Anaconda
Anaconda is a data science platform which includes Python and R.
Documentation
Usage
Multiple versions of Anaconda are available on Bridges and on Bridges-2. In addition, environments tailored for AI applications which include Anaconda and other popular AI/Machine Learning/Big Data packages, such as TensorFlow, Theano, Keras, pandas, opencv, scikit-learn, and more are set up for you to use.
General instructions
To see what versions of Anaconda are available, type
module avail anaconda # on Bridges module spider anaconda # on Briges-2
Note that anaconda2 modules use python2 and anaconda3 modules use python3.
To see what other modules are needed, what commands are available and how to get additional help type
module help anaconda-version # on Bridges module spider anaconda-version # on Bridges-2
To use Anaconda, include a command like this in your batch script or interactive session to load the Anaconda module:
module load anaconda-version
Be sure you also load any other modules needed, as listed by the module help or module spider anaconda command.
Storing your Anaconda environments
Your home directory has limited space, and Anaconda environment files can be very large. We recommend working in your pylon5 space ($SCRATCH) on Bridges or your ocean space ($PROJECT) on Bridges-2 as your quota there is much larger.
By default, Anaconda environments are created in your home directory space. If you have already created some there, they should be moved to $SCRATCH or $PROJECT. Check if you have environments in your home directory by looking for a .conda subdirectory. Because the subdirectory name begins with a “.”, you need the -a flag to the ls command to see it:
[username@login005]$ ls -a . .. .conda batch_defaults.out examples file.err [username@login005]$
To move your .conda directory and its contents to $SCRATCH or $PROJECT, use the appropriate command:
mv $HOME/.conda $SCRATCH/.conda mv $HOME/.conda $PROJECT/.conda
This may take a while to complete. Once it has, create a symbolic link to direct all new Anaconda environments to be created with the appropriate command:
ln -s $SCRATCH/.conda $HOME/.conda ln -s $PROJECT/.conda $HOME/.conda
Adding to an environment
If you need additional software, you can create a new environment and install it there. Steps to do this are:
- Get an interactive session with the
interactcommand. On Bridges, you must use the--egressoption so that you will be able to access the anaconda website. - Move to your pylon5 space ($SCRATCH) or your ocean space ($PROJECT) to allow enough file space.
- Load the anaconda module you want. Type
module avail anacondaon Bridges ormodule spider anacondaon Bridges-2 to see what versions are available. - Use the
conda createcommand to create your new environment. - Activate your new environment.
- Install the software you need.
This example session on Bridges creates a new environment and installs fitsio.
[username@login006 ~]$ interact --egress A command prompt will appear when your session begins "Ctrl+d" or "exit" will end your session srun: job 5897598 queued and waiting for resources srun: job 5897598 has been allocated resources [username@r003 ~]$ module load anaconda3 [username@r003 ~]$ conda create --name new-env Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.5.4 latest version: 4.6.14 Please update conda by running $ conda update -n base conda ## Package Plan ## environment location: /home/username/.conda/envs/new-env Proceed ([y]/n)? y Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use: # > source activate new-env # # To deactivate an active environment, use: # > source deactivate # [username@r003 ~]$ source activate new-env (new-env) [username@r003 ~]$ conda install -c conda-forge fitsio Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.5.4 latest version: 4.6.14 Please update conda by running $ conda update -n base conda ## Package Plan ## environment location: /home/username/.conda/envs/new-env added / updated specs: - fitsio The following packages will be downloaded: (a list of packages to be downloaded and installed will be displayed) . . . Proceed ([y]/n)? y Preparing transaction: done Verifying transaction: done Executing transaction: done (new-env) [username@r003 ~]$
At this point, a directory named /pylon5/groupname/username/.conda/envs/new-env will have been created for you. The /bin subdirectory will contain your new binaries.
PSC created environments for AI applications
We have built some environments that include software for AI, Big Data and machine learning applications.
The AI environments are built for the GPU nodes on Bridges and Bridges-2. Be sure to use one of the GPU partitions. See the Running jobs section of the Bridges User Guide or the Bridges-2 User Guide for information on Bridges and Bridges-2 partitions and how to choose one to use.
Type
module avail AI/anaconda # on Bridges
module spider AI/anaconda # on Bridges-2
to see the AI environments which you can use.
For additional help, type
module help AI/anaconda-version
Note that AI/anaconda2 environments use python2, while AI/anaconda3 environments use python3.
See what the PSC defined AI environment contains
To see the full list of software included in a given environment, first load the module and activate the environment with these commands:
module load AI/anaconda-version source activate $AI_ENV
To see what is included in $AI_ENV, type
conda list
Customize the PSC defined AI environment
If you need software that is not in the pre-built environment, you can create a new environment by cloning the PSC defined one and then customizing it. First load the module and activate the PSC defined environment, as above, then clone it with
conda create --name your-new-environment-name --clone $AI_ENV
Then you can activate the new environment and proceed with your customization. See the example below for more detail.
Examples
Example sessions are shown below for common uses of anaconda.
Use Tensorflow and python3
Use the following commands:
interact -gpu module load AI/anaconda3-5.1.0_gpu # choose an available AI/anaconda3 module source activate $AI_ENV python import tensorflow
Use Tensorflow and python2
Use the following commands.
interact -gpu module load AI/anaconda2-5.1.0_gpu # choose an available AI/anaconda2 module source activate $AI_ENV python import tensorflow
Customize the PSC defined environment
In this example, the user installs the h5py package in a new environment they are creating. Use the following commands. Note:
The conda list command shows what packages are currently installed. Check to see if what you need is already available. The conda list command also shows the version number of the installed packages.
The conda create command clones $AI_ENV to create a new environment. This can take a long time, so ask for an hour of time with the interact command.
Here, the new environment is named clone-env-1, and is stored in the user’s pylon5 or ocean directory. The –prefix flag names the full path to the where the environment will be stored. You can name the environment anything you like and store it in any directory you like.
interact -gpu --egress -t 01:00:00 module load AI/anaconda3-5.1.0_gpu source activate $AI_ENV conda list conda create --name clone-env-1 --clone $AI_ENV conda activate clone-env-1 conda install h5py
Conda install will install the newest version of the package. If you want to install a version of the package not available in the public installations use the –revision option to the conda install command.
Use the additional packages you installed in a subsequent session
You can use any additional packages you install in the same session in which you install them. To access them in subsequent sessions, follow these steps. In this example, the user created the environment clone-env-1 and installed h5py in it in a previous session.
interact -gpu module load AI/anaconda3-5.1.0_gpu source activate clone-env-1 python import h5py