[FIXED] PGF / LaTeX Backend in Matplotlib via Jupyter Notebook SLURM Job on HPC System

Issue

I am a university student using my university's computing cluster.

I installed Tex Live to my home directory at ~/.local/texlive/. I have a file called mplrc. The MATPLOTLIBRC environment variable is set to the mplrc file. The mplrc file contains the following lines

backend:            pgf  

pgf.rcfonts:        false  
pgf.texsystem:      pdflatex 
pgf.preamble:       \input{mpl_settings.tex} 

text.usetex:        true

font.family:        serif
font.size:          12

The mpl_settings.tex file is in the same directory as the mplrc file and contains the following

\usepackage{amsmath}
\usepackage[T1]{fontenc}
\usepackage{gensymb}
\usepackage{lmodern}
\usepackage{siunitx}

On the cluster I am using, I must submit a SLURM job to run the Jupyter notebook. The example code I am trying to run within the notebook is

formula = (
    r'$\displaystyle '
    r'N = \int_{E_\text{min}}^{E_\text{max}} '
    r'\int_0^A'
    r'\int_{t_\text{min}}^{t_\text{max}} '
    r'\Phi_0 \left(\frac{E}{\SI{1}{\GeV}}\right)^{\!\!-γ}'
    r' \, \symup{d}A \, \symup{d}t \, \symup{d}E'
    r'$'
)


def power_law_spectrum(energy, normalisation, spectral_index):
    return normalisation * energy**(-spectral_index)


bin_edges = np.logspace(2, 5, 15)
bin_centers = 0.5 * (bin_edges[:-1] + bin_edges[1:])

y = power_law_spectrum(bin_centers, 1e-5, 2.5)
relative_error = np.random.normal(1, 0.2, size=len(y))
y_with_err = relative_error * y

fig, ax = plt.subplots()
ax.errorbar(
    np.log10(bin_centers),
    y_with_err,
    xerr=[
        np.log10(bin_centers) - np.log10(bin_edges[:-1]),
        np.log10(bin_edges[1:]) - np.log10(bin_centers)
    ],
    yerr=0.5 * y_with_err,
    linestyle='',
)

ax.text(0.1, 0.1, formula, transform=plt.gca().transAxes)
ax.set_yscale('log')

fig.tight_layout(pad=0)

plt.show()

This generates an enormous error message, but the root of it is

RuntimeError: latex was not able to process the following string:
b'lp'

However, underneath that, I see what I think is the real problem

! LaTeX Error: File `article.cls' not found.

I've set my PATH so that it finds the right latex command, but what else needs to be set in order to find the article.cls file? It seems like it's something particular to the Python notebook. When running kpsewhich article.cls in a terminal within the Jupyterlab interface, the file gets found. But trying ! kpsewhich article.cls or subprocess.run(['kpsewhich', 'article.cls']) within the Python notebook does not find the file.

Solution

I figured it out. I forgot I had run a section of code which set

TEXINPUTS=/path/to/some/directory

Looks like I missed a : in my TEXINPUTS, so TeX was only looking in /path/to/some/directory

The solution was to have

TEXINPUTS=/path/to/some/directory:

That way it looked in my current directory, but also continued looking elsewhere.

Answered By - Will