Installation¶

Install XPRESSpipe¶

1. Open your command line interface and install conda, if not already installed.

# If on a MacOS
$ curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh

# If on a LinuxOS
$ curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash ~/Miniconda3-latest-MacOSX-x86_64.sh

# Enter yes for all successive prompts and allow the script to install Conda into your path
# After installation, the install script can be removed
rm ~/Miniconda3-latest-MacOSX-x86_64.sh

2. Download the latest version of XPRESSpipe by executing the lines of code in the code block below. Replace the URL for the version of XPRESSpipe for whatever version you want (these can be found under the releases tab on the XPRESSpipe GitHub repository).

$ cd ~
$ curl -L -O https://github.com/XPRESSyourself/XPRESSpipe/archive/refs/tags/v0.6.3.zip
$ unzip XPRESSpipe-v0.6.3.zip
$ cd XPRESSpipe-v0.6.3/

3. Install XPRESSpipe dependencies via Conda and activate the XPRESSpipe environment:

Note

20 Oct 2021 - Currently, base conda is having issues resolving the dependencies required for XPRESSpipe. We recommend installing dependencies using mamba instead, which appears to resolve dependencies without issues. mamba is also conveniently faster than base conda.

Installing dependencies using base conda:

$ conda env create -f requirements.yml
$ conda activate xpresspipe

Installing dependencies using mamba:

$ conda install -c conda-forge mamba
$ mamba env create -f requirements.yml
$ conda activate xpresspipe

4. This installation method will create a separate environment for XPRESSpipe and all its dependencies to live in. Each time you open the command line, you will need to type conda activate xpresspipe to use XPRESSpipe

5. Install XPRESSpipe and test that the installation was successful:

Note

v0.6.3 and later employs the bash install.sh method for installing XPRESSpipe. If using v0.6.2 or earlier, you should instead run pip install .

$ bash install.sh
$ xpresspipe test

If a summary menu appeared in the command line interface, it means we are good to go! Congrats! You are almost ready to use XPRESSpipe!

You can run xpresspipe --help to see a list of the available modules within XPRESSpipe. To see specific parameters for a module, type xpresspipe <module_name> --help.

Install in a supercomputing environment¶

If the dependencies for XPRESSpipe were installed to a conda environment as above, you will need to add a couple lines to you bash script to submit the supercomputing job.

For example, if using a SLURM job scheduler, you should include the following after the #SBATCH lines and before any calls to XPRESSpipe in the slurm script, as below:

#!/bin/bash
#SBATCH --time=72:00:00
#SBATCH --nodes=1
#SBATCH ...
...

source $(conda info --base)/etc/profile.d/conda.sh
source activate xpresspipe

... rest of the script