Installing PyGMT on Google Colab

[sudhir2016]

How do you install PyGMT on Google Colab notebook.

[seisman]

Try running following commands in Google Colab:

!wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
!chmod +x Miniconda3-latest-Linux-x86_64.sh
!bash ./Miniconda3-latest-Linux-x86_64.sh -bfp /usr/local
!conda update conda -y -q
!conda config --prepend channels conda-forge
!conda install -q -y --prefix /usr/local python=3.8 pygmt

import sys
import os
sys.path.append('/usr/local/lib/python3.8/site-packages')
os.environ["GMT_LIBRARY_PATH"]="/usr/local/lib"

Then you should be able to use pygmt:

import pygmt

[emetdan]

@seisman Worked well for me, thanks!

[ahmetanildindar]

Dear @seisman,
Do we have to install pygmt everytime we access Colab? Because after completing my work and come back couple of days later, I have to run your codes again.

Best regards from Istanbul.

++Ahmet

[seisman]

@ahmetanildindar

Do we have to install pygmt everytime we access Colab?

Yes, I believe so. Google colab doesn’t save your environment.

[ahmetanildindar]

Yeah, that was my belief, too. Pity.

[seismiclover]

It was working pretty well until a few days ago. Now I got this error;

[seisman]

I can reproduce your issue. Loading the libgmt.so gives me the following message:

OSError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /usr/local/lib/././libtiledb.so.2.1)

I think some other conda-forge packages are broken.

[liamtoney]

Did this ever get resolved, or is there an issue for this?

[seisman]

I’m not sure. The PyGMT tests all work well, but the try-gmt binder seems broken recently (GMT.jl is broken on Binder · Issue #15 · GenericMappingTools/try-gmt (github.com)).

[emetdan]

I have the same issue

[andrebelem]

Hello. Any news on this ?
I got the same problem (just runinng the colab test I got the same error)

Any help ?

[emetdan]

Solved here:

COLAB example on github "Try PyGMT online" not working any more

Worked ! The sequence was: (1) update VM colab !sudo apt update !sudo apt upgrade -y !sudo apt install -y build-essential cmake libcurl4-gnutls-dev libnetcdf-dev gdal-bin libgdal-dev libfftw3-dev libpcre3-dev liblapack-dev libblas-dev libglib2.0-dev ghostscript ghostscript-x graphicsmagick ffmpeg xdg-utils (2) Install gmt from github !git clone --depth 50 https://github.com/GenericMappingTools/gmt (3) make everthing ! !cmake /content/gmt (4) install !cmake --build . --target install …

[seisman]

To whom may concern, here is the latest solution to install PyGMT on Google Colab:

COLAB example on github "Try PyGMT online" not working any more

For anyone who reads this post: Currently, the best and simplest solution is to install conda using condacolab. Install conda!pip install -q condacolab import condacolab condacolab.install() Install PyGMT and its depenecies!mamba install pygmt Please refer to https://github.com/conda-incubator/condacolab and https://github.com/GenericMappingTools/try-gmt/blob/master/python-demo.ipynb for the detailed instructions.