Anaconda installation

All Platforms System Requirements

CMOR 3.6.1 on conda-forge has support for Python 3.6, 3.7, 3.8, and 3.9.
Anaconda

Make sure anaconda is in your PATH (assuming ananconda is installed in ${HOME}/anaconda)

export PATH=${HOME}/anaconda/bin:${PATH} # for [ba]sh
setenv PATH ${HOME}/anaconda/bin:${PATH} # for [t]csh

Bypassing firewalls

If your institution has a firewall
```
conda config --set ssl_verify False
```

Installing CMOR and PrePARE

Run the following commands

# install cmor
# ------------------------------------------------
conda create -n CMOR -c conda-forge cmor
conda activate CMOR

# Clone the CMIP6 table to your working directory.
# ------------------------------------------------
mkdir CMIP6_work
cd  CMIP6_work

# Disable SSL verification (firewall only).
# -----------------------------------------
export GIT_SSL_NO_VERIFY=true
git clone https://github.com/PCMDI/cmip6-cmor-tables.git

# Note:
# -----------------------------------------------------------
# UDUNITS2_XML_PATH is set automatically by activating CMOR. 
# export UDUNITS2_XML_PATH=${CONDA_PREFIX}/share/udunits/udunits2.xml
#

Testing

Run the CMIP6 CV Python tests

# Install cmor with cdms2 and testsrunner
# ------------------------------------------------
conda install -n CMOR -c cdat/label/nightly -c cdat -c conda-forge cdms2 testsrunner

# Clone the CMOR repository to your working directory.
# ------------------------------------------------
git clone https://github.com/PCMDI/cmor.git
cd cmor

# Update the CMIP6 tables submodule.
# ------------------------------------------------
git submodule init
git submodule update

# Set PYTHONPATH to the Test directory.
# ------------------------------------------------
export PYTHONPATH=Test/

# Run the tests.
# ------------------------------------------------
python run_tests.py -v2 -H -n1 Test/test_python_CMIP6_CV*.py

Run the full test suite for C, Fortran, and Python

Install gcc and gfortran and linking environment variable

Linux:

conda install -n CMOR -c conda-forge gcc_linux-64 gfortran_linux-64
export LDSHARED_FLAGS="-shared -pthread"

Mac:

conda install -n CMOR -c conda-forge clang_osx-64 gfortran_osx-64
export LDSHARED_FLAGS=" -bundle -undefined dynamic_lookup"

Build and run tests

# Set prefix for configure step.
# ------------------------------------------------
export PREFIX=$(python -c "import sys; print(sys.prefix)")

# Configure the Makefile.
# ------------------------------------------------
./configure --prefix=$PREFIX --with-python --with-uuid=$PREFIX --with-json-c=$PREFIX --with-udunits2=$PREFIX --with-netcdf=$PREFIX  --enable-verbose-test

# Run the tests with the Makefile (without rebuilding CMOR).
# ------------------------------------------------
make test -o cmor -o python

Conda environment

Create your different CMOR environment with anaconda.

conda create -n [YOUR_ENV_NAME_HERE] -c conda-forge cmor
source activate [YOUR_ENV_NAME_HERE]

To learn more about conda environments

Obtaining Nighlty builds

Create a dedicated environment for nightly (in between releases code):

conda create -n [YOUR_ENV_NAME_HERE] -c pcmdi/label/nightly -c conda-forge cmor
source activate [YOUR_ENV_NAME_HERE]

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