Commit 0a8af5f2 authored by Andrea Giannetti's avatar Andrea Giannetti
Browse files

Added apptainer definition to run on HPC environments.

parent 781b25ce

apptainer.def

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Bootstrap: docker

From: postgres:14.1-alpine



%environment

export POSTGRES_DB=$DB_NAME

export POSTGRES_USER=$DB_USER

export POSTGRES_PASSWORD=$DB_PASS

create_apptainer_image_file.sh

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rm swiss_army_knife_latest.sif

singularity pull --disable-cache docker://git.ia2.inaf.it:5050/andrea.giannetti/swiss_army_knife

documentation/radmc3d_install_local.sh

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#!/bin/bash

# Set PYCHARM_HOME, INSTALL_DEPENDENCIES environment variable

PYCHARM_HOME=${PYCHARM_HOME:=$HOME/PycharmProjects}

INSTALL_DEPENDENCIES="${INSTALL_DEPENDENCIES:=true}"

echo $PYCHARM_HOME

cd $PYCHARM_HOME

export RADMC_HOME=$PYCHARM_HOME/radmc3d-2.0

if [[ ! -d "$RADMC_HOME" ]]

then

    echo RADMC not found, cloning into "$(pwd)"

    git clone https://github.com/dullemond/radmc3d-2.0.git

fi



if $INSTALL_DEPENDENCIES

then

    sudo apt-get install gfortran build-essential python3-dev

fi



cd $RADMC_HOME/src

make

make install



# Add this to the .bashrc configuration file (or equivalent)

export PATH=$HOME/bin:$PATH

export PYTHONPATH=$HOME/bin/python:$PYTHONPATH



cd $RADMC_HOME/python/radmc3dPy

python setup.py install

etl/prs/prs_inspect_results.py

+36 −4
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@@ -2,12 +2,13 @@ import matplotlib.pyplot as plt 
import numpy as np

import os

import xarray as xr

from typing import Union

from typing import Union, Tuple

from itertools import product

from astropy.io import fits

from sqlalchemy.orm import Session

from sqlalchemy import and_, or_

from stg.stg_build_db_structure import (GridPars,

                                        GridFiles,

                                        StarsPars,

                                        ModelPars,

                                        RatioMaps,
@@ -34,9 +35,14 @@ def get_aggregated_ratio_from_db( 
    :param session: the SQLAlchemy session to use

    :return: the aggregated ratio

    """

    results = session.query(GridPars, RatioMaps).join(StarsPars, isouter=True).join(ModelPars).join(MomentZeroMaps).join(RatioMaps,

    results = session.query(GridPars, RatioMaps) \

        .join(StarsPars, isouter=True) \

        .join(ModelPars) \

        .join(MomentZeroMaps) \

        .join(RatioMaps,

              or_(RatioMaps.mom_zero_map_1,

                                                                                               RatioMaps.mom_zero_map_2)).filter(

                  RatioMaps.mom_zero_map_2)) \

        .filter(

        and_(GridPars.dust_temperature_at_reference == dust_temperature,

             GridPars.density_at_reference == gas_density,

             # GridPars.central_density == gas_density,
@@ -44,6 +50,32 @@ def get_aggregated_ratio_from_db( 
    return results[1].aggregated_ratio





def get_density_distribution(

        dust_temperature: float,

        gas_density: float,

        lines: Union[list, tuple],

        session: Session) -> Tuple[float, str, str, np.array, np.array]:

    results = session.query(GridPars, RatioMaps, GridFiles) \

        .join(GridFiles) \

        .join(StarsPars, isouter=True) \

        .join(ModelPars) \

        .join(MomentZeroMaps) \

        .join(RatioMaps,

              or_(RatioMaps.mom_zero_map_1,

                  RatioMaps.mom_zero_map_2)) \

        .filter(

        and_(GridPars.dust_temperature_at_reference == dust_temperature,

             GridPars.density_at_reference == gas_density,

             GridFiles.quantity == 'gas_number_density',

             ModelPars.iline.in_(lines),

             GridPars.run_id == '55d05c03-192a-47da-9dcf-c41df1882868')).order_by(GridPars.created_on.desc()).first()

    with fits.open(os.path.join('prs', 'fits', 'grids', results[2].fits_grid_name)) as fitsfile:

        grid_values = fitsfile[0].data

    with fits.open(os.path.join('prs', 'fits', 'ratios', results[1].ratio_map_name)) as ratio_fitsfile:

        ratio_values = ratio_fitsfile[0].data

    return results[1].aggregated_ratio, results[1].ratio_map_name, results[2].fits_grid_name, grid_values, ratio_values





def main():

    engine = get_pg_engine(logger=logger)

    config = load_config_file(os.path.join('config', 'config.yml'))

push_etl_image_to_gitlab.sh

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docker login git.ia2.inaf.it:5050

docker tag sak_etl:latest git.ia2.inaf.it:5050/andrea.giannetti/swiss_army_knife

docker push git.ia2.inaf.it:5050/andrea.giannetti/swiss_army_knife
 
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