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PEcAn 1.4.4: Remote execution from web interface
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@dlebauer dlebauer released this 12 Nov 16:52
· 17136 commits to master since this release
v1.4.4
c9e30e2

DOI

The major new feature of this release of PEcAn is the ability to launch workflows from the web interface that then run on remote machines (e.g. clusters, cloud services). For this to work you will need to have ssh access to that remote machine. PEcAn further supports both remote and local servers that use qsub to schedule job execution instead of just running the job, with PEcAn settings allowing the job submission to be tweaked to particular systems. Running PEcAn remote execution does not require a full PEcAn installation on the remote server; details on remote installation and set-up can be found at remote PEcAn setup

The web interface can now also be configured to control user access to visualizing and downloading existing outputs versus running new workflows. This allows you to provide broad access to model outputs and analyses on your server without risk that unauthorized users will burden compute resources with additional runs. User access is controlled using BETY to configure the users that can view and/or run new workflows.

changes to web interface

One new feature (besides the remote run capability) is the ability to leave notes with the workflow. This allows you to record information about the workflow. Right now this is part of the advanced features, but will be moved in the next release to a more prominent place (#679).

You will need to add the following to you config.php for the ability to control who can run a workflow.

# Require username/password, can set min level to 0 so nobody can
# run/delete.
# 4 = viewer
# 3 = creator
# 2 = manager
# 1 = administrator
$min_run_level=2;
$min_delete_level=2;

For the ability to remote launch instances you will need to add the following to your config.php:

# sshTunnel binary
$SSHtunnel=dirname(__FILE__) . DIRECTORY_SEPARATOR . "sshtunnel.sh";

# List of hosts that need qsub
$qsublist=array("geo.bu.edu");

# List of qsub options, this might only be needed for certain systems
# the list should be the server pointing to an array, the second array
# can contain 3 values (qsub, jobid and qstat).
$qsuboptions=array("geo.bu.edu" => 
                    array("qsub"   => "qsub -V -N @NAME@ -o @STDOUT@ -e @STDERR@ -S /bin/bash",
                          "jobid"  => "Your job ([0-9]+) .*",
                          "qstat"  => "qstat -j @JOBID@ || echo DONE",
                          "job.sh" => "module load udunits R/R-3.0.0_gnu-4.4.6",
                          "models" => array("ED2"    => "module load hdf5")),
                    "host2" => 
                    array( "job.sh" => "echo 'Hello Word'"));

Examples of both these settings are provided in the web/config.example.php file.

Database

This release now will have the ability to sync with the database hosted at the University of Wisconsin - Madison. We have also launched a status page for tracking the overall PEcAn network database synchronization: https://pecan2.bu.edu/pecan/status.php

Changes to PEcAn

As always bug fixes.

Updates to RTM package: additional documentation and vignette updates, support for sensor spectral response functions.

Photosynthesis package: added option for TPU limitation and temperature dependence on parameters

Coming down the pipeline for v1.4.5

The current release of PEcAn includes partial (incomplete) code adding additional models (CLM4.5, PRELES, a revised version of LINKAGES), utilities for benchmarking, support for global meteorology products, integration of remotely-sensed data, and additional generalizations in the state & parameter data assimilation schemes.

Downloads

A VM with this version of PEcAn can be downloaded from NCSA

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