Hi, I am trying to use the python API for doing some vapor work but am getting an error when trying to load a dataset that loads without issue in the GUI:
Could not find VAPOR installed UDUnits database
Attempting to fall back to system install
UDUnits failed to initialize
UDUnits Error: Can't open installed, default, unit database
Failed to initialized udunits2 library : Can't open installed, default, unit database
Could not find VAPOR installed UDUnits database
Attempting to fall back to system install
UDUnits failed to initialize
UDUnits Error: Can't open installed, default, unit database
Failed to initialize udunits2 library : Can't open installed, default, unit database
Failed to initialize data importer
Failure to open data set of type "cf"
When creating the environment, I didn’t notice any issues. I see udunits2 v2.2.28 in my environment.
Hi, is this on Casper?
If so, could you tell us the output of ncarenv in your console?
If not, could you tell us what OS you’re using, and the version of VAPOR you’re seeing this with (probably 3.10.0 but just want to make sure)?
Hi - yes, I’m running on Casper in a jupyter notebook with VAPOR 3.10.0 installed. I’m not sure if this is what you meant, but I have the ncarenv/24.12 module loaded. (If I’m supposed to run a command ncarenv somewhere, where should I run that? It doesn’t register as a command from the CLI or in python.)
Sorry, you’re right about that ncarenv part. But that’s the information I needed. I need to test this and discuss it with the team. Hopefully will get back to you tomorrow. Thank you for reporting this.
Could you share the script you’re using to produce this, on glade? Thanks.
Ok, sounds good - thanks a lot! If it’s easier to communicate via email or slack, let me know.
The script I am running is here: u/home/hawbecker/Code/Python/FastEddy/Vapor.ipynb
The code is very simple if you don’t have access to that file, this is what I’m running:
from vapor import session, renderer, dataset
from vapor.animation import Animation
from vapor.dataset import Dataset
import os
import glob
ses = session.Session()
f_dir = '/glade/derecho/scratch/hawbecker/Projects/ATEC/canopy_clearing_experiments/production/4m/output_canopyClearingCanopyQ/0'
files = sorted(glob.glob(os.path.join(f_dir,'FE_CANOPYhr*_cf.nc')))
f = files[0]
data = ses.OpenDataset(dataset.CF, f)
Strange, I’m able to run this. Could you show the output for ncarenv from a terminal?
Do you mean run module list and show the version that is loaded for ncarenv? That was 24.12 from a terminal. When you mention running it from a console, what do you mean?
Yes, module list will indicate other modules that are loaded. I’m running ncarenv 24.12 as well but it works for me, so I’m wondering if there’s another module that is causing this. You can run this from an ssh session, or from Casper’s console application, named “Konsole”.
Here’s the output from module list:
Currently Loaded Modules:
1) ncarenv/24.12 (S) 3) ncarcompilers/1.0.0 5) ucx/1.17.0 7) hdf5/1.12.3 9) ncview/2.1.9
2) intel/2024.2.1 4) cuda/12.3.2 6) openmpi/5.0.6 8) netcdf/4.9.2 10) conda/latest
I’m also putting the info from conda list here since I think that would maybe show the differences in our python environments that could be causing this:
# packages in environment at /glade/work/hawbecker/conda-envs/vapor_python:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alsa-lib 1.2.8 h166bdaf_0 conda-forge
anyio 4.9.0 pyh29332c3_0 conda-forge
anywidget 0.9.18 pyhd8ed1ab_0 conda-forge
aom 3.5.0 h27087fc_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_1 conda-forge
argon2-cffi-bindings 21.2.0 py39h8cd3c5a_5 conda-forge
arrow 1.3.0 pyhd8ed1ab_1 conda-forge
assimp 5.3.1 h378b44f_1 conda-forge
asttokens 3.0.0 pyhd8ed1ab_1 conda-forge
async-lru 2.0.5 pyh29332c3_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 25.3.0 pyh71513ae_0 conda-forge
babel 2.17.0 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.13.4 pyha770c72_0 conda-forge
binutils_impl_linux-64 2.39 he00db2b_1 conda-forge
binutils_linux-64 2.39 h5fc0e48_13 conda-forge
bleach 6.2.0 pyh29332c3_4 conda-forge
bleach-with-css 6.2.0 h82add2a_4 conda-forge
boost-cpp 1.78.0 h5adbc97_2 conda-forge
bqplot 0.12.43 pyhd8ed1ab_1 conda-forge
brotli 1.1.0 hb9d3cd8_2 conda-forge
brotli-bin 1.1.0 hb9d3cd8_2 conda-forge
brotli-python 1.1.0 py39hf88036b_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.4.26 hbd8a1cb_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.16.0 ha61ee94_1014 conda-forge
certifi 2025.4.26 py39h06a4308_0 anaconda
cffi 1.17.1 py39h15c3d72_0 conda-forge
cftime 1.6.4 py39hf3d9206_1 conda-forge
cfunits 3.3.7 pypi_0 pypi
charset-normalizer 3.4.2 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pyhd8ed1ab_1 conda-forge
contourpy 1.3.0 py39h74842e3_2 conda-forge
cppyy 2.2.0 py39ha3ed2ce_1 conda-forge
cppyy-backend 1.14.7 py39h1a9c180_0 conda-forge
cppyy-cling 6.25.2 py39h0f9e12e_1 conda-forge
cpycppyy 1.12.8 py39h1a9c180_1 conda-forge
curl 8.1.2 h409715c_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
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exceptiongroup 1.3.0 pyhd8ed1ab_0 conda-forge
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fftw 3.3.10 nompi_hf1063bd_110 conda-forge
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font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_3 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.58.0 py39h9399b63_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_1 conda-forge
freeglut 3.2.2 h9c3ff4c_1 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
gcc_impl_linux-64 9.5.0 h99780fb_19 conda-forge
gcc_linux-64 9.5.0 h4258300_13 conda-forge
geotiff 1.6.0 h2b14fbe_4 conda-forge
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gxx_impl_linux-64 9.5.0 h99780fb_19 conda-forge
gxx_linux-64 9.5.0 h43f449f_13 conda-forge
h11 0.16.0 pyhd8ed1ab_0 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
h5py 3.7.0 nompi_py39h817c9c5_102 conda-forge
harfbuzz 6.0.0 h8e241bc_0 conda-forge
hdf4 4.2.15 h9772cbc_5 conda-forge
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hdf5plugin 4.1.1 py39h1e10723_0 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
httpcore 1.0.9 pyh29332c3_0 conda-forge
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icu 70.1 h27087fc_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
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krb5 1.20.1 h81ceb04_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.14 h6ed2654_0 conda-forge
ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
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python 3.9.18 h0755675_0_cpython conda-forge
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python-fastjsonschema 2.21.1 pyhd8ed1ab_0 conda-forge
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python_abi 3.9 7_cp39 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py39h9399b63_2 conda-forge
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qt-main 5.15.8 h5d23da1_6 conda-forge
readline 8.2 h8c095d6_2 conda-forge
referencing 0.36.2 pyh29332c3_0 conda-forge
requests 2.32.3 pyhd8ed1ab_1 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_1 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rpds-py 0.24.0 py39h3506688_0 conda-forge
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tomli 2.2.1 pyhd8ed1ab_1 conda-forge
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typing-extensions 4.13.2 h0e9735f_0 conda-forge
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tzdata 2025b h78e105d_0 conda-forge
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uri-template 1.3.0 pyhd8ed1ab_1 conda-forge
urllib3 2.4.0 pyhd8ed1ab_0 conda-forge
vapor 3.10.0 h2bc3f7f_0 ncar-vapor
vapor-maps 1.0.0 0 ncar-vapor
wcwidth 0.2.13 pyhd8ed1ab_1 conda-forge
webcolors 24.11.1 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_1 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.14 pyhd8ed1ab_0 conda-forge
wrapt 1.17.2 py39h8cd3c5a_0 conda-forge
wurlitzer 3.1.1 pyhd8ed1ab_1 conda-forge
x264 1!164.3095 h166bdaf_2 conda-forge
x265 3.5 h924138e_3 conda-forge
xarray 2022.12.0 pyhd8ed1ab_0 conda-forge
xcb-util 0.4.0 h516909a_0 conda-forge
xcb-util-image 0.4.0 h166bdaf_0 conda-forge
xcb-util-keysyms 0.4.0 h516909a_0 conda-forge
xcb-util-renderutil 0.3.9 h166bdaf_0 conda-forge
xcb-util-wm 0.4.1 h516909a_0 conda-forge
xkeyboard-config 2.38 h0b41bf4_0 conda-forge
xorg-damageproto 1.2.1 hb9d3cd8_1003 conda-forge
xorg-fixesproto 5.0 hb9d3cd8_1003 conda-forge
xorg-glproto 1.4.17 hb9d3cd8_1003 conda-forge
xorg-inputproto 2.3.2 hb9d3cd8_1003 conda-forge
xorg-kbproto 1.0.7 hb9d3cd8_1003 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.4 h0b41bf4_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdamage 1.1.5 h7f98852_1 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrandr 1.5.2 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-randrproto 1.5.0 hb9d3cd8_1002 conda-forge
xorg-renderproto 0.11.1 hb9d3cd8_1003 conda-forge
xorg-util-macros 1.20.2 hb9d3cd8_0 conda-forge
xorg-xextproto 7.3.0 hb9d3cd8_1004 conda-forge
xorg-xf86vidmodeproto 2.3.1 hb9d3cd8_1005 conda-forge
xorg-xproto 7.0.31 hb9d3cd8_1008 conda-forge
xz 5.8.1 hbcc6ac9_1 conda-forge
xz-gpl-tools 5.8.1 hbcc6ac9_1 conda-forge
xz-tools 5.8.1 hb9d3cd8_1 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zeromq 4.3.5 h59595ed_1 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zlib 1.2.13 h4ab18f5_6 conda-forge
zstandard 0.23.0 py39h8cd3c5a_2 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
Running the python script from the command line (instead of in the notebook) produces a different error:
(vapor_python) hawbecker@casper-login1:FastEddy ➜ python Vapor.py
Vapor 3.10.0
Python 3.9.18 (/glade/work/hawbecker/conda-envs/vapor_python)
In file included from input_line_28:1:
In file included from /glade/work/hawbecker/conda-envs/vapor_python/include/python3.9/CPyCppyy/API.h:26:
In file included from /glade/work/hawbecker/conda-envs/vapor_python/include/python3.9/Python.h:50:
In file included from /glade/work/hawbecker/conda-envs/vapor_python/include/python3.9/pyport.h:212:
In file included from /glade/work/hawbecker/conda-envs/vapor_python/bin/../x86_64-conda-linux-gnu/sysroot/usr/include/sys/time.h:28:
/glade/work/hawbecker/conda-envs/vapor_python/bin/../x86_64-conda-linux-gnu/sysroot/usr/include/bits/time.h:30:8: error: redefinition of 'timeval'
struct timeval
^
/usr/include/bits/types/struct_timeval.h:8:8: note: previous definition is here
struct timeval
^
Traceback (most recent call last):
File "/glade/u/home/hawbecker/Code/Python/FastEddy/Vapor.py", line 1, in <module>
from vapor import session, renderer, dataset
File "/glade/work/hawbecker/conda-envs/vapor_python/lib/python3.9/site-packages/vapor/__init__.py", line 19, in <module>
link.Wasp.RegisterResourceFinder(config.GetResourceSafe)
TypeError: void Wasp::RegisterResourceFinder(std::string(*)(const std::string&) cb) =>
TypeError: could not convert argument 1
pearse
May 17, 2025, 12:23am
11
Sorry about this Patrick, I’m stumped on this one. I’ve tried loading the modules you’ve shown, and your conda list does indicate that udunits is present. Could you try re-installing vapor in a new environment that’s separate from the one you’re currently using and let us know if it persists?