Lluis.fita: /* Adding new packages/libraries to an existing environment */

2026-07-18T19:32:25Z

Adding new packages/libraries to an existing environment

← Revisión anterior		Revisión del 19:32 18 jul 2026
Línea 73:		Línea 73:

	To add new libraries, using mamba (preferred way)		To add new libraries, using mamba (preferred way)
	<PRE>		<PRE style="Shell">
	# /opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba install -n easy pyflextrkr		# /opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba install -n easy pyflextrkr
	</PRE>		</PRE>

Lluis.fita: /* Adding new packages/libraries to an existing environment */

2026-07-18T19:32:09Z

Adding new packages/libraries to an existing environment

← Revisión anterior		Revisión del 19:32 18 jul 2026
Línea 73:		Línea 73:

	To add new libraries, using mamba (preferred way)		To add new libraries, using mamba (preferred way)
	<PRE ~~style="Shell"~~># /opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba install -n easy pyflextrkr</PRE>		<PRE>
			# /opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba install -n easy pyflextrkr
			</PRE>

	Via pip		Via pip

Lluis.fita: /* Adding new packages/libraries to an existing environment */

2026-07-18T19:31:44Z

Adding new packages/libraries to an existing environment

← Revisión anterior		Revisión del 19:31 18 jul 2026
Línea 73:		Línea 73:

	To add new libraries, using mamba (preferred way)		To add new libraries, using mamba (preferred way)
	<PRE style="Shell">		<PRE style="Shell"># /opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba install -n easy pyflextrkr</PRE>
	# /opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba install -n easy pyflextrkr
	</PRE>

	Via pip		Via pip

Lluis.fita: /* Adding new packages/libraries to an existing environment */

2026-07-18T19:30:59Z

Adding new packages/libraries to an existing environment

← Revisión anterior		Revisión del 19:30 18 jul 2026
Línea 73:		Línea 73:

	To add new libraries, using mamba (preferred way)		To add new libraries, using mamba (preferred way)
	<PRE style="~~shell~~"># /opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba install -n easy pyflextrkr		<PRE style="Shell">
			# /opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba install -n easy pyflextrkr
	</PRE>		</PRE>

Lluis.fita: /* Adding new packages/libraries to an existing environment */

2026-07-18T19:30:36Z

Adding new packages/libraries to an existing environment

← Revisión anterior		Revisión del 19:30 18 jul 2026
Línea 73:		Línea 73:

	To add new libraries, using mamba (preferred way)		To add new libraries, using mamba (preferred way)
	<PRE style="shell">		<PRE style="shell"># /opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba install -n easy pyflextrkr
	# /opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba install -n easy pyflextrkr
	</PRE>		</PRE>

Lluis.fita: Página creada con «En esta sección se detallan los pasos seguidos para instalar librerías y/o programario específico. Dichas librerías se tendrán que instalar para cada usuarie desde la sesión jupyter. = Kernels = == Digital Earths - Global Hackathon == En la semana del 13 al 16 de Mayo aconteció el la [https://www.wcrp-esmo.org/activities/wcrp-global-km-scale-hackathon-2025 Digital Earths - Global Hackathon] en la cuál el CIMA/IFAECI participó con la organización de un nodo…»

2026-07-18T19:10:32Z

Página creada con «En esta sección se detallan los pasos seguidos para instalar librerías y/o programario específico. Dichas librerías se tendrán que instalar para cada usuarie desde la sesión jupyter. = Kernels = == Digital Earths - Global Hackathon == En la semana del 13 al 16 de Mayo aconteció el la [https://www.wcrp-esmo.org/activities/wcrp-global-km-scale-hackathon-2025 Digital Earths - Global Hackathon] en la cuál el CIMA/IFAECI participó con la organización de un nodo…»

Página nueva

En esta sección se detallan los pasos seguidos para instalar librerías y/o programario específico. Dichas librerías se tendrán que instalar para cada usuarie desde la sesión jupyter.

= Kernels =

== Digital Earths - Global Hackathon ==
En la semana del 13 al 16 de Mayo aconteció el la [https://www.wcrp-esmo.org/activities/wcrp-global-km-scale-hackathon-2025 Digital Earths - Global Hackathon] en la cuál el CIMA/IFAECI participó con la organización de un nodo en [https://git.cima.fcen.uba.ar/gvieytes/global-hackathon/-/wikis/home CABA]. Para esa actividad fue necesaria la instalación de un entorno de python el cuál se hizo accesible para todes les usuaries de Deimos. Estos son los pasos seguidos:

First download the Hachkathon's repository as root in <CODE>/opt/onda/mamba/DE-global_hackathon<CODE> (as root)
<PRE style="shell">
# git clone https://github.com/digital-earths-global-hackathon/tools.git
</PRE>

Go to directory with installation and make a copy for <CODE>deimos</CODE> and edit the prefix
<PRE style="shell">
# cd tools/python_envs
# cp install_python install_python_deimos
diff install_python install_python_orig install_python install_python_orig
4c4,5
< prefix=${prefix:-$HOME/python_envs}
---
> #prefix=${prefix:-$HOME/python_envs}
> prefix=/opt/conda/mamba/DE-global_hackathon
./install_python_deimos
```
We got the right installation
<PRE style="shell">
ls /opt/conda/mamba/DE-global_hackathon/
miniconda3 tools
</PRE>

Registering the new kernel [https://jupyterhub.readthedocs.io/en/stable/howto/configuration/config-user-env.html jupyerhub-doc] and [https://discourse.jupyter.org/t/add-multiple-python-kernels-like-3-6-x-and-3-7-x-to-jupyterhub/5458/3 multiple-kernels]
<PRE style="shell">
# /opt/tljh/user/bin/jupyter kernelspec list
Available kernels:
python3 /opt/tljh/user/share/jupyter/kernels/python3
bash /usr/local/share/jupyter/kernels/bash
ir /usr/local/share/jupyter/kernels/ir
python_conda_su /usr/local/share/jupyter/kernels/python_conda_su
# /opt/tljh/user/bin/jupyter-kernelspec remove python_conda_su
Kernel specs to remove:
python_conda_su /usr/local/share/jupyter/kernels/python_conda_su
Remove 1 kernel specs [y/N]: y
# /opt/tljh/user/bin/jupyter-kernelspec list
Available kernels:
python3 /opt/tljh/user/share/jupyter/kernels/python3
bash /usr/local/share/jupyter/kernels/bash
ir /usr/local/share/jupyter/kernels/ir
# /opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba install ipykernel
# /opt/conda/mamba/DE-global_hackathon/miniconda3/envs/easy/bin/python3 -m ipykernel install
Installed kernelspec python3 in /usr/local/share/jupyter/kernels/python3
# /opt/tljh/user/bin/jupyter-kernelspec install /usr/local/share/jupyter/kernels/python3 --name=python_DigEarth-Hack
[InstallKernelSpec] Installed kernelspec python_digearth-hack in /usr/local/share/jupyter/kernels/python_digearth-hack
# /opt/tljh/user/bin/jupyter-kernelspec list
Available kernels:
python3 /opt/tljh/user/share/jupyter/kernels/python3
bash /usr/local/share/jupyter/kernels/bash
ir /usr/local/share/jupyter/kernels/ir
python_digearth-hack /usr/local/share/jupyter/kernels/python_digearth-hack
</PRE>

Editing kernel name to be recognizible in jupyterHUB api and set-up environment (see [https://stackoverflow.com/questions/67914989/creating-virtual-environments-for-jupyterhub stackoverflow])
<PRE style="shell">
# vim /usr/local/share/jupyter/kernels/python_digearth-hack/kernel.json
"display_name": "Python 3 (D.E. Hachkathon)",
"env": {
"MAMBA_PREFIX":"/opt/conda/mamba/DE-global_hackathon/miniconda3/envs/easy",
"MAMBA_DEFAULT_ENV":"easy",
"PATH":"/opt/conda/mamba/DE-global_hackathon/miniconda3/envs/easy/bin:/opt/conda/mamba/DE-global_hackathon/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
},
</PRE>

=== Adding new packages/libraries to an existing environment ===

To add new libraries, using mamba (preferred way)
<PRE style="shell">
# /opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba install -n easy pyflextrkr
</PRE>

Via pip
<PRE style="shell">
# cd /opt/conda/mamba/DE-global_hackathon/miniconda3/envs/easy
# bin/pip3 install healpy
</PRE>

== ATRACKCS ==
El [https://github.com/ATRACKCS/ATRACKCS ATRACKCS] Esta herramienta está diseñada para realizar seguimientos de sistemas atmosféricos. Estos son los pasos seguidos para su instalación en Deimos

Creando el enclave del paquete
<PRE style="sell">
# cd /opt/conda/mamba/
# mkdir ATRACKCS
# cd ATRACKCS
</PRE>

Agarrando el software y preparando la instalación via la creación de un nuevo entorno de python
<PRE style="shell">
# git clone https://github.com/alramirezca/ATRACKCS
# cd ATRACKCS
# /opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba env create -f env_py3.yml
</PRE>

Activación del entorno y terminar la instalación
<PRE style="shell">
# eval "$(/opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba shell hook --shell bash)"
(base) # mamba activate atrackcs_py3
(atrackcs_py3) # pip install -e .
</PRE>

Registrando el nuevo kernel para deimos:
<PRE style="shell">
(atrackcs_py3) # pip3 install ipykernel
(atrackcs_py3) # mamba deactivate
(base) # mamba deactivate
# /opt/tljh/user/bin/jupyter kernelspec list
Available kernels:
python3 /opt/tljh/user/share/jupyter/kernels/python3
bash /usr/local/share/jupyter/kernels/bash
ir /usr/local/share/jupyter/kernels/ir
python_digearth-hack /usr/local/share/jupyter/kernels/python_digearth-hack
# /opt/conda/mamba/DE-global_hackathon/miniconda3/envs/atrackcs_py3/bin/python3 -m ipykernel install
# /opt/tljh/user/bin/jupyter-kernelspec install /usr/local/share/jupyter/kernels/python3 --name=python_atrackcs
# /opt/tljh/user/bin/jupyter-kernelspec list
Available kernels:
python3 /opt/tljh/user/share/jupyter/kernels/python3
bash /usr/local/share/jupyter/kernels/bash
ir /usr/local/share/jupyter/kernels/ir
python_atrackcs /usr/local/share/jupyter/kernels/python_atrackcs
python_digearth-hack /usr/local/share/jupyter/kernels/python_digearth-hack
</PRE>

Editando el nombre del kernel para identificarlo desde deimos:
<PRE style="shell">
# vim /usr/local/share/jupyter/kernels/python_atrackcs/kernel.json
"display_name": "Python 3 (atrackcs)",
"env": {
"MAMBA_PREFIX":"/opt/conda/mamba/DE-global_hackathon/miniconda3/envs/atrackcs_py3",
"MAMBA_DEFAULT_ENV":"atrackcs_py3",
"PATH":"/opt/conda/mamba/DE-global_hackathon/miniconda3/envs/atrackcs_py3/bin:/opt/conda/mamba/DE-global_hackathon/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
},
</PRE>

== ESMValTool ==
Herramientas para el análisis de datos CMIP. [https://esmvaltool.org/ ESMValTool] es una herramienta en python, abierta y desarrollada por la comunidad.

Los pasos para su instalación se detallan acá [[/ESMValToolInst]].

<I>El sistema papa-deimos, se pudo constituir en parte, gracias a fondos del [https://www.insu.cnrs.fr/fr INSU] - [https://programmes.insu.cnrs.fr/lefe/ LEFE]</I>

== ANDEX ==
Creación de un entorno para python3 desde cero.

Para eso vamos a utilizar el mamba que se instaló para la 'D.E. global Hackathon'

Localización de la creación del nuevo entorno de python
<PRE style="shell">
# cd /opt/conda/mamba/
# mkdir ANDEX
# cd ANDEX
</PRE>

Creación del entorno de python llamado <CODE>py3_andex</CODE> a partir del archivo creado <CODE>py3_andex_pkgs.yaml</CODE>:
<PRE style="Shell">
# /opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba create -n py3_andex -f py3_andex_pkgs.yaml
</PRE>
El archivo <CODDE>py3_andex_pkgs.yaml</CODE> contiene:
<PRE>
# cat py3_andex_pkgs.yaml
name: py3_andex
channels:
- conda-forge
dependencies:
- wrf-python
- xesmf
- netcdf4
- dask
- cartopy
</PRE>

Activación e instalación del paquete de kernels de jupyerHUB
<PRE style="Shell">
# eval "$(/opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba shell hook --shell bash)"
# mamba activate atrackcs_py3
(py3_andex) # pip3 install ipykernel
</PRE>

Registro del nuevo kernel para jupyerHUB. Eso desde fuera del entorno, por eso lo desactivamos
<PRE style="Shell">
(py3_andex) # mamba deactivate
# /opt/tljh/user/bin/jupyter kernelspec list
Available kernels:
python3 /opt/tljh/user/share/jupyter/kernels/python3
bash /usr/local/share/jupyter/kernels/bash
ir /usr/local/share/jupyter/kernels/ir
python_atrackcs /usr/local/share/jupyter/kernels/python_atrackcs
python_digearth-hack /usr/local/share/jupyter/kernels/python_digearth-hack
python_esmvaltools /usr/local/share/jupyter/kernels/python_esmvaltools
# /opt/conda/mamba/DE-global_hackathon/miniconda3/envs/py3_andex/bin/python3 -m ipykernel install
# /opt/tljh/user/bin/jupyter-kernelspec install /usr/local/share/jupyter/kernels/python3 --name=py3_andex
# /opt/tljh/user/bin/jupyter-kernelspec list
Available kernels:
python3 /opt/tljh/user/share/jupyter/kernels/python3
bash /usr/local/share/jupyter/kernels/bash
ir /usr/local/share/jupyter/kernels/ir
py3_andex /usr/local/share/jupyter/kernels/py3_andex
python_atrackcs /usr/local/share/jupyter/kernels/python_atrackcs
python_digearth-hack /usr/local/share/jupyter/kernels/python_digearth-hack
# vim /usr/local/share/jupyter/kernels/py3_andex/kernel.json
{
"argv": [
"/opt/conda/mamba/DE-global_hackathon/miniconda3/envs/py3_andex/bin/python3",
"-Xfrozen_modules=off",
"-m",
"ipykernel_launcher",
"-f",
"{connection_file}"
],
"display_name": "Python 3 (ANDEX)",
"env": {
"MAMBA_PREFIX":"/opt/conda/mamba/DE-global_hackathon/miniconda3/envs/py3_andex",
"MAMBA_DEFAULT_ENV":"py3_andex",
"PATH":"/opt/conda/mamba/DE-global_hackathon/miniconda3/envs/py3_andex/bin:/opt/conda/mamba/DE-global_hackathon/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
},
"language": "python",
"metadata": {
"debugger": true,
"supported_encryption": "curve"
},
"kernel_protocol_version": "5.5"
}
</PRE>

Listado de paquetes en el entorno:
<PRE style="shell">
(py3_andex) # pip3 freeze --local
asttokens==3.0.2
Cartopy==0.25.0
certifi==2026.6.17
cf_xarray @ file:///home/conda/feedstock_root/build_artifacts/cf_xarray_1781358794801/work
cftime==1.6.5
click==8.4.2
cloudpickle==3.1.2
comm==0.2.3
contourpy==1.3.3
cycler==0.12.1
dask==2026.7.1
debugpy==1.8.21
decorator==5.3.1
esmpy @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_esmpy_1767783521/work/src/addon/esmpy
executing==2.2.1
fonttools==4.63.0
fsspec==2026.6.0
ipykernel==7.3.0
ipython==9.15.0
ipython_pygments_lexers==1.1.1
jedi==0.20.0
jupyter_client==8.9.1
jupyter_core==5.9.1
kiwisolver==1.5.0
llvmlite==0.48.0
locket==1.0.0
matplotlib==3.11.0
matplotlib-inline==0.2.2
nest-asyncio2==1.7.2
netCDF4==1.7.4
numba @ file:///home/conda/feedstock_root/build_artifacts/numba_1784209014097/work
numpy @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_numpy_1779169198/work/dist/numpy-2.4.6-cp314-cp314-linux_x86_64.whl#sha256=67bfc5dc678227ea6ad6cc75838ae920b11bc7da7649fc19c624fda3aaec691a
packaging @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_packaging_1777103621/work
pandas @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_pandas_1778602611/work
parso==0.8.7
partd==1.4.2
pexpect==4.9.0
pillow==12.3.0
platformdirs==4.10.0
prompt_toolkit==3.0.52
psutil==7.2.2
ptyprocess==0.7.0
pure_eval==0.2.3
Pygments==2.20.0
pyparsing==3.3.2
pyproj==3.7.2
pyshp==3.1.4
python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_python-dateutil_1751104122/work
PyYAML==6.0.3
pyzmq==27.1.0
setuptools==83.0.0
shapely @ file:///home/conda/feedstock_root/build_artifacts/shapely_1762523525223/work
six @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_six_1753199211/work
sparse @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_sparse_1782985176/work
stack-data==0.6.3
toolz==1.1.0
tornado==6.5.7
traitlets==5.15.1
typing_extensions==4.16.0
wcwidth==0.8.2
wrapt @ file:///home/conda/feedstock_root/build_artifacts/wrapt_1782133551393/work
wrf-python @ file:///home/conda/feedstock_root/build_artifacts/wrf-python_1771438235011/work
xarray @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_xarray_1783633473/work
xesmf @ file:///home/conda/feedstock_root/build_artifacts/xesmf_1764332232756/work
</pre>

>>>
import os

os.environ["OMP_NUM_THREADS"] = "2"
os.environ["MKL_NUM_THREADS"] = "2"
os.environ["OPENBLAS_NUM_THREADS"] = "2"
os.environ["VECLIB_MAXIMUM_THREADS"] = "2"
os.environ["NUMEXPR_NUM_THREADS"] = "2"

import dask
import numpy

# Set global constraints
dask.config.set(scheduler='threads', num_workers=2)
>>>

= Librerías =

== PyNCplot3 ==
Librerías genéricas de Lluís Fita Borrell, CIMA [https://git.cima.fcen.uba.ar/lluis.fita/pyncplot/-/wikis/home PyNCplot]

Des de una sesión <CODE>bash</CODE> del jupyterHUB:
<PRE style="Shell">
git clone -b numpy20 https://git.cima.fcen.uba.ar/lluis.fita/pyncplot.git PyNCplot3
cd PyNCplot3
ln -s Makefile.deimos-jupyterHub ./Makefile
make all >& run_make.log
ls *so
module_ForDef.cpython-39-x86_64-linux-gnu.so
module_ForDiag.cpython-39-x86_64-linux-gnu.so
module_ForDistriCorrect.cpython-39-x86_64-linux-gnu.so
module_ForGen.cpython-39-x86_64-linux-gnu.so
module_ForInt.cpython-39-x86_64-linux-gnu.so
module_ForSci.cpython-39-x86_64-linux-gnu.so
</PRE>
Después desde un directorio de trabajo del estudio concreto (e.j. <CODE>EstudioXY12</CODE>) almacenado dentro del directrio <CODE>estudios</CODE> del home del usuario de jupyteHUB. Desde la misma notebook de <CODE>bash</CODE>
<PRE style="shell">
cd
mkdir -p estudios/EstudioXY12
cd estudios/EstudioXY12
/home/jupyter-[usuario_JupyterHUB]/PyNCplot3/link_essentials_PWD.bash
</PRE>
Ahora ya se puede abrir un notebook the python en el directorio <CODE>estudios/EstudioXY12</CODE> (aparecerá en el home del juyterHUB del usuario) y poder utilizar sin problemas las scripts de PyNCplot

Kernels - Historial de revisiones

Lluis.fita: /* Adding new packages/libraries to an existing environment */

Lluis.fita: /* Adding new packages/libraries to an existing environment */

Lluis.fita: /* Adding new packages/libraries to an existing environment */

Lluis.fita: /* Adding new packages/libraries to an existing environment */

Lluis.fita: /* Adding new packages/libraries to an existing environment */