Skip to main content

Utilities for remote submission and collection of GridEngine jobs.

Project description

# remote_sge: Remotely submit jobs to GridEngine

* Remotely submit jobs to a GridEngine cluster.
* Retrieve job results.
* Automated transfer of jobs from one cluster to another.

Remote SGE is a tool for transferring queued jobs to a remote SGE cluster,
as well as for submitting jobs to SGE from a machine other than the cluster's
master host.

* [See here]( for common configuration problems.

# Usage

# Holds jobs with ids in the given range, collects all the required data, and
# sends them to the configured remote.
remote_sge shuttle 12300-12399

# Later...
# Downloads results from any remote jobs that have finished, and unpacks the
# results in the working directory of the local jobs.
# Finally, terminates (deletes) the original jobs from the local queue.
remote_sge collect

# Installation

The installation utility targets Centos 6.x and Amazon Linux 1 (cfncluster).

## Install Base Packages (Client AND Server)

# Feel free to change PY_VERSION to the latest, or to pypy or your favorite
# version available within pyenv.
curl -o \
-L \
&& chmod +x
./ <path to wheel file>

# Restart your shell, you can log out and log in again, or else:

This will:

* Install YUM packages required for pyenv.
* Install latest version of pyenv.
* Install Python 3.6.4 and create a virtualenv called `remote_sge`, based on that version.

## Install the Remote SGE package. (Client AND Server)

You can also type `pyenv activate remote_sge` and then `pip` and other executables will be added
to your path.

First, download the latest wheel from

# Activate your virtualenv:
pyenv activate remote_sge
# Install the package:
pip install /path/to/remote-sge-xxx.whl

## Install the Remote SGE Server Components.

# Activate your virtualenv if not already active:
pyenv activate remote_sge
# Type remote_sge install_server -h for a full list of command-line options.
# The below assumes that vim is installed and you know how to use it.
remote_sge install_server -i

The installer will ask you to edit a number of configuration files. Make changes as needed,
save and quit the editor, and the file will be copied into place.

Here are the particular settings to pay attention to:

### Main Config File:

* Client Section:
* You can safely remove this section from the server component; won't be used.
* Server Section:
* `work_root` should reflect the location where each job's working directory should run.
Each job will be given a randomly-named working directory within this location.
* `completed_files_root` should reflect the location where job results will be placed.
* `nginx_listen` can be a port number, or an `ip_address:port` assignment.
* Command Environment Section:
* A list of environment variables. Use this section to configure locations of any resources
your jobs might use, which are located outside of the job's working directory.

## Test the function of the server component:

# Change the location of the config dir, if you changed the default for config files.
remote_sge test_server ~/.config/remote_sge -P 443 -h localhost

If the server is configured correctly and running, you'll see `It works!`, and you should continue.

## Configure the client component:

The server install will have placed the required client certificates in a tgz file at

# Copy the certificate files to the client machine
ssh <client_machine>
scp me@server_machine:~/remote_sge_client_certs.tgz .

# Do the base install (see Install Base Packages above):
curl -L | PY_VERSION=3.6.4 bash

# Restart your shell:

pyenv activate remote_sge
# Ensure that the wheel file has been downloaded to this machine, and then:
pip install /path/to/remote-sge-xxx.whl

remote_sge install_client -i -c /path/to/remote_sge_client_certs.tgz

You'll be prompted to correct the hostname and port number of your server instance.
The other settings can likely be left alone.

## Test client connectivity

Just to make sure that you have connectivity to the server:

remote_sge test_server ~/.config/remote_sge -P 443 -h

# Set up for development:

``pip install -e .[testing]``

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for remote-sge, version 0.2.8
Filename, size File type Python version Upload date Hashes
Filename, size remote_sge-0.2.8-py3-none-any.whl (50.5 kB) File type Wheel Python version py3 Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page