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miguelraz/gist:536bd341c5d024f2e5148afcc9e00ccd

Last active April 5, 2017 04:09
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Chris Rackauckas vs Pycall - Round 1
Raw
gistfile1.txt
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
@miguelraz
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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>

@miguelraz
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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>

@miguelraz
Copy link
Author 

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>

@miguelraz
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Author 

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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