This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
conda [2022/02/01 17:38] jpummil |
conda [2024/03/01 19:25] (current) jpummil |
||
---|---|---|---|
Line 1: | Line 1: | ||
- | ==== Conda ==== | + | ==== Conda Package Manager==== |
- | ==Conda== | + | ===Conda=== |
[[http:// | [[http:// | ||
Line 14: | Line 14: | ||
< | < | ||
- | $ module load python/ | + | $ module load python/ |
- | $ source / | + | |
</ | </ | ||
Line 26: | Line 25: | ||
conda config --add channels conda-forge | conda config --add channels conda-forge | ||
</ | </ | ||
+ | |||
+ | With everything above resolved, one can now search for relevant software that might be useful for their research... | ||
+ | (*The following two commands should be done on a compute node as login nodes no longer have reliable access to the outside world.) | ||
+ | |||
+ | < | ||
+ | conda search <package name> | ||
+ | </ | ||
+ | |||
+ | Once you find the package you wish to install, you would use the following example to perform the following task: | ||
+ | < | ||
+ | conda create -n < | ||
+ | </ | ||
+ | |||
+ | One may also use the following command to see what environments are already installed on Pinnacle and activate if suitable: | ||
+ | < | ||
+ | conda env list | ||
+ | </ | ||
+ | |||
+ | As most users will utilize their new software installs in conjunction with a SLURM job script, below is a quick example of how this process would be implemented: | ||
+ | |||
+ | < | ||
+ | #SBATCH -J < | ||
+ | #SBATCH --partition comp06 | ||
+ | #SBATCH -o < | ||
+ | #SBATCH -e < | ||
+ | #SBATCH --mail-type=ALL | ||
+ | #SBATCH --mail-user=< | ||
+ | #SBATCH --nodes=1 | ||
+ | #SBATCH --ntasks-per-node=32 | ||
+ | #SBATCH --time=06: | ||
+ | |||
+ | export OMP_NUM_THREADS=32 | ||
+ | |||
+ | module load python/ | ||
+ | conda activate < | ||
+ | </ | ||
+ | |||
+ | The Anaconda group maintain a very helpful "Cheat Sheet" for all things conda. If you have further questions, you can find it here: [[https:// | ||
Line 31: | Line 68: | ||
* If a “conda install xxx” asks you to downgrade or revert anything…STOP! Don’t do it. In this case, create a unique environment for that specific software tool alone. | * If a “conda install xxx” asks you to downgrade or revert anything…STOP! Don’t do it. In this case, create a unique environment for that specific software tool alone. | ||
- | * If it says “requires Python 2.7”….we’d also just create an isolated environment. | + | * If it says “requires Python 2.7”….we’d also just create an isolated environment |
- | * If “conda install xxx” shows just an enormous number of dependencies (Rstudio, BUSCO, and Qiime are prime examples)…best to Google before installing. These occasionally have “gotcha’s” that require a bit of additional effort. | + | * If “conda install xxx” shows just an enormous number of dependencies (Rstudio, BUSCO, GATK, and Qiime are prime examples)…best to Google before installing. These occasionally have “gotcha’s” that require a bit of additional effort. |
* Check developer page to see what the most current version of the software you need is…on occasion, the latest version on conda will be a couple of releases behind. | * Check developer page to see what the most current version of the software you need is…on occasion, the latest version on conda will be a couple of releases behind. | ||
* Though the situation improves daily, not ALL software packages are available thru conda repositories. | * Though the situation improves daily, not ALL software packages are available thru conda repositories. | ||
+ | * While conda does make GPU accelerated packages available, it isn't as straightforward getting those to run properly due to the necessity of activating the appropriate NVIDIA run time tools. | ||