Re: [python-users] miniconda error message

  • To: "Weber, Jim" <Jim.Weber@xxxxxxx>, "python-users@xxxxxxxxxxxxxxxx" <python-users@xxxxxxxxxxxxxxxx>
  • Subject: Re: [python-users] miniconda error message
  • From: "Herzmann, Daryl E [AGRON]" <akrherz@xxxxxxxxxxx>
  • Date: Thu, 19 May 2022 13:15:25 +0000
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Greetings,

Thanks.  That pyproj from pypi looks to be trouble.  Can we try this?

 conda install --force-reinstall pyproj

Also, how are you running these python processes?  From cron?  From pqact ?

daryl

________________________________________
From: Weber, Jim <Jim.Weber@xxxxxxx>
Sent: Wednesday, May 18, 2022 6:30 PM
To: Herzmann, Daryl E [AGRON]; python-users@xxxxxxxxxxxxxxxx
Subject: RE: miniconda error message

Hi,  it is a long list, but here it is:   (Thanks!)


# packages in environment at /home/ldm/miniconda3:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
brotli                    1.0.9                h166bdaf_7    conda-forge
brotli-bin                1.0.9                h166bdaf_7    conda-forge
brotlipy                  0.7.0           py39hb9d737c_1004    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2021.10.8            ha878542_0    conda-forge
cartopy                   0.20.2           py39h0ddd56c_4    conda-forge
certifi                   2021.10.8        py39hf3d152e_2    conda-forge
cffi                      1.15.0           py39h4bc2ebd_0    conda-forge
cftime                    1.6.0            py39hd257fcd_1    conda-forge
charset-normalizer        2.0.12             pyhd8ed1ab_0    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
conda                     4.12.0           py39hf3d152e_0    conda-forge
conda-package-handling    1.8.1            py39hb9d737c_1    conda-forge
cryptography              36.0.2           py39hd97740a_1    conda-forge
curl                      7.83.1               h7bff187_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
esmf                      8.2.0           nompi_h61edca3_0    conda-forge
expat                     2.4.8                h27087fc_0    conda-forge
fonttools                 4.33.3           py39hb9d737c_0    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
geos                      3.10.2               h9c3ff4c_0    conda-forge
giflib                    5.2.1                h36c2ea0_2    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
hdf4                      4.2.15               h10796ff_3    conda-forge
hdf5                      1.12.1          nompi_h2386368_104    conda-forge
idna                      3.3                pyhd8ed1ab_0    conda-forge
importlib-metadata        4.11.3           py39hf3d152e_1    conda-forge
importlib_metadata        4.11.3               hd8ed1ab_1    conda-forge
importlib_resources       5.7.1              pyhd8ed1ab_1    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jpeg                      9e                   h166bdaf_1    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.2            py39hf939315_1    conda-forge
krb5                      1.19.3               h3790be6_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      3.0                  h9c3ff4c_0    conda-forge
libblas                   3.9.0           14_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h166bdaf_7    conda-forge
libbrotlidec              1.0.9                h166bdaf_7    conda-forge
libbrotlienc              1.0.9                h166bdaf_7    conda-forge
libcblas                  3.9.0           14_linux64_openblas    conda-forge
libcurl                   7.83.1               h7bff187_0    conda-forge
libdeflate                1.10                 h7f98852_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.1.0              h8d9b700_16    conda-forge
libgfortran-ng            12.1.0              h69a702a_16    conda-forge
libgfortran5              12.1.0              hdcd56e2_16    conda-forge
libgomp                   12.1.0              h8d9b700_16    conda-forge
liblapack                 3.9.0           14_linux64_openblas    conda-forge
libnetcdf                 4.8.1           nompi_h329d8a1_102    conda-forge
libnghttp2                1.47.0               h727a467_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.20          pthreads_h78a6416_0    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-ng              12.1.0              ha89aaad_16    conda-forge
libtiff                   4.3.0                h542a066_3    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libwebp                   1.2.2                h3452ae3_0    conda-forge
libwebp-base              1.2.2                h7f98852_1    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libzip                    1.8.0                h4de3113_1    conda-forge
libzlib                   1.2.11            h166bdaf_1014    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
matplotlib                3.4.3                    pypi_0    pypi
matplotlib-base           3.5.2            py39h700656a_0    conda-forge
metpy                     1.3.0              pyhd8ed1ab_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nco                       5.0.3                hcfc2ecc_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
netcdf-fortran            4.5.4           nompi_h2b6e579_100    conda-forge
netcdf4                   1.5.8           nompi_py39h64b754b_101    conda-forge
numpy                     1.22.3           py39hc58783e_2    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openssl                   1.1.1o               h166bdaf_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.3.3                    pypi_0    pypi
pillow                    8.3.2                    pypi_0    pypi
pint                      0.19.2             pyhd8ed1ab_0    conda-forge
pip                       22.1               pyhd8ed1ab_0    conda-forge
pooch                     1.6.0              pyhd8ed1ab_0    conda-forge
proj                      9.0.0                h93bde94_1    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pycosat                   0.6.3           py39hb9d737c_1010    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyproj                    3.2.1                    pypi_0    pypi
pyshp                     2.3.0              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1            py39hf3d152e_5    conda-forge
python                    3.9.12          h9a8a25e_1_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pytz                      2022.1             pyhd8ed1ab_0    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
requests                  2.27.1             pyhd8ed1ab_0    conda-forge
ruamel_yaml               0.15.80         py39h3811e60_1006    conda-forge
scipy                     1.8.0            py39hee8e79c_1    conda-forge
setuptools                62.3.1           py39hf3d152e_0    conda-forge
shapely                   1.8.2            py39h73b9895_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.38.5               h4ff8645_0    conda-forge
tempest-remap             2.1.3                h1a2fe09_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tqdm                      4.64.0             pyhd8ed1ab_0    conda-forge
traitlets                 5.2.1.post0        pyhd8ed1ab_0    conda-forge
typing_extensions         4.2.0              pyha770c72_1    conda-forge
tzdata                    2022a                h191b570_0    conda-forge
udunits2                  2.2.28               hc3e0081_0    conda-forge
unicodedata2              14.0.0           py39hb9d737c_1    conda-forge
urllib3                   1.26.9             pyhd8ed1ab_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
xarray                    2022.3.0           pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zipp                      3.8.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h166bdaf_1014    conda-forge
zstd                      1.5.2                h8a70e8d_1    conda-forge

Jim Weber



-----Original Message-----
From: Herzmann, Daryl E [AGRON] <akrherz@xxxxxxxxxxx>
Sent: Wednesday, May 18, 2022 4:11 PM
To: Weber, Jim <Jim.Weber@xxxxxxx>; python-users@xxxxxxxxxxxxxxxx
Subject: Re: miniconda error message

Greetings,

It may be good to list out your environment and see which packages are coming 
from conda and which are coming from pip/pypi

conda list

daryl

________________________________________
From: Weber, Jim <Jim.Weber@xxxxxxx>
Sent: Wednesday, May 18, 2022 2:38 PM
To: Herzmann, Daryl E [AGRON]; python-users@xxxxxxxxxxxxxxxx
Subject: RE: miniconda error message

Daryl,
 Miniconda is installed and started in the .bashrc so all path variables are 
set then. It seems to be tied to when I did the metpy update, it installed many 
other updates at that time also. One of them seems to have caused a small issue 
to get things out of sync. Admittedly, I am not very proficent in the conda 
enviroment as this is still new to me.

I did realize there was one more part of the line that I did not include in my 
original email.  The entire error message is below when I run a python script. 
Specifically I am using a reciepe created by Brian Blaylock called 
https://urldefense.proofpoint.com/v2/url?u=http-3A__mapping-5FGOES16-5FTrueColor.py&d=DwIFAg&c=uw6TLu4hwhHdiGJOgwcWD4AjKQx6zvFcGEsbfiY9-EI&r=KKIRMcmZ6BcKOjHM4171gGDDLEx31ZuiUy6Gn81J_cs&m=GK5ToT1IGxzCtZQ4TGNSte6MpAce6NleCh1_Oyl6KH4zpjRbsgDs9uSaaGrpC1OV&s=HzdaanOdDVeq5SmtFckKKa13UW6KEaJv5ESyxg_fzV0&e=
   where I have modified it for my local use.

/home/ldm/miniconda3/lib/python3.9/site-packages/pyproj/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwIFAg&c=uw6TLu4hwhHdiGJOgwcWD4AjKQx6zvFcGEsbfiY9-EI&r=KKIRMcmZ6BcKOjHM4171gGDDLEx31ZuiUy6Gn81J_cs&m=GK5ToT1IGxzCtZQ4TGNSte6MpAce6NleCh1_Oyl6KH4zpjRbsgDs9uSaaGrpC1OV&s=_ZlMxA_xtyV5Rn7Gb1lYxiIQDK_VOIujYyTlBWfxF6U&e=
 :89: UserWarning: pyproj unable to set database path.
  _pyproj_global_context_initialize()



It seems to be tied to the import metpy in the beginning as that specific error 
goes away if I comment it out (of course other parts do not work).

When I do a printenv, I do see "PROJ_LIB=/home/ldm/miniconda3/share/proj" 
listed so the variable is set.

Looking back  through my notes of when I originally installed everything I see 
that I had reached out regarding an error message with pandas. A user gave me a 
quick fixed of typing "pip uninstall pandas" followed by "pip install -U 
pandas" but then warned me about a mixed pip-conda environment getting out of 
sync.  Could this be what is going on that I did a metpy update but something 
got out of sync because one other part was installed with pip?  Not to get too 
far off topic, my notes suggest my first command during the installed was "pip 
install metpy" followed by "conda install -c conda-forge metpy"

I guess I am also asking is my install correct or am I on a wrong tangent with 
my install that future updates will cause me headache.

Sorry for the confusion and rambling, this is still a learning process for me.

Jim


-----Original Message-----
From: Herzmann, Daryl E [AGRON] <akrherz@xxxxxxxxxxx>
Sent: Tuesday, May 17, 2022 11:46 PM
To: Weber, Jim <Jim.Weber@xxxxxxx>; python-users@xxxxxxxxxxxxxxxx
Subject: Re: miniconda error message

Greetings,

How are you instantiating miniconda?  If you are just manually setting a $PATH 
variable, then your shell is missing out on other variables that miniconda may 
be wishing to set at activation time.  In this case PROJ_LIB.  see: 
etc/conda/activate.d/https://urldefense.proofpoint.com/v2/url?u=http-3A__proj4-2Dactivate.sh&d=DwIFAg&c=uw6TLu4hwhHdiGJOgwcWD4AjKQx6zvFcGEsbfiY9-EI&r=KKIRMcmZ6BcKOjHM4171gGDDLEx31ZuiUy6Gn81J_cs&m=GK5ToT1IGxzCtZQ4TGNSte6MpAce6NleCh1_Oyl6KH4zpjRbsgDs9uSaaGrpC1OV&s=HkVKv1y68hqUOUGwuU95_PnesHJmrIUuqo_Tf1Gx0g4&e=

Additionally, a best practice is to install packages into a dedicated 
environment and not the base environment.

Now for LDM, having each shell invocation run a conda environment activation 
can create horrible latency for some workflows.  In such case, just add the 
needed PROJ_LIB setting when you set your PATH.  For your example I am setting

export PROJ_LIB=/home/ldm/miniconda3/share/proj

daryl

________________________________________
From: python-users <python-users-bounces@xxxxxxxxxxxxxxxx> on behalf of Weber, 
Jim <Jim.Weber@xxxxxxx>
Sent: Tuesday, May 17, 2022 2:15 PM
To: python-users@xxxxxxxxxxxxxxxx
Subject: [python-users] miniconda error message

Hi,

I upgraded to metpy 1.3.0 last month and notice a little after I was getting a 
warning message.  It does not seem to affect the end result of anything that I 
run, but it throws it out for anything that I run. Any idea of how I can 
resolve the issue for this error:


/home/ldm/miniconda3/lib/python3.9/site-packages/pyproj/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwIFAg&c=uw6TLu4hwhHdiGJOgwcWD4AjKQx6zvFcGEsbfiY9-EI&r=KKIRMcmZ6BcKOjHM4171gGDDLEx31ZuiUy6Gn81J_cs&m=BMlerE2UKcRw0Su-YOnb-GIQ3I318UBjkUf-J0Z77Y2bWkl_YC86KWmjfx_kpi2W&s=kSytVwiagj1W9KzuBn7HlnxnOmKIOwean1FjmjUTwIw&e=
 :89: UserWarning: pyproj unable to set database path.



Thanks for any help!

Jim Weber



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