PbsExecutorSiwenna
Instructions for installing and configuring a WMT executor for the PBS application on siwenna.
--Mpiper (talk) 14:15, 15 March 2019 (MDT)
--Mpiper (talk) 09:27, 30 July 2018 (MDT)
Set install directory
The install directory for this executor is /home/csdms/wmt/pbs.
install_dir=/home/csdms/wmt/pbs 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.
Start by installing an obsolete dependency from the anaconda channel:
conda install libgfortran-ng=7.3 -c anaconda
To (hopefully) ensure all the packages meet the same dependencies, install the base software for the PBS executor through a conda requirements file.
mkdir -p $install_dir/opt && cd $install_dir/opt git clone https://github.com/csdms/wmt-executor-config-files cd wmt-executor-config-files nice conda install --file pbs.txt -c csdms-stack -c defaults -c conda-forge
(It might take awhile for conda to harmonize the dependencies.)
When running/testing interactively on siwenna, activate the base conda environment
source activate base
and set
export MPLBACKEND=Agg
Install executor software
Install the `wmt-exe` package from source.
cd $install_dir/opt git clone https://github.com/csdms/wmt-exe cd wmt-exe git checkout mdpiper/activate-conda-env python setup.py develop
Note that I'm installing from a branch that I haven't merged into the master branch.
Create a site configuration file that describes the executor and symlink it to the executor's etc/ diectory.
scratch_dir='/scratch/$USER/wmt/pbs' python setup.py configure --wmt-prefix=$install_dir --launch-dir=$scratch_dir --exec-dir=$scratch_dir ln -s "$(realpath wmt.cfg)" $install_dir/conda/etc
Here I've configured the executor to do stuff in the /scratch directory instead of the default ~/.wmt.
Install and test CSDMS components
Each section below describes how to install and test a particular CSDMS component.
Currently installed components:
- BenchmarkIngestTool
- ILAMB
- ModelIngestTool
ILAMB
We installed ILAMB above. Test it by starting a Python session in $install_dir/test and executing the setup and IRF methods.
from pymt.components import ILAMB comp = ILAMB() comp.get_component_name() comp.setup('.')
At this point, stop and edit bmi_ilamb.yaml, updating the `ilamb_root` attribute with the appropriate location on siwenna, /home/csdms/ilamb. All other attributes can be left unchanged with their default values.
comp.initialize('bmi_ilamb.yaml') comp.get_start_time() comp.get_end_time() comp.get_current_time() comp.update() comp.finalize()
ILAMB is run at the call to `update`. The default run takes about 75 min.
PBS
Download and install the `pbs-executor` software from source.
cd $install_dir/opt git clone https://github.com/permamodel/pbs-executor cd pbs-executor python setup.py install
Babelize the PBS components.
cd $install_dir mkdir -p build && cd build bmi-babelize $install_dir/opt/pbs-executor --prefix=$install_dir/conda
The first attempt to babelize fails because a file, libltdl.la, is missing. I copied it from another install, modified the path at the end, then re-babelized (be sure to remove existing babelization).
Test a component (here, ModelIngestTool) by starting a Python session in $install_dir/test and executing the setup and IRF methods.
from pymt.components import ModelIngestTool comp = ModelIngestTool() comp.get_component_name() comp.setup('.')
At this point, suspend the IPython session and copy a sample config file and data from the `pbs-executor` repo. (This could be improved.)
cd $install_dir/opt/pbs-executor/pbs_executor/data cp ingest.yaml sftlf_fx_PBS-test_historical_r9i0p0.nc $install_dir/test cd -
Restore the IPython session and continue.
comp.initialize('ingest.yaml') comp.update() comp.finalize()
View the index.html file that results.