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ocean-transport / lcs-ml

Lagrangian Coherent Structure identification for machine learning
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Error running batch scripts, 'pyqg' not found #36

Closed hscannell closed 2 years ago

hscannell commented 2 years ago

I am getting the following error when running either spin_up.sh or ensemble_generator.sh in batch mode. 

1
Traceback (most recent call last):
  File "ensemble_generator.py", line 3, in <module>
    import pyqg
ModuleNotFoundError: No module named 'pyqg'

To run either process, I type the following at the terminal:

sbatch spin_up.sh

sbatch --array=1-3 ensemble_generator.sh

My environment is lcs-ml and contains pyqg version 0.4.0, and I specify the exact environment in my batch script, so I'm at a loss as to why this error is occurring.

Using the lcs-ml in the notebook version of the script causes no errors.

rabernat commented 2 years ago

There is a typo here

https://github.com/ocean-transport/lcs-ml/blob/7bcb9a32177d7bec248df2b8154a8bdebda74bc4/spin_up/spin_up.sh#L15

Could that be relevant?

hscannell commented 2 years ago

Nice catch! That line was hastily added while I was trying to debug. It should be removed.

Otherwise, the problem still stands.

hscannell commented 2 years ago

Here are my ~/.bashrc file contents:

# .bashrc

# User specific aliases and functions

alias rm='rm -i'
alias cp='cp -i'
alias mv='mv -i'

# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/burg/opt/anaconda3-2020.11/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/burg/opt/anaconda3-2020.11/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/burg/opt/anaconda3-2020.11/anaconda3/etc/profile.d/conda.sh"
    else
        export PATH="/burg/opt/anaconda3-2020.11/anaconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<
rabernat commented 2 years ago

My best guess would be that the environment is not actually loading correctly.

Add the following lines to your script before calling the python script to debug:

which python
conda info
conda list
hscannell commented 2 years ago

**For reference

/burg/opt/anaconda3-2021.05/bin/python

2.

active environment : lcs-ml
    active env location : /burg/home/hs3277/.conda/envs/lcs-ml
            shell level : 2
       user config file : /burg/home/hs3277/.condarc
 populated config files :
          conda version : 4.9.2
    conda-build version : 3.20.5
         python version : 3.8.5.final.0
       virtual packages : __glibc=2.28=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /burg/opt/anaconda3-2020.11/anaconda3  (read only)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /burg/opt/anaconda3-2020.11/anaconda3/pkgs
                          /burg/home/hs3277/.conda/pkgs
       envs directories : /burg/home/hs3277/.conda/envs
                          /burg/opt/anaconda3-2020.11/anaconda3/envs
               platform : linux-64
             user-agent : conda/4.9.2 requests/2.24.0 CPython/3.8.5 Linux/4.18.0-193.el8.x86_64 rhel/8.2 glibc/2.28
                UID:GID : 545216:500
             netrc file : None
           offline mode : False

3.

# packages in environment at /burg/home/hs3277/.conda/envs/lcs-ml:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
argcomplete               1.12.3             pyhd3eb1b0_0
argon2-cffi               20.1.0           py37h27cfd23_1
asciitree                 0.3.3                      py_2
asn1crypto                1.4.0                      py_0
async_generator           1.10             py37h28b3542_0
atk                       2.36.0               h06a4308_0
atk-1.0                   2.36.0               h28cd5cc_0
attrs                     21.2.0             pyhd3eb1b0_0
backcall                  0.2.0              pyhd3eb1b0_0
blas                      1.0                    openblas
bleach                    4.0.0              pyhd3eb1b0_0
bokeh                     2.3.2            py37h06a4308_0
brotli                    1.0.9                he6710b0_2
brotlipy                  0.7.0           py37h27cfd23_1003
bzip2                     1.0.8                h7b6447c_0
ca-certificates           2021.10.8            ha878542_0    conda-forge
cairo                     1.16.0            h18b612c_1001    conda-forge
certifi                   2021.10.8        py37h89c1867_1    conda-forge
cffi                      1.14.0           py37h2e261b9_0
cftime                    1.5.0            py37h6323ea4_0
charset-normalizer        2.0.4              pyhd3eb1b0_0
click                     8.0.3              pyhd3eb1b0_0
cloudpickle               2.0.0              pyhd3eb1b0_0
colorcet                  2.0.6              pyhd3eb1b0_0
cryptography              2.3.1            py37hc365091_0
curl                      7.64.0               h646f8bb_0    conda-forge
cycler                    0.10.0                   py37_0
cython                    0.29.24          py37hcd2ae1e_0    conda-forge
cytoolz                   0.11.0           py37h7b6447c_0
dask                      2021.10.0          pyhd8ed1ab_0    conda-forge
dask-core                 2021.10.0          pyhd3eb1b0_0
datashader                0.13.0             pyhd3eb1b0_1
datashape                 0.5.4            py37h06a4308_1
dbus                      1.13.18              hb2f20db_0
debugpy                   1.4.1            py37h295c915_0
decorator                 5.1.0              pyhd3eb1b0_0
defusedxml                0.7.1              pyhd3eb1b0_0
distributed               2021.10.0        py37h06a4308_0
entrypoints               0.3                      py37_0
expat                     2.4.1                h2531618_2
fasteners                 0.16.3             pyhd3eb1b0_0
fontconfig                2.13.1            he4413a7_1000    conda-forge
fonttools                 4.25.0             pyhd3eb1b0_0
freetype                  2.11.0               h70c0345_0
fribidi                   1.0.10               h7b6447c_0
fsspec                    2021.8.1           pyhd3eb1b0_0
gdk-pixbuf                2.42.2               h19a9c64_1    conda-forge
gettext                   0.21.0               hf68c758_0
giflib                    5.2.1                h7b6447c_0
glib                      2.66.3               h58526e2_0    conda-forge
gobject-introspection     1.66.1           py37h9019ea4_3    conda-forge
graphite2                 1.3.14               h23475e2_0
gstreamer                 1.14.5               h36ae1b5_2    conda-forge
gtk2                      2.24.32              h90f3771_0    conda-forge
h5netcdf                  0.11.0             pyhd8ed1ab_0    conda-forge
h5py                      2.10.0           py37h7918eee_0
harfbuzz                  2.4.0                h37c48d4_1    conda-forge
hdf4                      4.2.13               h3ca952b_2
hdf5                      1.10.4               hb1b8bf9_0
heapdict                  1.0.1              pyhd3eb1b0_0
holoviews                 1.14.6             pyhd3eb1b0_1
icu                       58.2                 he6710b0_3
idna                      3.2                pyhd3eb1b0_0
importlib-metadata        4.8.1            py37h06a4308_0
importlib_metadata        4.8.1                hd3eb1b0_0
ipykernel                 6.4.2            py37h6531663_0    conda-forge
ipython                   7.29.0           py37hb070fc8_0
ipython_genutils          0.2.0              pyhd3eb1b0_1
jedi                      0.18.0           py37h06a4308_1
jinja2                    3.0.2              pyhd3eb1b0_0
jpeg                      9d                   h7f8727e_0
jsonschema                3.2.0              pyhd3eb1b0_2
jupyter_client            7.0.1              pyhd3eb1b0_0
jupyter_core              4.8.1            py37h06a4308_0
jupyterlab_pygments       0.1.2                      py_0
kiwisolver                1.3.1            py37h2531618_0
krb5                      1.16.3            hc83ff2d_1000    conda-forge
lcms2                     2.12                 h3be6417_0
libblas                   3.9.0                8_openblas    conda-forge
libcblas                  3.9.0                8_openblas    conda-forge
libcurl                   7.64.0               h01ee5af_0    conda-forge
libedit                   3.1.20210216         h27cfd23_1
libffi                    3.2.1             hf484d3e_1007
libgcc-ng                 11.2.0              h1d223b6_11    conda-forge
libgfortran-ng            7.5.0               ha8ba4b0_17
libgfortran4              7.5.0               ha8ba4b0_17
libglib                   2.66.3               hbe7bbb4_0    conda-forge
libgomp                   11.2.0              h1d223b6_11    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0                8_openblas    conda-forge
libllvm10                 10.0.1               hbcb73fb_5
libnetcdf                 4.6.2             hbdf4f91_1001    conda-forge
libopenblas               0.3.12          pthreads_hb3c22a3_1    conda-forge
libpng                    1.6.37               hbc83047_0
libsodium                 1.0.18               h7b6447c_0
libssh2                   1.8.0             h1ad7b7a_1003    conda-forge
libstdcxx-ng              9.3.0               hd4cf53a_17
libtiff                   4.2.0                h85742a9_0
libuuid                   2.32.1            h7f98852_1000    conda-forge
libwebp                   1.2.0                h89dd481_0
libwebp-base              1.2.0                h27cfd23_0
libxcb                    1.14                 h7b6447c_0
libxml2                   2.9.12               h03d6c58_0
llvmlite                  0.36.0           py37h612dafd_4
locket                    0.2.1            py37h06a4308_1
lz4-c                     1.9.3                h295c915_1
markdown                  3.3.4            py37h06a4308_0
markupsafe                2.0.1            py37h27cfd23_0
matplotlib                3.4.3            py37h89c1867_1    conda-forge
matplotlib-base           3.4.3            py37hbbc1b5f_0
matplotlib-inline         0.1.2              pyhd3eb1b0_2
mistune                   0.8.4           py37h14c3975_1001
msgpack-python            1.0.2            py37hff7bd54_1
multipledispatch          0.6.0                    py37_0
munkres                   1.1.4                      py_0
nbclient                  0.5.3              pyhd3eb1b0_0
nbconvert                 6.1.0            py37h06a4308_0
nbformat                  5.1.3              pyhd3eb1b0_0
ncurses                   6.2                  he6710b0_1
nest-asyncio              1.5.1              pyhd3eb1b0_0
netcdf4                   1.5.1.2          py37had58050_0    conda-forge
ninja                     1.10.2               hff7bd54_1
notebook                  6.4.5            py37h06a4308_0
numba                     0.53.1           py37ha9443f7_0
numcodecs                 0.8.0            py37h2531618_0
numpy                     1.21.3           py37h31617e3_0    conda-forge
olefile                   0.46                     py37_0
openssl                   1.0.2u               h516909a_0    conda-forge
packaging                 21.0               pyhd3eb1b0_0
pandas                    1.2.0            py37ha9443f7_0
pandocfilters             1.4.3            py37h06a4308_1
panel                     0.8.3                    pypi_0    pypi
pango                     1.42.4               h7062337_4    conda-forge
param                     1.11.1             pyhd3eb1b0_0
parso                     0.8.2              pyhd3eb1b0_0
partd                     1.2.0              pyhd3eb1b0_0
pcre                      8.45                 h295c915_0
pexpect                   4.8.0              pyhd3eb1b0_3
pickleshare               0.7.5           pyhd3eb1b0_1003
pillow                    8.4.0            py37h5aabda8_0
pip                       21.0.1           py37h06a4308_0
pixman                    0.38.0            h516909a_1003    conda-forge
prometheus_client         0.11.0             pyhd3eb1b0_0
prompt-toolkit            3.0.20             pyhd3eb1b0_0
psutil                    5.8.0            py37h27cfd23_1
ptyprocess                0.7.0              pyhd3eb1b0_2
pycparser                 2.20                       py_2
pyct                      0.4.8                    py37_0
pyfftw                    0.11.1          py37h240ffea_1002    conda-forge
pygments                  2.10.0             pyhd3eb1b0_0
pyopenssl                 19.0.0                   py37_0
pyparsing                 3.0.4              pyhd3eb1b0_0
pyqg                      0.4.0            py37hb1e94ed_0    conda-forge
pyqt                      5.6.0           py37h13b7fb3_1008    conda-forge
pyrsistent                0.18.0           py37heee7806_0
pysocks                   1.7.1                    py37_1
python                    3.7.0             hd21baee_1006    conda-forge
python-dateutil           2.8.2              pyhd3eb1b0_0
python_abi                3.7                     2_cp37m    conda-forge
pytz                      2021.3             pyhd3eb1b0_0
pyviz_comms               2.0.2              pyhd3eb1b0_0
pyyaml                    6.0              py37h5e8e339_0    conda-forge
pyzmq                     22.2.1           py37h295c915_1
qt                        5.6.2             hce4f676_1013    conda-forge
readline                  7.0                  h7b6447c_5
requests                  2.26.0             pyhd3eb1b0_0
scipy                     1.3.0            py37he2b7bc3_0
send2trash                1.8.0              pyhd3eb1b0_1
setuptools                58.0.4           py37h06a4308_0
sip                       4.18.1          py37hf484d3e_1000    conda-forge
six                       1.16.0             pyhd3eb1b0_0
sortedcontainers          2.4.0              pyhd3eb1b0_0
sqlite                    3.28.0               h8b20d00_0    conda-forge
tbb                       2020.3               hfd86e86_0
tblib                     1.7.0              pyhd3eb1b0_0
terminado                 0.9.4            py37h06a4308_0
testpath                  0.5.0              pyhd3eb1b0_0
tk                        8.6.11               h1ccaba5_0
toolz                     0.11.1             pyhd3eb1b0_0
tornado                   6.1              py37h27cfd23_0
tqdm                      4.62.3             pyhd3eb1b0_1
traitlets                 5.1.0              pyhd3eb1b0_0
typing_extensions         3.10.0.2           pyh06a4308_0
urllib3                   1.26.7             pyhd3eb1b0_0
wcwidth                   0.2.5              pyhd3eb1b0_0
webencodings              0.5.1                    py37_1
wheel                     0.37.0             pyhd3eb1b0_1
xarray                    0.19.0             pyhd8ed1ab_1    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h27cfd23_1007
xz                        5.2.5                h7b6447c_0
yaml                      0.2.5                h7b6447c_0
zarr                      2.8.1              pyhd3eb1b0_0
zeromq                    4.3.4                h2531618_0
zict                      2.0.0              pyhd3eb1b0_0
zipp                      3.6.0              pyhd3eb1b0_0
zlib                      1.2.11               h7b6447c_3
zstd                      1.4.9                haebb681_0
rabernat commented 2 years ago

/burg/opt/anaconda3-2021.05/bin/python

So this is not the python from your conda environment. That python should be in /burg/home/hs3277/.conda/envs/lcs-ml. This explains why it is not working.

hscannell commented 2 years ago

I discovered that the anaconda version was not the same in bashrc vs. what I was loading in the script.

I changed this in the bash script and things seem to work!

module load anaconda/3-2021.05
conda init bash