Problem using pygmt with pip install

Q&A
1

Hi, after installing pygmt (using pip) and creating a test file importing pygmt, when I run the file I get the following error: (I already tried in my computer with anaconda and everything run fine but I used anaconda, I want to install this with pip because I am installing it in a centos server with a little amount of space (only have 8gb left) and anaconda is quite heavy (6.3 Gb))

Traceback (most recent call last):
File “test.py”, line 1, in
import pygmt
File “/usr/local/lib/python3.8/site-packages/pygmt/init.py”, line 71, in
_begin()
File “/usr/local/lib/python3.8/site-packages/pygmt/session_management.py”, line 16, in begin
with Session() as lib:
File “/usr/local/lib/python3.8/site-packages/pygmt/clib/session.py”, line 183, in enter
self.create(“pygmt-session”)
File “/usr/local/lib/python3.8/site-packages/pygmt/clib/session.py”, line 330, in create
c_create_session = self.get_libgmt_func(
File “/usr/local/lib/python3.8/site-packages/pygmt/clib/session.py”, line 282, in get_libgmt_func
self._libgmt = load_libgmt()
File “/usr/local/lib/python3.8/site-packages/pygmt/clib/loading.py”, line 59, in load_libgmt
raise GMTCLibNotFoundError("\n".join(error_msg))
pygmt.exceptions.GMTCLibNotFoundError: Error loading GMT shared library at ‘libgmt.so’.
libgmt.so: cannot open shared object file: No such file or directory

The documentation I use for the installation is this https://www.pygmt.org/latest/install.html, I believe the problem is that I need to export the path of pygmt but it seem I am doing this wrong.
What I try was:

export GMT_LIBRARY_PATH=/usr/local/lib/python3.8/site-packages/pygmt/clib

But I still get the error above.
Thanks for reading until here.

2

PyGMT relies on GMT. When you run pip install pygmt, you only install the PyGMT package. The required GMT package (which is not written in Python) is still missing.

I think you have two choices:

  1. Install miniconda instead, which is much smaller than anaconda.
  2. Build GMT from source code, and then set GMT_LIBRARY_PATH to the path of the GMT library
1 Like
3

Thanks, I already installed miniconda3 and build from source, the environment is working fine and pygmt is working correctly.