PermafrostExecutorBlanca

wmt-permafrost executor on blanca

Instructions for installing and configuring a WMT executor on blanca.

--Mpiper (talk) 16:48, 19 March 2018 (MDT)

Set install directory

The install directory for this executor is /projects/mapi8461/wmt/permafrost.

install_dir=/projects/mapi8461/wmt/permafrost
mkdir -p $install_dir

Install Python

Install a Python distribution to be used locally by WMT. We like to use Miniconda.

cd $install_dir
curl https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -o miniconda.sh
bash ./miniconda.sh -f -b -p $(pwd)/conda
export PATH=$(pwd)/conda/bin:$PATH

If working with an existing Miniconda install, be sure to update everything before continuing:

conda update conda
conda update --all

Install the CSDMS software stack

A limiting factor in setting up this executor is the componentized version of ILAMB can only be run with `pymt=0.2`; in particular, the BMI I wrote for ILAMB is incompatible with the `model_metadata` package in newer versions of PyMT. Further, as of 2018-03-20, the `netcdf-fortran` package needs to be wound back so that HDF5 1.8.18 is used because of problems with HDF5 1.10.1 and ESMF, used in PyMT. To ensure all the packages meet the same dependencies (looking at you, numpy), simultaneously install `cca-tools`, `netcdf-fortran`, `pymt=0.2` and `csdms-ilamb` using the csdms-stack conda channel (the Bakery),

conda install cca-tools netcdf-fortran=4.4.4=5 pymt=0.2 csdms-ilamb -c csdms-stack -c defaults -c conda-forge

Install the `babelizer` for components that need to be built from source.

conda install -c csdms-stack babelizer

Optionally install IPython for testing.

conda install ipython

Note that when running IPython remotely on siwenna, it's helpful to set

export MPLBACKEND=Agg

Install executor software

Load blanca's `git` module.

module load git

Install the `wmt-exe` package from source.

mkdir -p $install_dir/opt && cd $install_dir/opt
git clone https://github.com/csdms/wmt-exe
cd wmt-exe
python setup.py develop

Create a site configuration file that describes the executor and symlink it to the executor's etc/ diectory.

python setup.py configure --wmt-prefix=$install_dir --launch-dir='/rc_scratch/$USER/wmt/permafrost' --exec-dir='/rc_scratch/$USER/wmt/permafrost'
#ln -s "$(realpath wmt.cfg)" $install_dir/conda/etc # "realpath" not installed on blanca :(
cd $install_dir/conda/etc
ln -s $install_dir/opt/wmt-exe/wmt.cfg

Note that we're using rc_scratch for the launch and execution directories instead of the default ~/.wmt. Also note that we needed an SbatchLauncher class for wmt-exe because blanca uses Slurm instead of Torque for job control.