Closed daxsoule closed 5 years ago
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commented
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PaulWessel
commented
5 years ago Not sure, but sounds like a mix of two GDAL versions and it is getting the wrong one during lookup. @leouieda, any other ideas?
daxsoule
commented
5 years ago @leouieda let me know if you have any ideas or would like to chat briefly.
leouieda
commented
5 years ago @daxsoule thanks for reporting. Which version of GMT did you install from conda (what command did you run to install)? The 6.0.0 alpha builds are no longer being supported (we'll wait until there is an official release to rebuild those).
Could you please paste the output of conda list here?
daxsoule
commented
5 years ago Here you go:
jovyan@jupyter-daxsoule:~$ conda list
# packages in environment at /opt/conda:
#
# Name Version Build Channel
alembic 0.9.9 py_0 conda-forge
appdirs 1.4.3 py_1 conda-forge
arpack 3.6.3 blas_openblash6d6ea35_1002 [blas_openblas] conda-forge
arrow-cpp 0.11.1 py36h3bd774a_0 conda-forge
asciitree 0.3.3 py_2 conda-forge
asn1crypto 0.24.0 py36_0 conda-forge
atk 2.25.90 h05f3006_1 conda-forge
atomicwrites 1.2.1 py_0 conda-forge
attrs 18.2.0 py_0 conda-forge
av 6.1.0 py36h7273d18_0 conda-forge
azure-common 1.1.16 <pip>
azure-storage-blob 1.4.0 <pip>
azure-storage-common 1.4.0 <pip>
backcall 0.1.0 py_0 conda-forge
blas 1.1 openblas conda-forge
bleach 2.1.3 py_0 conda-forge
blinker 1.4 py_1 conda-forge
blosc 1.15.1 hfc679d8_0 conda-forge
bokeh 1.0.2 py36_1000 conda-forge
boost-cpp 1.68.0 h3a22d5f_0 conda-forge
bzip2 1.0.6 h470a237_2 conda-forge
ca-certificates 2019.3.9 hecc5488_0 conda-forge
cachetools 2.1.0 py_0 conda-forge
cairo 1.14.12 h276e583_5 conda-forge
cartopy 0.17.0 py36h0aa2c8f_1004 conda-forge
certifi 2019.3.9 py36_0 conda-forge
cffi 1.11.5 py36_0 conda-forge
cftime 1.0.3.4 py36h7eb728f_0 conda-forge
chardet 3.0.4 py36_0 conda-forge
click 7.0 py_0 conda-forge
click-plugins 1.0.4 py_0 conda-forge
cligj 0.5.0 py_0 conda-forge
cloudpickle 0.6.1 py_0 conda-forge
cmake 3.14.0 hf94ab9c_0 conda-forge
colorcet 1.0.0 py_0 conda-forge
conda 4.5.11 py36_1000 conda-forge
conda-env 2.6.0 0 conda-forge
configurable-http-proxy 3.1.0 node8_1 conda-forge
cryptography 2.6.1 py36h72c5cf5_0 conda-forge
curl 7.64.1 hf8cf82a_0 conda-forge
cycler 0.10.0 py_1 conda-forge
cython 0.29.1 py36hfc679d8_0 conda-forge
cytoolz 0.9.0.1 py36h470a237_1 conda-forge
dask 1.0.0 py_0 conda-forge
dask-core 1.0.0 py_0 conda-forge
dask-kubernetes 0.6.0 py_0 conda-forge
datashader 0.6.8 py_0 conda-forge
datashape 0.5.4 py36_0 conda-forge
dbus 1.13.0 h3a4f0e9_0 conda-forge
dcw-gmt 1.1.4 1001 conda-forge
decorator 4.3.0 py_0 conda-forge
descartes 1.1.0 py_2 conda-forge
distributed 1.25.0 py36_1000 conda-forge
driveanon 0.1.0 <pip>
entrypoints 0.2.3 py36_1 conda-forge
expat 2.2.5 hfc679d8_2 conda-forge
fasteners 0.14.1 py_3 conda-forge
fastparquet 0.2.0 py36h7eb728f_0 conda-forge
ffmpeg 4.0.2 ha0c5888_2 conda-forge
fftw 3.3.8 h470a237_1 conda-forge
fiona 1.8.4 py36heb36068_1001 conda-forge
fontconfig 2.13.1 h65d0f4c_0 conda-forge
freetype 2.9.1 h6debe1e_4 conda-forge
freexl 1.0.5 h470a237_2 conda-forge
future 0.17.0 py36_1000 conda-forge
gdal 2.3.3 py36hf242f0b_1 conda-forge
gdk-pixbuf 2.36.12 h4ab6910_1 conda-forge
geopandas 0.4.0 py_1 conda-forge
geos 3.7.1 hf484d3e_1000 conda-forge
geotiff 1.4.3 h1105359_1000 conda-forge
geoviews 1.6.0a3 py_0 pyviz/label/dev
geoviews-core 1.6.0a3 py_0 pyviz/label/dev
gettext 0.19.8.1 h5e8e0c9_1 conda-forge
ghostscript 9.22 hf484d3e_1001 conda-forge
giflib 5.1.7 h516909a_1 conda-forge
glib 2.56.2 h464dc38_1 conda-forge
gmp 6.1.2 hfc679d8_0 conda-forge
gmt 6.0.0a18 blas_openblash4f9c4ba_0 [blas_openblas] conda-forge
gnutls 3.5.19 h2a4e5f8_1 conda-forge
gobject-introspection 1.56.1 py36haaf12d0_1 conda-forge
google-api-core 0.1.4 py_0 conda-forge
google-auth 1.6.1 py_0 conda-forge
google-cloud-core 0.28.1 py_0 conda-forge
google-cloud-storage 1.12.0 py_0 conda-forge
google-resumable-media 0.3.1 py_0 conda-forge
googleapis-common-protos 1.5.5 py_0 conda-forge
graphite2 1.3.12 hfc679d8_1 conda-forge
graphviz 2.38.0 h08bfae6_9 conda-forge
gshhg-gmt 2.3.7 1002 conda-forge
gst-plugins-base 1.12.5 hde13a9d_0 conda-forge
gstreamer 1.12.5 h5856ed1_0 conda-forge
gtk2 2.24.31 hde048ef_0 conda-forge
harfbuzz 1.9.0 h04dbb29_1 conda-forge
hdf4 4.2.13 h951d187_2 conda-forge
hdf5 1.10.4 nompi_h3c11f04_1106 conda-forge
heapdict 1.0.0 py36_1000 conda-forge
holoviews 1.11.0a11 pyh39e3cac_0 pyviz/label/dev
html5lib 1.0.1 py_0 conda-forge
hvplot 0.3.0a6 py_0 pyviz/label/dev
icu 58.2 hfc679d8_0 conda-forge
idna 2.7 py36_0 conda-forge
imagehash 4.0 py_0 conda-forge
imageio 2.4.1 py36_1000 conda-forge
intake 0.3.0 py_0 intake
intake-xarray 0.2.4 py_0 intake
ipykernel 4.8.2 py36_0 conda-forge
ipython 6.4.0 py36_0 conda-forge
ipython_genutils 0.2.0 py36_0 conda-forge
ipywidgets 7.4.2 py_0 conda-forge
jedi 0.12.0 py36_0 conda-forge
jinja2 2.10 py36_0 conda-forge
jpeg 9c h470a237_1 conda-forge
json-c 0.13.1 h14c3975_1001 conda-forge
jsonschema 2.6.0 py36_1 conda-forge
julia 1.0.3 blas_openblash12d65f3_2 [blas_openblas] conda-forge
jupyter 1.0.0 py_1 conda-forge
jupyter_client 5.2.3 py_1 conda-forge
jupyter_console 5.2.0 py36_1 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
jupyterhub 0.8.1 py36_0 conda-forge
jupyterlab 0.35.4 py36_0 conda-forge
jupyterlab_launcher 0.13.1 py_2 conda-forge
jupyterlab_server 0.2.0 py_0 conda-forge
kealib 1.4.10 h1978553_1003 conda-forge
kiwisolver 1.0.1 py36h2d50403_2 conda-forge
krb5 1.16.3 h05b26f9_1001 conda-forge
libcurl 7.64.1 hda55be3_0 conda-forge
libdap4 3.19.1 h8fe5423_1 conda-forge
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libffi 3.2.1 3 conda-forge
libgcc 7.2.0 h69d50b8_2 defaults
libgcc-ng 8.2.0 hdf63c60_1 defaults
libgdal 2.3.3 hdb8f723_1 conda-forge
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.3.0 hdf63c60_0 defaults
libgit2 0.28.1 heeda6b9_1 conda-forge
libiconv 1.15 h470a237_3 conda-forge
libkml 1.3.0 h328b03d_1009 conda-forge
libnetcdf 4.6.2 hbdf4f91_1001 conda-forge
libpng 1.6.36 ha92aebf_0 conda-forge
libpq 11.2 h4770945_0 conda-forge
libprotobuf 3.6.1 hd28b015_0 conda-forge
libsodium 1.0.16 0 conda-forge
libspatialindex 1.8.5 hfc679d8_3 conda-forge
libspatialite 4.3.0a hb5ec416_1026 conda-forge
libssh2 1.8.2 h22169c7_2 conda-forge
libstdcxx-ng 8.2.0 hdf63c60_1 defaults
libtiff 4.0.10 he6b73bb_0 conda-forge
libtool 2.4.6 h470a237_2 conda-forge
libuuid 2.32.1 h470a237_2 conda-forge
libuv 1.26.0 h14c3975_0 conda-forge
libxcb 1.13 h470a237_2 conda-forge
libxml2 2.9.8 h422b904_5 conda-forge
libxslt 1.1.32 h88dbc4e_2 conda-forge
llvmlite 0.26.0 py36hd28b015_0 conda-forge
locket 0.2.0 py_2 conda-forge
lxml 4.2.5 py36hc9114bc_0 conda-forge
lz4 1.1.0 py36h3b97293_1 conda-forge
lz4-c 1.8.1.2 0 conda-forge
lzo 2.10 h470a237_0 conda-forge
mako 1.0.7 py36_0 conda-forge
markdown 2.6.11 py_0 conda-forge
markupsafe 1.0 py36_0 conda-forge
matplotlib 3.0.3 py36_0 conda-forge
matplotlib-base 3.0.3 py36h167e16e_0 conda-forge
metis 5.1.0 hfc679d8_3 conda-forge
mistune 0.8.3 py36_1 conda-forge
monotonic 1.5 py_0 conda-forge
more-itertools 4.3.0 py36_1000 conda-forge
mpfr 4.0.1 h16a7912_0 conda-forge
msgpack-numpy 0.4.4.2 py_0 conda-forge
msgpack-python 0.6.0 py36h2d50403_0 conda-forge
multipledispatch 0.6.0 py_0 conda-forge
munch 2.3.2 py_0 conda-forge
nbconvert 5.3.1 py_1 conda-forge
nbformat 4.4.0 py36_0 conda-forge
nbserverproxy 0.8.6 py_1000 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
netcdf4 1.5.0 py36had58050_0 conda-forge
nettle 3.3 0 conda-forge
networkx 2.2 py_1 conda-forge
nodejs 8.10.0 0 conda-forge
nomkl 3.0 0 defaults
notebook 5.5.0 py36_0 conda-forge
numba 0.41.0 py36hf8a1672_0 conda-forge
numcodecs 0.6.2 py36hfc679d8_0 conda-forge
numexpr 2.6.8 py36hf8a1672_0 conda-forge
numpngw 0.0.7 <pip>
numpy 1.16.2 py36_blas_openblash1522bff_0 [blas_openblas] conda-forge
oauthlib 2.1.0 py_0 conda-forge
obspy 1.1.0 py36h7eb728f_2 conda-forge
olefile 0.46 py_0 conda-forge
openblas 0.3.3 h9ac9557_1001 conda-forge
openh264 1.8.0 hd28b015_0 conda-forge
openjpeg 2.3.0 h0e734dc_3 conda-forge
openlibm 0.5.4 h470a237_0 conda-forge
openspecfun 0.5.3 h26a2512_0 conda-forge
openssl 1.1.1b h14c3975_1 conda-forge
owslib 0.17.0 py_0 conda-forge
packaging 18.0 py_0 conda-forge
pamela 0.3.0 py36_0 conda-forge
pandas 0.23.4 py36hf8a1672_0 conda-forge
pandoc 2.2.1 0 conda-forge
pandocfilters 1.4.2 py36_0 conda-forge
panel 0.3.1 py_0 pyviz/label/dev
pango 1.40.14 he752989_2 conda-forge
param 1.8.1 py_0 conda-forge
parquet-cpp 1.5.1 2 conda-forge
parso 0.2.1 py_0 conda-forge
partd 0.3.9 py_0 conda-forge
pcre 8.41 hfc679d8_3 conda-forge
pcre2 10.23 2 conda-forge
pexpect 4.6.0 py36_0 conda-forge
pickleshare 0.7.4 py36_0 conda-forge
pillow 5.3.0 py36hc736899_0 conda-forge
pip 9.0.3 py36_0 conda-forge
pip 18.1 <pip>
pixman 0.34.0 h470a237_3 conda-forge
pluggy 0.8.0 py_0 conda-forge
poppler 0.67.0 hdf8a1b3_2 conda-forge
poppler-data 0.4.9 0 conda-forge
postgresql 11.2 h61314c7_0 conda-forge
proj4 5.2.0 h14c3975_1001 conda-forge
prompt_toolkit 1.0.15 py36_0 conda-forge
protobuf 3.6.1 py36hfc679d8_1 conda-forge
psutil 5.4.8 py36h470a237_0 conda-forge
psycopg2 2.7.7 py36h72c5cf5_2 conda-forge
pthread-stubs 0.4 h470a237_1 conda-forge
ptyprocess 0.5.2 py36_0 conda-forge
py 1.7.0 py_0 conda-forge
pyarrow 0.11.1 py36hfc679d8_0 conda-forge
pyasn1 0.4.4 py_1 conda-forge
pyasn1-modules 0.2.1 py_0 conda-forge
pycamhd 0.7.0 <pip>
pycosat 0.6.3 py36_0 conda-forge
pycparser 2.18 py36_0 conda-forge
pyct 0.4.5 py_0 conda-forge
pyct-core 0.4.5 py_0 conda-forge
pyepsg 0.4.0 py_0 conda-forge
pygments 2.2.0 py36_0 conda-forge
pyjwt 1.6.4 py_0 conda-forge
pykdtree 1.3.1 py36h7eb728f_2 conda-forge
pyopenssl 18.0.0 py36_0 conda-forge
pyparsing 2.3.0 py_0 conda-forge
pyproj 1.9.6 py36hc0953d3_1000 conda-forge
pyqt 4.11.4 py36_3 conda-forge
pysal 1.14.4.post2 py36_1001 conda-forge
pyshp 2.0.0 py_0 conda-forge
pysocks 1.6.8 py36_1 conda-forge
pytables 3.4.4 py36h5d69a80_1004 conda-forge
pytest 3.9.1 py36_1000 conda-forge
python 3.6.7 h0371630_0 defaults
python-blosc 1.6.2 py36hfc679d8_1 conda-forge
python-dateutil 2.7.3 py_0 conda-forge
python-editor 1.0.3 py36_0 conda-forge
python-graphviz 0.8.4 py36_1002 conda-forge
python-kubernetes 4.0.0 py36_1 conda-forge
python-oauth2 1.0.1 py36_0 conda-forge
python-snappy 0.5.3 py36h00d4201_0 conda-forge
pytz 2018.7 py_0 conda-forge
pyviz_comms 0.6.0 py_0 conda-forge
pywavelets 1.0.1 py36h7eb728f_0 conda-forge
pyyaml 3.13 py36h470a237_1 conda-forge
pyzmq 17.0.0 py36_4 conda-forge
qt 4.8.7 2 defaults
qtconsole 4.4.3 py_0 conda-forge
readline 7.0 hf8c457e_1001 conda-forge
requests 2.19.1 py36_0 conda-forge
requests-oauthlib 1.0.0 py_1 conda-forge
rhash 1.3.6 h14c3975_1001 conda-forge
rsa 3.4.2 py_1 conda-forge
rtree 0.8.3 py36_1000 conda-forge
ruamel_yaml 0.15.40 py36h470a237_0 conda-forge
scikit-image 0.14.1 py36hfc679d8_1 conda-forge
scipy 1.2.1 py36_blas_openblash1522bff_0 [blas_openblas] conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 39.2.0 py36_0 conda-forge
shapely 1.6.4 py36h2afed24_1003 conda-forge
simplegeneric 0.8.1 py36_0 conda-forge
sip 4.18 py36_1 conda-forge
six 1.11.0 py36_1 conda-forge
snappy 1.1.7 hfc679d8_2 conda-forge
sortedcontainers 2.1.0 py_0 conda-forge
sqlalchemy 1.2.8 py36_0 conda-forge
sqlite 3.26.0 h67949de_1001 conda-forge
suitesparse 4.5.6 blas_openblash17e8c26_1201 [blas_openblas] conda-forge
tbb 2019.3 h2d50403_0 conda-forge
tblib 1.3.2 py_1 conda-forge
terminado 0.8.1 py36_0 conda-forge
testpath 0.3.1 py36_0 conda-forge
thrift 0.11.0 py36hfc679d8_1 conda-forge
tk 8.6.9 ha92aebf_0 conda-forge
toolz 0.9.0 py_1 conda-forge
tornado 5.0.2 py36_0 conda-forge
traitlets 4.3.2 py36_0 conda-forge
tzcode 2018g h14c3975_1001 conda-forge
urllib3 1.23 py36_0 conda-forge
wcwidth 0.1.7 py36_0 conda-forge
webencodings 0.5 py36_0 conda-forge
websocket-client 0.40.0 py36_0 conda-forge
wheel 0.31.0 py36_0 conda-forge
widgetsnbextension 3.4.2 py36_1000 conda-forge
x264 1!152.20180717 h470a237_1 conda-forge
xarray 0.11.0 py36_1000 conda-forge
xerces-c 3.2.2 hac72e42_1001 conda-forge
xorg-kbproto 1.0.7 h470a237_2 conda-forge
xorg-libice 1.0.9 h470a237_4 conda-forge
xorg-libsm 1.2.3 h8c8a85c_0 conda-forge
xorg-libx11 1.6.6 h470a237_0 conda-forge
xorg-libxau 1.0.8 h470a237_6 conda-forge
xorg-libxdmcp 1.1.2 h470a237_7 conda-forge
xorg-libxext 1.3.3 h470a237_4 conda-forge
xorg-libxpm 3.5.12 h470a237_2 conda-forge
xorg-libxrender 0.9.10 h470a237_2 conda-forge
xorg-libxt 1.1.5 h470a237_2 conda-forge
xorg-renderproto 0.11.1 h470a237_2 conda-forge
xorg-xextproto 7.3.0 h470a237_2 conda-forge
xorg-xproto 7.0.31 h470a237_7 conda-forge
xz 5.2.4 h470a237_1 conda-forge
yaml 0.1.7 0 conda-forge
zarr 2.2.0 py_1 conda-forge
zeromq 4.2.5 1 conda-forge
zict 0.1.3 py_0 conda-forge
zlib 1.2.11 h470a237_3 conda-forgeThanks! I see you have the gmt 6.0.0a18 from conda-forge, which is strange because that should not be there. This is what is causing you trouble. I imagine that your environment file only specifies gmt without a version, right? Could you try using gmt=5.4.* instead? (note that this version would not with pygmt)
I opened conda-forge/gmt-feedstock#63 to address this issue. Thanks for bringing this to our attention! I would not have noticed this otherwise.
seisman
commented
5 years ago Closed as the issue should be fixed now. Please reopen the issue if you still have the same issue.
I am trying to get started running GMT in on a PANGEO cluster. I have Conda installed gmt
$gmt returns >>
gmt: symbol lookup error: /opt/conda/bin/../lib/libgdal.so.20: undefined symbol: _ZNK6libdap5Error17get_error_messageB5cxx11EvTesting further using the tutorial scripts that are found in gmt/doc/scripts from the git repo:
source GMT_tut_17.shreturns:
gmt: symbol lookup error: /opt/conda/bin/../lib/libgdal.so.20: undefined symbol: _ZNK6libdap5Error17get_error_messageB5cxx11EvSystem information python 3.6.7 |Anaconda, Inc.| (default, Oct 23 2018, 19:16:44)
[GCC 7.3.0] on linux