrector = <bound method EquilibriumCurve._MoorePenrose of PyCont curve EQ1 (type EP-C)> | |
UseAuto = False | |
StopAtPoints = [] | |
SPOut = None | |
Special Points | |
-------------- | |
P1, P2, LP1, LP2 | |
PyCont curve SN1 (type LP-C) | |
Using model: Calcium channel model | |
Model Info | |
---------- | |
Variables : v, w | |
Parameters: gca, vca, c, i, vl, v1, v2, gl | |
Continuation Parameters | |
----------------------- | |
name = SN1 | |
auxpars = [] | |
freepars = ['i', 'gca'] | |
MaxNumPoints = 200 | |
MaxCorrIters = 5 | |
MaxTestIters = 10 | |
MaxStepSize = 2 | |
MinStepSize = 1e-05 | |
StepSize = 2 | |
VarTol = 1e-06 | |
FuncTol = 1e-06 | |
TestTol = 0.0001 | |
LocBifPoints = ['CP'] | |
verbosity = 1 | |
ClosedCurve = 50 | |
SaveJacobian = False | |
SaveEigen = True | |
Corrector = <bound method FoldCurve._MoorePenrose of PyCont curve SN1 (type LP-C)> | |
UseAuto = False | |
StopAtPoints = [] | |
SPOut = None | |
Special Points | |
-------------- | |
P1, P2 | |
25.663171 seconds (1.06 M allocations: 45.910 MB, 0.05% gc time) | |
LP Point found | |
LP Point found | |
PyCont curve EQ1 (type EP-C) | |
Using model: Calcium | |
Model Info | |
---------- | |
Variables : v, w | |
Parameters: gca, vca, c, i, vl, v1, v2, gl | |
Continuation Parameters | |
----------------------- | |
name = EQ1 | |
auxpars = [] | |
freepars = ['i'] | |
MaxNumPoints = 450 | |
MaxCorrIters = 5 | |
MaxTestIters = 10 | |
MaxStepSize = 2 | |
MinStepSize = 1e-05 | |
StepSize = 2 | |
VarTol = 1e-06 | |
FuncTol = 1e-06 | |
TestTol = 0.0001 | |
LocBifPoints = ['B', 'SP', 'BP', 'LP', 'H'] | |
verbosity = 1 | |
ClosedCurve = 50 | |
SaveJacobian = False | |
SaveEigen = True | |
Corrector = <bound method EquilibriumCurve._MoorePenrose of PyCont curve EQ1 (type EP-C)> | |
UseAuto = False | |
StopAtPoints = [] | |
SPOut = None | |
Special Points | |
-------------- | |
P1, P2, LP1, LP2 | |
8.823612 seconds (1.75 M allocations: 74.445 MB, 0.20% gc time) | |
elapsed time: 37.052887826 seconds | |
INFO: PyDSTool tests passed | |
INFO: No packages to install, update or remove |
Author
miguelraz
commented
Apr 5, 2017
•
mrg@mrg:~/.julia/v0.6/Conda/deps/usr/bin$ julia
_
_ _ _(_)_ | A fresh approach to technical computing
(_) | (_) (_) | Documentation: http://docs.julialang.org
_ _ _| |_ __ _ | Type "?help" for help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 0.6.0-dev.1557 (2016-12-13 22:41 UTC)
_/ |\__'_|_|_|\__'_| | Commit 1f8006d (112 days old master)
|__/ | x86_64-linux-gnu
julia> Pkg.clone("https://github.com/JuliaDiffEq/FEniCS.jl"); Pkg.build("FEniCS")
INFO: Cloning FEniCS from https://github.com/JuliaDiffEq/FEniCS.jl
INFO: Computing changes...
INFO: No packages to install, update or remove
INFO: Building Conda
INFO: Building PyCall
Fetching package metadata .........
Solving package specifications: .
# All requested packages already installed.
# packages in environment at /home/mrg/.julia/v0.6/Conda/deps/usr:
#
numpy 1.12.1 py27_0
INFO: PyCall is using /home/mrg/.julia/v0.6/Conda/deps/usr/bin/python (Python 2.7.13) at /home/mrg/.julia/v0.6/Conda/deps/usr/bin/python, libpython = /home/mrg/.julia/v0.6/Conda/deps/usr/lib/libpython2.7
INFO: /home/mrg/.julia/v0.6/PyCall/deps/deps.jl has not changed
INFO: /home/mrg/.julia/v0.6/PyCall/deps/PYTHON has not changed
INFO: Building FEniCS
Fetching package metadata ...........
Solving package specifications: .
Package plan for installation in environment /home/mrg/.julia/v0.6/Conda/deps/usr:
The following NEW packages will be INSTALLED:
blas: 1.1-openblas conda-forge
boost: 1.63.0-np112py27_6 conda-forge
boost-cpp: 1.63.0-2 conda-forge
bzip2: 1.0.6-1 conda-forge
cloog: 0.18.0-0
cmake: 3.7.1-4 conda-forge
curl: 7.52.1-0 conda-forge
eigen: 3.3.1-0 conda-forge
expat: 2.1.0-2 conda-forge
fastcache: 1.0.2-py27_1
fenics: 2016.2.0-py27_6 conda-forge
gcc: 4.8.5-7
gmp: 6.1.2-0 conda-forge
icu: 58.1-1 conda-forge
isl: 0.12.2-0
jsoncpp: 0.10.6-1 conda-forge
libarchive: 3.2.1-2 conda-forge
libgcc: 5.2.0-0
libgfortran: 3.0.0-1
libiconv: 1.14-4 conda-forge
libuv: 1.11.0-0 conda-forge
metis: 5.1.0-3 conda-forge
mpc: 1.0.3-4 conda-forge
mpfr: 3.1.5-0 conda-forge
mpich: 3.2-4 conda-forge
mpmath: 0.19-py27_2 conda-forge
ncurses: 5.9-10 conda-forge
openblas: 0.2.19-1 conda-forge
pcre: 8.39-0 conda-forge
petsc: 3.7.4-blas_openblas_5 conda-forge [blas_openblas]
petsc4py: 3.7.0-py27_1 conda-forge
pkg-config: 0.29.1-1 conda-forge
ply: 3.9-py27_0 conda-forge
ptscotch: 6.0.4-2 conda-forge
slepc: 3.7.1-2 conda-forge
slepc4py: 3.7.0-py27_0 conda-forge
subprocess32: 3.2.7-py27_0 conda-forge
suitesparse: 4.5.4-blas_openblas_200 conda-forge [blas_openblas]
swig: 3.0.11-0 conda-forge
sympy: 1.0-py27_0 conda-forge
tbb: 2017_20170226-0 conda-forge
xz: 5.2.2-0 conda-forge
The following packages will be UPDATED:
numpy: 1.12.1-py27_0 --> 1.12.1-py27_blas_openblas_200 conda-forge [blas_openblas]
The following packages will be SUPERSEDED by a higher-priority channel:
conda: 4.3.16-py27_0 --> 4.2.13-py27_0 conda-forge
conda-env: 2.6.0-0 --> 2.6.0-0 conda-forge
bzip2-1.0.6-1. 100% |################################################################| Time: 0:00:00 521.80 kB/s
conda-env-2.6. 100% |################################################################| Time: 0:00:00 2.20 MB/s
eigen-3.3.1-0. 100% |################################################################| Time: 0:00:00 1.32 MB/s
expat-2.1.0-2. 100% |################################################################| Time: 0:00:01 383.39 kB/s
icu-58.1-1.tar 100% |################################################################| Time: 0:00:19 1.23 MB/s
jsoncpp-0.10.6 100% |################################################################| Time: 0:00:00 1.14 MB/s
libgcc-5.2.0-0 100% |################################################################| Time: 0:00:00 1.35 MB/s
libgfortran-3. 100% |################################################################| Time: 0:00:00 1.56 MB/s
libiconv-1.14- 100% |################################################################| Time: 0:00:02 1.04 MB/s
libuv-1.11.0-0 100% |################################################################| Time: 0:00:00 1.29 MB/s
metis-5.1.0-3. 100% |################################################################| Time: 0:00:00 1.70 MB/s
ncurses-5.9-10 100% |################################################################| Time: 0:00:00 1.32 MB/s
pcre-8.39-0.ta 100% |################################################################| Time: 0:00:00 1.29 MB/s
tbb-2017_20170 100% |################################################################| Time: 0:00:00 1.40 MB/s
xz-5.2.2-0.tar 100% |################################################################| Time: 0:00:00 1.49 MB/s
boost-cpp-1.63 100% |################################################################| Time: 0:00:15 1.22 MB/s
curl-7.52.1-0. 100% |################################################################| Time: 0:00:00 1.61 MB/s
isl-0.12.2-0.t 100% |################################################################| Time: 0:00:00 1.34 MB/s
libarchive-3.2 100% |################################################################| Time: 0:00:02 1.08 MB/s
mpich-3.2-4.ta 100% |################################################################| Time: 0:00:04 1.28 MB/s
openblas-0.2.1 100% |################################################################| Time: 0:00:11 1.26 MB/s
pkg-config-0.2 100% |################################################################| Time: 0:00:00 1.72 MB/s
blas-1.1-openb 100% |################################################################| Time: 0:00:00 2.93 MB/s
cloog-0.18.0-0 100% |################################################################| Time: 0:00:00 1.61 MB/s
cmake-3.7.1-4. 100% |################################################################| Time: 0:00:07 1.21 MB/s
fastcache-1.0. 100% |################################################################| Time: 0:00:00 2.16 MB/s
mpmath-0.19-py 100% |################################################################| Time: 0:00:00 1.42 MB/s
ply-3.9-py27_0 100% |################################################################| Time: 0:00:00 1.11 MB/s
ptscotch-6.0.4 100% |################################################################| Time: 0:00:01 1.34 MB/s
subprocess32-3 100% |################################################################| Time: 0:00:00 98.21 kB/s
conda-4.2.13-p 100% |################################################################| Time: 0:00:00 544.18 kB/s
gcc-4.8.5-7.ta 100% |################################################################| Time: 0:01:00 1.15 MB/s
numpy-1.12.1-p 100% |################################################################| Time: 0:00:11 736.79 kB/s
suitesparse-4. 100% |################################################################| Time: 0:00:02 993.26 kB/s
sympy-1.0-py27 100% |################################################################| Time: 0:00:06 969.44 kB/s
boost-1.63.0-n 100% |################################################################| Time: 0:00:00 1.21 MB/s
petsc-3.7.4-bl 100% |################################################################| Time: 0:00:07 661.64 kB/s
petsc4py-3.7.0 100% |################################################################| Time: 0:00:05 674.66 kB/s
slepc-3.7.1-2. 100% |################################################################| Time: 0:00:01 867.99 kB/s
swig-3.0.11-0. 100% |################################################################| Time: 0:00:00 1.22 MB/s
slepc4py-3.7.0 100% |################################################################| Time: 0:00:01 618.25 kB/s
fenics-2016.2. 100% |################################################################| Time: 0:00:42 1.13 MB/s
julia>
julia> using PyCall; pyimport("fenics")
PyObject <module 'fenics' from '/home/mrg/.julia/v0.6/Conda/deps/usr/lib/python2.7/site-packages/fenics/__init__.pyc'>
julia>
julia> Pkg.build("FEniCS")
INFO: Building Conda
INFO: Building PyCall
Fetching package metadata .........
Solving package specifications: ..........
# All requested packages already installed.
# packages in environment at /home/mrg/.julia/v0.6/Conda/deps/usr:
#
numpy 1.12.1 py27_blas_openblas_200 [blas_openblas] conda-forge
INFO: PyCall is using /home/mrg/.julia/v0.6/Conda/deps/usr/bin/python (Python 2.7.13) at /home/mrg/.julia/v0.6/Conda/deps/usr/bin/python, libpython = /home/mrg/.julia/v0.6/Conda/deps/usr/lib/libpython2.7
INFO: /home/mrg/.julia/v0.6/PyCall/deps/deps.jl has not changed
INFO: /home/mrg/.julia/v0.6/PyCall/deps/PYTHON has not changed
INFO: Building FEniCS
Warning: 'conda-forge' already in 'channels' list, moving to the top
Fetching package metadata .........
Solving package specifications: ..........
# All requested packages already installed.
# packages in environment at /home/mrg/.julia/v0.6/Conda/deps/usr:
#
fenics 2016.2.0 py27_6 conda-forge
julia>
julia> Pkg.build("DifferentialEquations")
INFO: Building Rmath
INFO: Building Sundials
INFO: Building Conda
INFO: Building SymEngine
INFO: Building PyCall
Fetching package metadata .........
Solving package specifications: ..........
# All requested packages already installed.
# packages in environment at /home/mrg/.julia/v0.6/Conda/deps/usr:
#
numpy 1.12.1 py27_blas_openblas_200 [blas_openblas] conda-forge
INFO: PyCall is using /home/mrg/.julia/v0.6/Conda/deps/usr/bin/python (Python 2.7.13) at /home/mrg/.julia/v0.6/Conda/deps/usr/bin/python, libpython = /home/mrg/.julia/v0.6/Conda/deps/usr/lib/libpython2.7
INFO: /home/mrg/.julia/v0.6/PyCall/deps/deps.jl has not changed
INFO: /home/mrg/.julia/v0.6/PyCall/deps/PYTHON has not changed
INFO: Building PyDSTool
Fetching package metadata .........
Solving package specifications: ..........
Package plan for installation in environment /home/mrg/.julia/v0.6/Conda/deps/usr:
The following packages will be downloaded:
package | build
---------------------------|-----------------
pip-9.0.1 | py27_0 1.6 MB conda-forge
The following packages will be SUPERCEDED by a higher-priority channel:
pip: 9.0.1-py27_1 --> 9.0.1-py27_0 conda-forge
Fetching packages ...
pip-9.0.1-py27 100% |################################################################| Time: 0:00:02 833.52 kB/s
Extracting packages ...
[ COMPLETE ]|###################################################################################| 100%
Unlinking packages ...
[ COMPLETE ]|###################################################################################| 100%
Linking packages ...
[ COMPLETE ]|###################################################################################| 100%
Requirement already satisfied: pydstool in /home/mrg/.julia/v0.6/Conda/deps/usr/lib/python2.7/site-packages
Requirement already satisfied: six in /home/mrg/.julia/v0.6/Conda/deps/usr/lib/python2.7/site-packages (from pydstool)
Requirement already satisfied: scipy>=0.9 in /home/mrg/.julia/v0.6/Conda/deps/usr/lib/python2.7/site-packages (from pydstool)
Requirement already satisfied: numpy>=1.6 in /home/mrg/.julia/v0.6/Conda/deps/usr/lib/python2.7/site-packages (from pydstool)
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