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oscode's Issues

(even?) spacing of "time" array in pyoscode

documentation @ version (0.1.2)

Does pyoscode assume that the grid of timepoints ts passed to pyoscode.solve is evenly spaced?

In the documentation it says for the C++ interface that

  • For the sake of speed, oscode will assume the grid of timepoints \omega and \gamma are given on is evenly spaced. It is possible not to supply an evenly spaced grid, this will be discussed later.

The pyscode documentation does not specify this. There it only says (note also awkward splitting of word independent):

ts: numpy.ndarray [float] or list [float]
    An array of real numbers representing the values of the independe
    nt variable at which the frequency and friction term are evaluated. 

If it indeed is assuming ts to be evenly spaced, then it would probably be good to

  1. update the pyoscode documentation accordingly
  2. check the ts input accordingly and raise an error or at least a warning if the condition is violated

Possibly nice features:

  • allow uneven spacing of ts
  • have option of log spacing of ts, i.e. for np.logspace time arrays as input

How to include Eigen

I remember having had issues previously with installing pyoscode (python setup.py install) because of the error

pyoscode/_pyoscode.hpp:6:10: fatal error: Eigen/Dense: No such file or directory

and I'm running into this again now.

I have Eigen on my system, but how do I let pyoscode know where it is? What would be the best way of handling this? Do I need to create symlinks as mentioned in Eigen's Getting started?

Installation on windows 10

It seems that there is an error for the installation on windows 10. The error message is "Microsoft Visual C++ 14.0 or greater is required'. It fails to build wheels for pyoscode.

travis CI not using Python 3 as intended

As seen in #9, the travis CI is not actually using the Python versions that are requested in .travis.yml. It seems to ignore the python field completely and always uses the system Python, which typically is Python 2.7.

This becomes very clear with the commit cb90a3d that makes travis print out the used python version. See for example the job 195.1, where it shows that Python 2.7.17 was used instead of the expected Python 3.7.

pip install fails

solver@solver-mbook ~ % pip install pyoscode
Collecting pyoscode
  Downloading pyoscode-1.0.0.tar.gz (70.2 MB)
     |████████████████████████████████| 70.2 MB 498 kB/s 
Collecting numpy
  Using cached numpy-1.19.4-cp37-cp37m-macosx_10_9_x86_64.whl (15.3 MB)
Building wheels for collected packages: pyoscode
  Building wheel for pyoscode (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/tt/c5pb_r2131d25c9f_b2z7jrc0000gp/T/pip-install-qiallowx/pyoscode_a2904fd97ae3468e899ba2642c231cd0/setup.py'"'"'; __file__='"'"'/private/var/folders/tt/c5pb_r2131d25c9f_b2z7jrc0000gp/T/pip-install-qiallowx/pyoscode_a2904fd97ae3468e899ba2642c231cd0/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/tt/c5pb_r2131d25c9f_b2z7jrc0000gp/T/pip-wheel-jlqo7fx3
       cwd: /private/var/folders/tt/c5pb_r2131d25c9f_b2z7jrc0000gp/T/pip-install-qiallowx/pyoscode_a2904fd97ae3468e899ba2642c231cd0/
  Complete output (73 lines):
  WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip.
  Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue.
  To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
  Requirement already satisfied: numpy in /usr/local/lib/python3.7/site-packages (1.19.4)
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.15-x86_64-3.7
  creating build/lib.macosx-10.15-x86_64-3.7/pyoscode
  copying pyoscode/__init__.py -> build/lib.macosx-10.15-x86_64-3.7/pyoscode
  running egg_info
  writing pyoscode.egg-info/PKG-INFO
  writing dependency_links to pyoscode.egg-info/dependency_links.txt
  writing requirements to pyoscode.egg-info/requires.txt
  writing top-level names to pyoscode.egg-info/top_level.txt
  reading manifest file 'pyoscode.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  writing manifest file 'pyoscode.egg-info/SOURCES.txt'
  copying pyoscode/__init__.pyc -> build/lib.macosx-10.15-x86_64-3.7/pyoscode
  copying pyoscode/_pyoscode.cpp -> build/lib.macosx-10.15-x86_64-3.7/pyoscode
  copying pyoscode/_pyoscode.hpp -> build/lib.macosx-10.15-x86_64-3.7/pyoscode
  copying pyoscode/_python.hpp -> build/lib.macosx-10.15-x86_64-3.7/pyoscode
  creating build/lib.macosx-10.15-x86_64-3.7/pyoscode/__pycache__
  copying pyoscode/__pycache__/__init__.cpython-36.pyc -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/__pycache__
  copying pyoscode/__pycache__/__init__.cpython-38.pyc -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/__pycache__
  creating build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs
  copying pyoscode/docs/Makefile -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs
  creating build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs/source
  copying pyoscode/docs/source/conf.py -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs/source
  copying pyoscode/docs/source/index.rst -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs/source
  copying pyoscode/docs/source/introduction.rst -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs/source
  copying pyoscode/docs/source/oscode.rst -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs/source
  copying pyoscode/docs/source/pyoscode.rst -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs/source
  creating build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
  copying pyoscode/images/airy-example.png -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
  copying pyoscode/images/burst-example.png -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
  copying pyoscode/images/gamma.png -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
  copying pyoscode/images/omega.png -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
  copying pyoscode/images/oscillator.gif -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
  copying pyoscode/images/oscillator.png -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
  copying pyoscode/images/spectra.gif -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
  running build_ext
  building '_pyoscode' extension
  Warning: Can't read registry to find the necessary compiler setting
  Make sure that Python modules winreg, win32api or win32con are installed.
  C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers
  
  creating build/temp.macosx-10.15-x86_64-3.7
  creating build/temp.macosx-10.15-x86_64-3.7/pyoscode
  compile options: '-Iinclude -Ipyoscode -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.6_1/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
  extra options: '-std=c++11 -Wall'
  clang: pyoscode/_pyoscode.cpp
  In file included from pyoscode/_pyoscode.cpp:4:
  In file included from include/system.hpp:2:
  include/interpolator.hpp:74:20: warning: unused variable 'x1' [-Wunused-variable]
              double x1 = xstart + (i+1)*dx;
                     ^
  include/interpolator.hpp:75:20: warning: unused variable 'x0' [-Wunused-variable]
              double x0 = xstart + i*dx;
                     ^
  In file included from pyoscode/_pyoscode.cpp:5:
  include/solver.hpp:280:38: warning: unused variable 'dx_dense_rk' [-Wunused-variable]
      std::complex<double> x_dense_rk, dx_dense_rk;
                                       ^
  include/solver.hpp:280:26: warning: unused variable 'x_dense_rk' [-Wunused-variable]
      std::complex<double> x_dense_rk, dx_dense_rk;
                           ^
  pyoscode/_pyoscode.cpp:7:10: fatal error: 'numpy/arrayobject.h' file not found
  #include <numpy/arrayobject.h>
           ^~~~~~~~~~~~~~~~~~~~~
  4 warnings and 1 error generated.
  error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -Iinclude -Ipyoscode -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.6_1/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c pyoscode/_pyoscode.cpp -o build/temp.macosx-10.15-x86_64-3.7/pyoscode/_pyoscode.o -std=c++11 -Wall" failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for pyoscode
  Running setup.py clean for pyoscode
Failed to build pyoscode
Installing collected packages: numpy, pyoscode
    Running setup.py install for pyoscode ... error
    ERROR: Command errored out with exit status 1:
     command: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/tt/c5pb_r2131d25c9f_b2z7jrc0000gp/T/pip-install-qiallowx/pyoscode_a2904fd97ae3468e899ba2642c231cd0/setup.py'"'"'; __file__='"'"'/private/var/folders/tt/c5pb_r2131d25c9f_b2z7jrc0000gp/T/pip-install-qiallowx/pyoscode_a2904fd97ae3468e899ba2642c231cd0/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/tt/c5pb_r2131d25c9f_b2z7jrc0000gp/T/pip-record-kbjhui_b/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.7m/pyoscode
         cwd: /private/var/folders/tt/c5pb_r2131d25c9f_b2z7jrc0000gp/T/pip-install-qiallowx/pyoscode_a2904fd97ae3468e899ba2642c231cd0/
    Complete output (73 lines):
    WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip.
    Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue.
    To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
    Requirement already satisfied: numpy in /usr/local/lib/python3.7/site-packages (1.19.4)
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.15-x86_64-3.7
    creating build/lib.macosx-10.15-x86_64-3.7/pyoscode
    copying pyoscode/__init__.py -> build/lib.macosx-10.15-x86_64-3.7/pyoscode
    running egg_info
    writing pyoscode.egg-info/PKG-INFO
    writing dependency_links to pyoscode.egg-info/dependency_links.txt
    writing requirements to pyoscode.egg-info/requires.txt
    writing top-level names to pyoscode.egg-info/top_level.txt
    reading manifest file 'pyoscode.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'pyoscode.egg-info/SOURCES.txt'
    copying pyoscode/__init__.pyc -> build/lib.macosx-10.15-x86_64-3.7/pyoscode
    copying pyoscode/_pyoscode.cpp -> build/lib.macosx-10.15-x86_64-3.7/pyoscode
    copying pyoscode/_pyoscode.hpp -> build/lib.macosx-10.15-x86_64-3.7/pyoscode
    copying pyoscode/_python.hpp -> build/lib.macosx-10.15-x86_64-3.7/pyoscode
    creating build/lib.macosx-10.15-x86_64-3.7/pyoscode/__pycache__
    copying pyoscode/__pycache__/__init__.cpython-36.pyc -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/__pycache__
    copying pyoscode/__pycache__/__init__.cpython-38.pyc -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/__pycache__
    creating build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs
    copying pyoscode/docs/Makefile -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs
    creating build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs/source
    copying pyoscode/docs/source/conf.py -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs/source
    copying pyoscode/docs/source/index.rst -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs/source
    copying pyoscode/docs/source/introduction.rst -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs/source
    copying pyoscode/docs/source/oscode.rst -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs/source
    copying pyoscode/docs/source/pyoscode.rst -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/docs/source
    creating build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
    copying pyoscode/images/airy-example.png -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
    copying pyoscode/images/burst-example.png -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
    copying pyoscode/images/gamma.png -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
    copying pyoscode/images/omega.png -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
    copying pyoscode/images/oscillator.gif -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
    copying pyoscode/images/oscillator.png -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
    copying pyoscode/images/spectra.gif -> build/lib.macosx-10.15-x86_64-3.7/pyoscode/images
    running build_ext
    building '_pyoscode' extension
    Warning: Can't read registry to find the necessary compiler setting
    Make sure that Python modules winreg, win32api or win32con are installed.
    C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers
    
    creating build/temp.macosx-10.15-x86_64-3.7
    creating build/temp.macosx-10.15-x86_64-3.7/pyoscode
    compile options: '-Iinclude -Ipyoscode -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.6_1/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
    extra options: '-std=c++11 -Wall'
    clang: pyoscode/_pyoscode.cpp
    In file included from pyoscode/_pyoscode.cpp:4:
    In file included from include/system.hpp:2:
    include/interpolator.hpp:74:20: warning: unused variable 'x1' [-Wunused-variable]
                double x1 = xstart + (i+1)*dx;
                       ^
    include/interpolator.hpp:75:20: warning: unused variable 'x0' [-Wunused-variable]
                double x0 = xstart + i*dx;
                       ^
    In file included from pyoscode/_pyoscode.cpp:5:
    include/solver.hpp:280:38: warning: unused variable 'dx_dense_rk' [-Wunused-variable]
        std::complex<double> x_dense_rk, dx_dense_rk;
                                         ^
    include/solver.hpp:280:26: warning: unused variable 'x_dense_rk' [-Wunused-variable]
        std::complex<double> x_dense_rk, dx_dense_rk;
                             ^
    pyoscode/_pyoscode.cpp:7:10: fatal error: 'numpy/arrayobject.h' file not found
    #include <numpy/arrayobject.h>
             ^~~~~~~~~~~~~~~~~~~~~
    4 warnings and 1 error generated.
    error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -Iinclude -Ipyoscode -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.6_1/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c pyoscode/_pyoscode.cpp -o build/temp.macosx-10.15-x86_64-3.7/pyoscode/_pyoscode.o -std=c++11 -Wall" failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/tt/c5pb_r2131d25c9f_b2z7jrc0000gp/T/pip-install-qiallowx/pyoscode_a2904fd97ae3468e899ba2642c231cd0/setup.py'"'"'; __file__='"'"'/private/var/folders/tt/c5pb_r2131d25c9f_b2z7jrc0000gp/T/pip-install-qiallowx/pyoscode_a2904fd97ae3468e899ba2642c231cd0/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/tt/c5pb_r2131d25c9f_b2z7jrc0000gp/T/pip-record-kbjhui_b/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.7m/pyoscode Check the logs for full command output.

Problems with dense output of the `Solution` class

I found an issue when instantiating the Solution class via e.g. passing a std::vector<double> to the const X &do_times variable (same for a list). The time ordering of the dense output class member lists is off, which is also reflected in the associated output file. Another issue is that a part of the solution (probably the parts obtained with the RK solver) seem to have been set to 0.

To reproduce this in a minimal example, I modified the burst.cpp file as follows (currently only non-dense output is included).

std::vector<double> temp;
for (int i = 0; i < 1000; ++i) { temp.push_back(-2*n + 4*n*i*0.001); }

de_system sys(&w, &g);
Solution solution(sys, x0, dx0, ti, tf, temp, 3, 1e-4, 0.0, 1, "native_do.dat");
solution.solve();

std::vector<double> do_ts(std::begin(solution.dotimes), std::end(solution.dotimes));
std::vector<std::complex<double> > do_xs(std::begin(solution.dosol), std::end(solution.dosol));

for (int i = 0; i < do_xs.size(); ++i)
{
     std::cout << temp[i] << " " << do_ts[i] << " " << do_xs[i] << std::endl;
}

Both the printed lines and the contents of native_do.dat should show the issues mentioned above.

burst example gives segmentation fault

@absurd-zipper Noted that when running burst.cpp, a segmentation fault occurs.

Steps to reproduce the error (with g++ (GCC) 10.2.0):

git clone "https://github.com/fruzsinaagocs/oscode"
cd oscode
g++ -g -Wall -I include -std=c++11 -c -o examples/burst.o examples/burst.cpp
g++ -g -Wall -std=c++11 -o examples/burst examples/burst.o
./examples/burst

One more problem with dense output of the `Solution` class

This is similar to #13 in that the dense output variables and hence also the data written to file are incorrect, e.g. set to 0. This only happens when both these conditions are met: (a) t_i > t_f and (b) the times in const X &do_times are also decreasing.

To reproduce this in a minimal example, I again modified the burst.cpp file as follows

ti = 2*n;
tf = -2*n;

std::vector<double> temp;
for (int i = 0; i < 1000; ++i) { temp.push_back(2*n - 4*n*i*0.001); }

de_system sys(&w, &g);
Solution solution(sys, x0, dx0, ti, tf, temp, 3, 1e-4, 0.0, 1, "native_do.dat");
solution.solve();

std::vector<double> do_ts(std::begin(solution.dotimes), std::end(solution.dotimes));
std::vector<std::complex<double> > do_xs(std::begin(solution.dosol), std::end(solution.dosol));

for (int i = 0; i < do_xs.size(); ++i)
{
     std::cout << temp[i] << " " << do_ts[i] << " " << do_xs[i] << std::endl;
}

I guess one way to solve this is to ensure that the dense output times are always sorted in increasing order, as the issues does not seem to appear then.

How to reduce warnings about about low step acceptance ratio?

At the moment my output gets flooded by warnings of the form:

Warning: the solver took 5000 steps, and may take a while to converge.
Warning: the step acceptance ratio is below 5%, the solver may take a while to converge.

Since things are running fine otherwise and timings don't seem to be catastrophic, the threshold of 5000 steps seems much too low for me. Does Oscode provide an option of reducing/suppressing these warnings? Else I might just hard code the threshold differently for me.

numpy version 1.19.5 not working with pyoscode

Just tried installing pyoscode on a different cluster and got this error:

>>> import pyoscode
RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/lh561/Documents/Projects/OscodePrj/oscode/pyoscode/__init__.py", line 3, in <module>
    import _pyoscode
ImportError: numpy.core.multiarray failed to import

Updating from numpy==1.19.5 to numpy>=1.20 solved this issue for me.

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