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psconvert [ERROR]: Cannot execute Ghostscript (gs). #393

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tjcrone opened this issue Feb 4, 2020 · 11 comments
Closed

psconvert [ERROR]: Cannot execute Ghostscript (gs). #393

tjcrone opened this issue Feb 4, 2020 · 11 comments

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@tjcrone
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tjcrone commented Feb 4, 2020

After a fresh install in a conda environment as per the installation instructions, I get the following error when trying to make my first figure:

psconvert [ERROR]: Cannot execute Ghostscript (gs).
---------------------------------------------------------------------------
GMTCLibError                              Traceback (most recent call last)
<ipython-input-5-6ebedab27258> in <module>
----> 1 fig.show()

~/.conda/envs/axial/lib/python3.8/site-packages/pygmt/figure.py in show(self, dpi, width, method)
    269             img = None
    270         elif method == "static":
--> 271             png = self._preview(
    272                 fmt="png", dpi=dpi, anti_alias=True, as_bytes=True, transparent=True
    273             )

~/.conda/envs/axial/lib/python3.8/site-packages/pygmt/figure.py in _preview(self, fmt, dpi, as_bytes, **kwargs)
    342         """
    343         fname = os.path.join(self._preview_dir.name, "{}.{}".format(self._name, fmt))
--> 344         self.savefig(fname, dpi=dpi, **kwargs)
    345         if as_bytes:
    346             with open(fname, "rb") as image:

~/.conda/envs/axial/lib/python3.8/site-packages/pygmt/figure.py in savefig(self, fname, transparent, crop, anti_alias, show, **kwargs)
    223             kwargs["W"] = "+k"
    224 
--> 225         self.psconvert(prefix=prefix, fmt=fmt, crop=crop, **kwargs)
    226         if show:
    227             launch_external_viewer(fname)

~/.conda/envs/axial/lib/python3.8/site-packages/pygmt/helpers/decorators.py in new_module(*args, **kwargs)
    181                 if alias in kwargs:
    182                     kwargs[arg] = kwargs.pop(alias)
--> 183             return module_func(*args, **kwargs)
    184 
    185         new_module.aliases = aliases

~/.conda/envs/axial/lib/python3.8/site-packages/pygmt/helpers/decorators.py in new_module(*args, **kwargs)
    291                         )
    292             # Execute the original function and return its output
--> 293             return module_func(*args, **kwargs)
    294 
    295         return new_module

~/.conda/envs/axial/lib/python3.8/site-packages/pygmt/figure.py in psconvert(self, **kwargs)
    163             kwargs["A"] = ""
    164         with Session() as lib:
--> 165             lib.call_module("psconvert", build_arg_string(kwargs))
    166 
    167     def savefig(

~/.conda/envs/axial/lib/python3.8/site-packages/pygmt/clib/session.py in call_module(self, module, args)
    496         )
    497         if status != 0:
--> 498             raise GMTCLibError(
    499                 "Module '{}' failed with status code {}:\n{}".format(
    500                     module, status, self._error_message

GMTCLibError: Module 'psconvert' failed with status code 78:
psconvert [ERROR]: Cannot execute Ghostscript (gs).

Here is the output from conda list:

(axial) jovyan@jupyter-tjcrone:~$ conda list
# packages in environment at /home/jovyan/.conda/envs/axial:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       0_gnu    conda-forge
atk                       2.32.0               haf93ef1_0    conda-forge
backcall                  0.1.0                      py_0    conda-forge
boost-cpp                 1.70.0               h8e57a91_2    conda-forge
bzip2                     1.0.8                h516909a_2    conda-forge
ca-certificates           2019.11.28           hecc5488_0    conda-forge
cairo                     1.16.0            hfb77d84_1002    conda-forge
certifi                   2019.11.28               py38_0    conda-forge
cfitsio                   3.470                hb60a0a2_2    conda-forge
cftime                    1.0.4.2                  pypi_0    pypi
chrpath                   0.16              h14c3975_1001    conda-forge
curl                      7.65.3               hf8cf82a_0    conda-forge
dbus                      1.13.6               he372182_0    conda-forge
dcw-gmt                   1.1.4                      1001    conda-forge
decorator                 4.4.1                      py_0    conda-forge
entrypoints               0.3                   py38_1000    conda-forge
expat                     2.2.9                he1b5a44_2    conda-forge
ffmpeg                    4.2                  h167e202_0    conda-forge
fftw                      3.3.8           nompi_h7f3a6c3_1110    conda-forge
fontconfig                2.13.1            h86ecdb6_1001    conda-forge
freetype                  2.10.0               he983fc9_1    conda-forge
freexl                    1.0.5             h14c3975_1002    conda-forge
fribidi                   1.0.5             h516909a_1002    conda-forge
gdal                      3.0.4            py38hbb6b9fb_0    conda-forge
gdk-pixbuf                2.38.2               h3f25603_0    conda-forge
geos                      3.8.0                he1b5a44_0    conda-forge
geotiff                   1.5.1                h38872f0_8    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
ghostscript               9.22              hf484d3e_1001    conda-forge
giflib                    5.2.1                h516909a_1    conda-forge
glib                      2.58.3          py38h6f030ca_1002    conda-forge
gmp                       6.2.0                he1b5a44_1    conda-forge
gmt                       6.0.0                hed9e446_1    conda-forge
gnuplot                   5.2.7                h0fb2448_3    conda-forge
gnutls                    3.6.5             hd3a4fd2_1002    conda-forge
gobject-introspection     1.58.2          py38h5503ade_1002    conda-forge
graphicsmagick            1.3.33               h40aeb3c_0    conda-forge
graphite2                 1.3.13            hf484d3e_1000    conda-forge
gshhg-gmt                 2.3.7                      1002    conda-forge
gst-plugins-base          1.14.5               h0935bb2_1    conda-forge
gstreamer                 1.14.5               h36ae1b5_1    conda-forge
gtk2                      2.24.32              h586f36d_1    conda-forge
harfbuzz                  2.4.0                h9f30f68_3    conda-forge
hdf4                      4.2.13            hf30be14_1003    conda-forge
hdf5                      1.10.5          nompi_h3c11f04_1104    conda-forge
icu                       64.2                 he1b5a44_1    conda-forge
ipykernel                 5.1.4            py38h5ca1d4c_0    conda-forge
ipython                   7.12.0           py38h5ca1d4c_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jedi                      0.16.0                   py38_0    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
json-c                    0.13.1            h14c3975_1001    conda-forge
jupyter_client            5.3.4                    py38_1    conda-forge
jupyter_core              4.6.1                    py38_0    conda-forge
kealib                    1.4.10            h58c409b_1005    conda-forge
krb5                      1.16.4               h2fd8d38_0    conda-forge
lame                      3.100             h14c3975_1001    conda-forge
ld_impl_linux-64          2.33.1               h53a641e_8    conda-forge
libblas                   3.8.0               14_openblas    conda-forge
libcblas                  3.8.0               14_openblas    conda-forge
libclang                  9.0.1           default_hde54327_0    conda-forge
libcurl                   7.65.3               hda55be3_0    conda-forge
libdap4                   3.20.4               hd3bb157_0    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
libgd                     2.2.5             h307a58e_1007    conda-forge
libgdal                   3.0.4                h20022a4_0    conda-forge
libgfortran-ng            7.3.0                hdf63c60_5    conda-forge
libgomp                   9.2.0                h24d8f2e_2    conda-forge
libiconv                  1.15              h516909a_1005    conda-forge
libkml                    1.3.0             h4fcabce_1010    conda-forge
liblapack                 3.8.0               14_openblas    conda-forge
libllvm9                  9.0.1                hc9558a2_0    conda-forge
libnetcdf                 4.7.3           nompi_h9f9fd6a_101    conda-forge
libopenblas               0.3.7                h5ec1e0e_6    conda-forge
libpng                    1.6.37               hed695b0_0    conda-forge
libpq                     12.1                 hd9ab2ff_0    conda-forge
libsodium                 1.0.17               h516909a_0    conda-forge
libspatialite             4.3.0a            ha48a99a_1034    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
libtiff                   4.1.0                hc3755c2_3    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libwebp                   1.0.2                h56121f0_5    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxkbcommon              0.9.1                hebb1f50_0    conda-forge
libxml2                   2.9.10               hee79883_0    conda-forge
lz4-c                     1.8.3             he1b5a44_1001    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
netcdf4                   1.5.3                    pypi_0    pypi
nettle                    3.4.1             h1bed415_1002    conda-forge
nspr                      4.24                 he1b5a44_0    conda-forge
nss                       3.47                 he751ad9_0    conda-forge
numpy                     1.18.1           py38h95a1406_0    conda-forge
openh264                  1.8.0             hdbcaa40_1000    conda-forge
openjpeg                  2.3.1                h981e76c_3    conda-forge
openssl                   1.1.1d               h516909a_0    conda-forge
packaging                 20.1                       py_0    conda-forge
pandas                    1.0.0            py38hb3f55d8_0    conda-forge
pango                     1.42.4               ha030887_1    conda-forge
parso                     0.6.1                      py_0    conda-forge
pcre                      8.43                 he1b5a44_0    conda-forge
pexpect                   4.8.0                    py38_0    conda-forge
pickleshare               0.7.5                 py38_1000    conda-forge
pip                       20.0.2                   py38_1    conda-forge
pixman                    0.38.0            h516909a_1003    conda-forge
poppler                   0.67.0               h14e79db_8    conda-forge
poppler-data              0.4.9                         1    conda-forge
postgresql                12.1                 hc63931a_0    conda-forge
proj                      6.3.0                hc80f0dc_0    conda-forge
prompt_toolkit            3.0.3                      py_0    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
ptyprocess                0.6.0                   py_1001    conda-forge
pygments                  2.5.2                      py_0    conda-forge
pygmt                     0.0.1a0+69.g320a728          pypi_0    pypi
pyparsing                 2.4.6                      py_0    conda-forge
python                    3.8.1                h357f687_2    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
pytz                      2019.3                     py_0    conda-forge
pyzmq                     18.1.1           py38h1768529_0    conda-forge
qt                        5.12.5               hd8c4c69_1    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
setuptools                45.1.0                   py38_0    conda-forge
six                       1.14.0                   py38_0    conda-forge
sqlite                    3.30.1               hcee41ef_0    conda-forge
tbb                       2018.0.5             h2d50403_0    conda-forge
tiledb                    1.7.0                hcde45ca_2    conda-forge
tk                        8.6.10               hed695b0_0    conda-forge
tornado                   6.0.3            py38h516909a_0    conda-forge
traitlets                 4.3.3                    py38_0    conda-forge
tzcode                    2019a             h516909a_1002    conda-forge
wcwidth                   0.1.8                      py_0    conda-forge
wheel                     0.34.2                   py38_0    conda-forge
x264                      1!152.20180806       h14c3975_0    conda-forge
xarray                    0.15.0                     py_0    conda-forge
xerces-c                  3.2.2             h8412b87_1004    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.9                h516909a_0    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-libxt                1.2.0                h516909a_0    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
zeromq                    4.3.2                he1b5a44_2    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge
zstd                      1.4.4                h3b9ef0a_1    conda-forge

Any thoughts on what might be going on? Thanks!
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@tjcrone
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tjcrone commented Feb 4, 2020

Is it possible that GMT cannot find the Ghostscript executable? I wonder if there is a way of passing the location of my Ghostscript executable to fig.show() as a kwarg?

(axial) jovyan@jupyter-tjcrone:~$ which gs
/home/jovyan/.conda/envs/axial/bin/gs

@tjcrone
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tjcrone commented Feb 4, 2020

By hardcoding kwargs["G"] = '/home/jovyan/.conda/envs/axial/bin/gs' just after the following line:

pygmt/pygmt/figure.py

Line 160 in 320a728

kwargs = self._preprocess(**kwargs)
I was able to get pygmt working in my environment.

I'm happy to submit a PR that allows the location of the Ghostscript executable to be found by GMT. One way is to pass **kwargs to fig.show(), but I doubt this is the best way. Another way is to set another environment variable. Any thoughts on how to best approach this? Or is there already another solution that I do not know about? Thanks!

@seisman
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seisman commented Feb 4, 2020

It's really weird. Your gs is in your PATH, and GMT should be able to find it without any extra settings.

@tjcrone
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tjcrone commented Feb 4, 2020

I'm not sure what we see in the Jupyterlab terminal window is the environment seen by a notebook when using conda environments inside Jupyterlab.

@seisman
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seisman commented Feb 4, 2020 •
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Maybe you could try following steps:

  1. Open a terminal (not the Jupyterlab terminal)
  2. activate your conda environment (i.e. axial)
  3. Run python or ipython
  4. Run the example you mentioned and see if it works

@tjcrone
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tjcrone commented Feb 4, 2020

Well, I am running this on Pangeo, which is built on a z2jh foundation using Kubernetes in the cloud. So opening a terminal separate from Jupyterlab isn't quite possible the way it would be if I was running all this locally. I'm switching to the conda environment using nb_conda_kernels. You are probably right that I just need to figure out how to set up my environment correctly.

We don't normally use/need conda environments on Pangeo, but I am unable to conda install gmt==6.0.0 on Pangeo because all sorts of conflicts and I decided to try inside a conda environment. I can at least install GMT, but now we have environment issues. Another solution is to figure out why gmt==6.0.0 cannot be installed on Pangeo.

@tjcrone
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tjcrone commented Feb 4, 2020

@ocefpaf, hope you are doing well. One potential solution to the issue here is figuring out how to conda install gmt==6.0.0 on Pangeo. Any suggestions on how to make this work?

@ocefpaf
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ocefpaf commented Feb 4, 2020

@ocefpaf, hope you are doing well. One potential solution to the issue here is figuring out how to conda install gmt==6.0.0 on Pangeo. Any suggestions on how to make this work?

Sure. I can help you debug that. Can you open an issue outside of pygmt, probably in a pangeo repo, so we can track this? I will need to check the current environment.yaml file pangeo. Can you point me to the one you are using? (Sorry, at this point I should know that already.)

(It may be as simple as a re-render/rebuild of gmt. But probably not that easy ;-p)

@tjcrone
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tjcrone commented Feb 4, 2020

Thank you for the quick response @ocefpaf! New issue here: pangeo-data/pangeo-cloud-federation#525

@tjcrone tjcrone mentioned this issue Feb 4, 2020
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@tjcrone
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tjcrone commented Feb 6, 2020

Working with @ocefpaf, I figured out how to install gmt=6 using conda inside Pangeo without a conda env, and this configuration issue was resolved. Thank you!

@tjcrone tjcrone closed this as completed Feb 6, 2020
@weiji14 weiji14 mentioned this issue Jan 31, 2021
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@ocefpaf @seisman @tjcrone