thomasaarholt

screen -aAxR -S x # Connect without disconnecting
screen -dRaA -S x # Connect and disconnect others

thomasaarholt

Using Jupyter notebook remotely via a ssh tunnel.

Especially good for running on headless devices, such as supercomputers or clusters.

Remotely:

# remote_port should be value between 8888 and 9000
jupyter notebook --no-browser --port=remote_port

Locally, new terminal window

thomasaarholt

# Add to ~/.zshrc
autoload -U up-line-or-beginning-search
autoload -U down-line-or-beginning-search
zle -N up-line-or-beginning-search
zle -N down-line-or-beginning-search
bindkey "^[[A" up-line-or-beginning-search # Up
bindkey "^[[B" down-line-or-beginning-search # Down

thomasaarholt

Project Name: stemsalabim_test
2019-01-10 05:45:34.431 [compute-7-22.local, 0] Hello from compute-7-22.local, MPI rank 0/16, about to spawn 1 threads.
2019-01-10 05:45:34.431 [compute-7-22.local, 1] Hello from compute-7-22.local, MPI rank 1/16, about to spawn 1 threads.
2019-01-10 05:45:34.431 [compute-7-22.local, 2] Hello from compute-7-22.local, MPI rank 2/16, about to spawn 1 threads.
2019-01-10 05:45:34.431 [compute-7-22.local, 3] Hello from compute-7-22.local, MPI rank 3/16, about to spawn 1 threads.
2019-01-10 05:45:34.431 [compute-7-22.local, 4] Hello from compute-7-22.local, MPI rank 4/16, about to spawn 1 threads.
2019-01-10 05:45:34.431 [compute-7-22.local, 5] Hello from compute-7-22.local, MPI rank 5/16, about to spawn 1 threads.
2019-01-10 05:45:34.431 [compute-7-22.local, 6] Hello from compute-7-22.local, MPI rank 6/16, about to spawn 1 threads.
2019-01-10 05:45:34.431 [compute-7-22.local, 7] Hello from compute-7-22.local, MPI rank 7/16, about to spawn 1 threads.
2019-01-10 05:45:34.431 [compute-

thomasaarholt

$ make
[  5%] Building CXX object src/CMakeFiles/stemsalabim_lib.dir/classes/Crystal.cpp.o
In file included from /usit/abel/u1/thomasaar/software/STEMsalabim/src/classes/Slice.hpp(28),
                 from /usit/abel/u1/thomasaar/software/STEMsalabim/src/classes/Crystal.cpp(29):
/usit/abel/u1/thomasaar/software/STEMsalabim/src/classes/../utilities/Wave.hpp(110): error: namespace "std" has no member "complex"
          typedef std::vector<std::complex<float>, fftwAllocator<std::complex<float>>> data_type;
                                   ^

In file included from /usit/abel/u1/thomasaar/software/STEMsalabim/src/classes/Slice.hpp(28),
                 from /usit/abel/u1/thomasaar/software/STEMsalabim/src/classes/Crystal.cpp(29):

thomasaarholt

# Open terminal, locally call:
ssh-copy-id -i ~/.ssh/id_rsa.pub user@somehost

thomasaarholt

import matplotlib.pyplot as plt

def save(filepath="image.png", fig=None):
    '''Save the current image with no whitespace
    Example filepath: "myfig.png" or r"C:\myfig.pdf" 
    Based on answers from https://stackoverflow.com/questions/11837979/
    '''
    import matplotlib.pyplot as plt
    if not fig:
        fig = plt.gcf()

thomasaarholt

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-39-840bfeb05f2a> in <module>()
----> 1 m.fit_background(bounded=True)

c:\users\me\documents\github\hyperspy\hyperspy\models\edsmodel.py in fit_background(self, start_energy, end_energy, windows_sigma, kind, **kwargs)
    445                         windows_sigma[1] * component.sigma.value)
    446             if kind == 'single':
--> 447                 self.fit(**kwargs)
    448             if kind == 'multi':

thomasaarholt

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-4-825396d5c1d6> in <module>()
----> 1 m.plot()

c:\users\me\documents\github\hyperspy\hyperspy\models\model1d.py in plot(self, plot_components, **kwargs)
    668         # Add the line to the figure
    669         _plot.signal_plot.add_line(l2)
--> 670         l2.plot()
    671         _plot.signal_plot.events.closed.connect(self._close_plot, [])

thomasaarholt

# Need nodejs version 9, not latest, as of July 2018
conda install jupyterlab ipywidgets ipympl nodejs=9
jupyter labextension install @jupyter-widgets/jupyterlab-manager