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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:~$ /home/mrg/.julia/v0.6/Conda/deps/usr/bin
bash: /home/mrg/.julia/v0.6/Conda/deps/usr/bin: Is a directory
mrg@mrg:~$ cd /home/mrg/.julia/v0.6/Conda/deps/usr/bin
mrg@mrg:~/.julia/v0.6/Conda/deps/usr/bin$ ls
2to3 conda-env easy_install idle pydoc python2.7 sqlite3 wish8.5
activate c_rehash easy_install-2.7 openssl python python-config tclsh8.5
conda deactivate f2py pip python2 smtpd.py wheel
mrg@mrg:~/.julia/v0.6/Conda/deps/usr/bin$ python2.7
Python 2.7.12 (default, Nov 19 2016, 06:48:10)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> help('modules')
Please wait a moment while I gather a list of all available modules...
/usr/local/lib/python2.7/dist-packages/IPython/kernel/__init__.py:13: ShimWarning: The `IPython.kernel` package has been deprecated. You should import from ipykernel or jupyter_client instead.
"You should import from ipykernel or jupyter_client instead.", ShimWarning)
Warning: matplotlib failed to import properly and so is not
providing a graphing interface
/usr/local/lib/python2.7/dist-packages/matplotlib/cbook.py:137: MatplotlibDeprecationWarning: The matplotlib.delaunay module was deprecated in version 1.4. Use matplotlib.tri.Triangulation instead.
warnings.warn(message, mplDeprecation, stacklevel=1)
/usr/lib/python2.7/pkgutil.py:110: UserWarning: The DICOM readers are highly experimental, unstable, and only work for Siemens time-series at the moment
Please use with caution. We would be grateful for your help in improving them
__import__(name)
/usr/lib/python2.7/pkgutil.py:110: FutureWarning: The pandas.rpy module is deprecated and will be removed in a future version. We refer to external packages like rpy2.
See here for a guide on how to port your code to rpy2: http://pandas.pydata.org/pandas-docs/stable/r_interface.html
__import__(name)
BaseHTTPServer bsddb jsonschema scipy
Bastion bz2 jupyter scour
CDROM cPickle jupyter_client select
CGIHTTPServer cProfile jupyter_console sets
Canvas cStringIO jupyter_core setuptools
ConfigParser cairo keyword sgmllib
Cookie calendar leveldb sha
Cython certifi lib2to3 shelve
DLFCN cgi line_search shlex
Dialog cgitb linecache shutil
DocXMLRPCServer chunk linuxaudiodev shutil_backports
FileDialog cmath locale signal
FixTk cmd logging simplegeneric
HTMLParser code lsb_release singledispatch
IN codecs macpath singledispatch_helpers
IPython codeop macurl2path site
MimeWriter collections mailbox sitecustomize
PIL colorsys mailcap six
PyDSTool commands markupbase sklearn
Pyste compileall markupsafe smtpd
Queue compiler marshal smtplib
ScrolledText configparser math sndhdr
SimpleDialog contextlib matplotlib socket
SimpleHTTPServer cookielib md5 softwareproperties
SimpleXMLRPCServer copy mhlib spwd
SocketServer copy_reg mimetools sqlite3
StringIO criterion mimetypes sre
TYPES crypt mimify sre_compile
Tix csv mistune sre_constants
Tkconstants ctypes mmap sre_parse
Tkdnd curl modulefinder ssl
Tkinter curses multifile stat
UserDict cycler multiprocessing statvfs
UserList cython mutex step
UserString cythonmagic nbconvert storemagic
_LWPCookieJar dask nbformat string
_MozillaCookieJar datetime netrc stringold
__builtin__ dateutil networkx stringprep
__future__ dbhash new strop
_abcoll dbm nibabel struct
_ast debconf nis subprocess
_bisect decimal nisext sunau
_bsddb decorator nntplib sunaudio
_codecs defaults nose symbol
_codecs_cn difflib notebook sympyprinting
_codecs_hk dircache ntpath symtable
_codecs_iso2022 dis nturl2path sys
_codecs_jp distutils numbers sysconfig
_codecs_kr doctest numpy syslog
_codecs_tw dsextras opcode tabnanny
_collections dumbdbm operator talloc
_csv dummy_thread optimizer tarfile
_ctypes dummy_threading optparse telnetlib
_ctypes_test easy_install os tempfile
_curses email os2emxpath tensorflow
_curses_panel encodings ossaudiodev terminado
_elementtree ensurepip pandas termios
_functools entrypoints pango test
_hashlib enum pangocairo tests
_heapq errno parser textwrap
_hotshot exceptions pathlib2 this
_io external pdb thread
_json fcntl pexpect threading
_locale filecmp pickle time
_lsprof fileinput pickleshare timeit
_md5 fnmatch pickletools tkColorChooser
_multibytecodec formatter pip tkCommonDialog
_multiprocessing fpectl pipes tkFileDialog
_osx_support fpformat pkg_resources tkFont
_pyio fractions pkgutil tkMessageBox
_random ftplib platform tkSimpleDialog
_sha functools plistlib tlz
_sha256 functools32 popen2 toaiff
_sha512 future_builtins poplib token
_socket gc posix tokenize
_sqlite3 genericpath posixfile toolz
_sre getopt posixpath toree
_ssl getpass powerline tornado
_strptime gettext pprint trace
_struct gflags profile traceback
_symtable gio prompt_toolkit traitlets
_sysconfigdata glib pstats ttk
_sysconfigdata_nd glob pty tty
_testcapi gobject ptyprocess turtle
_threading_local google pwd types
_warnings grp py4j unicodedata
_weakref gtk py_compile unittest
_weakrefset gtkunixprint pyclbr urllib
abc gyp pycurl urllib2
aifc gzip pydoc urlparse
antigravity h5py pydoc_data user
anydbm hashlib pyexpat uu
apt heapq pygments uuid
apt_inst helpers pygtk virtualenv
apt_pkg hmac pylab warnings
aptsources hotshot pynotify wave
argparse htmlentitydefs pyparsing wcwidth
array htmllib pytz weakref
ast httplib pyximport webbrowser
asynchat ihooks qtconsole wheel
asyncore imaplib quopri whichdb
atexit imghdr random widgetsnbextension
atk imp re wsgiref
audiodev importlib readline xdrlib
audioop imputil repr xml
autoreload indicator_keyboard resource xmllib
backports inspect rexec xmlrpclib
backports_abc io rfc822 xxsubtype
base64 ipykernel rlcompleter yaml
bdb ipython_genutils rmagic youtube_dl
binascii ipywidgets robotparser zipfile
binhex itertools run zipimport
bisect jinja2 runpy zlib
boost json sched zmq
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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