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The usage is:
module load anaconda3/2019.07.py3
OR
module load anaconda/4.00py2.7
OR:
module load anaconda/4.00py3.5
You need to run this after loading the modules:
source /sw/anaconda/py27-ver400/etc/profile.d/conda.sh #if using module load anaconda/4.00py2.7
OR source /sw/anaconda/py3-ver400/etc/profile.d/conda.sh #if using “module load anaconda/4.00py3.5”
Manual Usage:
You will need to activate the environment. For example, to activate biopython
source activate biopython
discarding /sw/anaconda/2.0.1/bin from PATH
prepending /sw/anaconda/2.0.1/envs/biopython/bin to PATH
To deactivate this environment, use:
source deactivate
Module Usage:
=============
For example,You can use this to load biopython using python 2.7 version (anaconda) :
module load anaconda/py27biopython1.66
For python 3.5 (anaconda env), use this:
module load anaconda/py35biopython1.66
Anaconda environment need not be loaded separately.
However, it can be loaded as follows if needed for other reasons:
module load anaconda/4.00py2.7
module load anaconda/4.00py3.5
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Installed Environment
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Useful commands
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Useful commands: conda info --envs conda list conda activate |
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#!/bin/bash #PBS -N condatest #PBS -m abe #PBS -M YourEMAIL@griffith.edu.au #PBS -l select=1:ncpus=1:mem=4gb,walltime=10:00:00 module load anaconda/4.00py2.7 source /sw/anaconda/py27-ver400/etc/profile.d/conda.sh ##use /sw/anaconda/py3-ver400/etc/profile.d/conda.sh if using “module load anaconda/4.00py3.5” echo "Starting job: " cd $PBS_O_WORKDIR python <pythonFile> >>>An example of the python file>>>>>>>>> cat pythonFile.py import tensorflow as tf >>>>>>>>>>>>>> |
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Activate an environment
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source /sw/anaconda/py27-ver400/etc/profile.d/conda.sh OR source /sw/anaconda/py3-ver400/etc/profile.d/conda.sh if using “module load module load anaconda/4.00py3.5” source activate biopython e.g: source activate biopython discarding /sw/anaconda/2.0.1/bin from PATH prepending /sw/anaconda/2.0.1/envs/biopython/bin to PATH |
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conda remove -n biopython |
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n060 anaconda installation
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Instructions from: https://medium.com/@danielwzou/installing-spacy-and-other-packages-without-sudo-or-root-privileges-using-anaconda-59571ec0ecad
First, navigate to your home directory.
module load anaconda/5.3.1py3
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh
Now, we have a local installation of the Conda package manager at ~/miniconda3
Let’s add conda to our bash profile so that we can call it from the command line
vim .bash_profile
i
Add this line to the file:
export PATH=$HOME/miniconda3/bin:$PATH
esc :wq
Now, let’s reload our .bash_profile
source .bash_profile
And check that our installation was completed successfully
which conda
Which should return ~/miniconda3/bin/conda
Now that Conda is installed, we can install Spacy or other Python packages
conda install spacy
python -m spacy download en
Now, let’s make sure that Spacy is installed correctly
python
import spacy
nlp = spacy.load('en')
doc = nlp(u'Hello World!')
print([w.lemma_ for w in doc])
Now that you have Conda installed, you can use it to install many packages locally. |
Reference
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Anaconda on the new cluster
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module load anaconda3/2019.07py3
This should have packages like the tensorflow env. You can find with this:
conda info --envs
>>>>>
conda info --envs
# conda environments:
#
/sw/anaconda2/2019.07/envs/bio
/sw/anaconda2/2019.07/envs/bioinfoPy27
base * /sw/anaconda3/2019.07
3point6 /sw/anaconda3/2019.07/envs/3point6
R /sw/anaconda3/2019.07/envs/R
bioinformatics /sw/anaconda3/2019.07/envs/bioinformatics
>>>>>>>
This will give the packages in the base:
conda list
source activate 3point6
Next run: " conda list"
This will list the packages installed in that environment.
It shows among many others:
pytorch 1.3.1 cuda100py36h53c1284_0
tensorboard 2.0.0 pyhb230dea_0
tensorflow 2.0.0 mkl_py36hef7ec59_0
tensorflow-base 2.0.0 mkl_py36h9204916_0
tensorflow-estimator 2.0.0 pyh2649769_0
termcolor 1.1.0 py_2 conda-forge
theano 1.0.4 py36hf484d3e_1000 conda-forge
Remember this cluster has no GPU (currently) |
Another sample pbs file
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#!/bin/bash
#PBS -N condatest
#PBS -m abe
#PBS -M YourEMAIL@griffith.edu.au
#PBS -l select=1:ncpus=1:mem=4gb,walltime=10:00:00
cd $PBS_O_WORKDIR
module load anaconda3/2019.07py3
source activate bioinformatics
trinity <trinityinput>
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Sample python code to write out a plot
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vi plot.py
>>>>>>>>>>>>>>>>>
import matplotlib.pyplot as plt
import numpy as np
np.random.seed(19680801)
data = np.random.randn(2, 100)
fig, axs = plt.subplots(2, 2, figsize=(5, 5))
axs[0, 0].hist(data[0])
axs[1, 0].scatter(data[0], data[1])
axs[0, 1].plot(data[0], data[1])
axs[1, 1].hist2d(data[0], data[1])
plt.show()
plt.savefig('test')
>>>>>>>>>>>>>>>>>>
module load anaconda3/2022.10
source activate yourenv #this should have the matlibplot packages and others.
python plot.py would generate a plot named test.png
Reference: https://matplotlib.org/3.4.3/tutorials/introductory/sample_plots.html
Sample codes are here:
https://matplotlib.org/3.4.3/_downloads/55a714c8a6e4dde456b09326202fe492/sample_plots.py
https://matplotlib.org/3.4.3/_downloads/003118d8eb1e7df55671bcdf18bfac3c/sample_plots.ipynb |
Reference
1. http://davebehnke.com/using-python-anaconda-distribution.html
2. https://store.continuum.io/cshop/anaconda/
3. https://medium.com/@danielwzou/installing-spacy-and-other-packages-without-sudo-or-root-privileges-using-anaconda-59571ec0ecad
4. http://continuum.io/downloads#all