Content Comparison

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The “conda install” on the above page gives the installation commands:

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The conda part in the red circle needs to be changed to mamba, and the bioconda part in the blue box is the channel name of this multiqc package. Channel is similar to the name of an online folder, that mamba can find and download the correct package. This is important for the next step.

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1. Connect to the VPN

2. Open a command line interface on Sol by navigating to sol.asu.edu on your browser and
   selecting the "Sol Shell Access" option from the "System" menu option. Or by SSHing into
   Sol using the command ssh <asurite>@sol.asu.edu

3. interactive -p htc -c 4 -t 30

4. module load mamba/latest module load cuda-12.4.1-gcc-12.1.0

5. If the package is for running codes on GPUs, a compatible cuda module is also needed.

6. Now we are ready to create env and install packages. It can be done in seperated separated commands, but the fastest way is to do it in a single command, here is how:

   1. Create an environment:

      Code Block
      mamba create -n myENV -c conda-forge python=3 source activate myENV

   2. Install Pytorch using the command found in step 1

      Code Block
      mamba install -c pytorch -c nvidia pytorch torchvision torchaudio pytorch-cuda=12.4

      Install Multiqc using the command found in step 1

      Code Block
      mamba install -c bioconda multiqc

   3. Combine commands from a, b, c into the fastest single command:

      Code Block
      mamba create -n myENV -c conda-forge -c pytorch -c nvidia -c bioconda python=3 multiqc pytorch torchvision torchaudio pytorch-cuda=12.4

7. And answer Y to the promoted question, if everything looks fine

8. Wait till the installation finish

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As explained in Python Package Installation Method Comparison , the only correct way to use pip on the ASU supercomputers at the moment, is to use it inside an activated mamba env.

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Almost all of the Python packages can be found on anaconda.org, and mamba is always preferred.

There are some packages can only be found on pypi.org but not anaconda.org, then the only option to install them is via pip, inside an activated mamba env. Notably that the current official installation guide for both tensorflow and pytorch prefers pip, but the conda-forge channel still supports them, and our public tensorflow/pytorch environments were built via mamba.

The example Here we take a python package called q2-greengenes2 as an example. The commands to have a package it installed via pip to a mamba env are:

1. Connect to the VPN

2. Open a command line interface on Sol by navigating to sol.asu.edu on your browser and
   selecting the "Sol Shell Access" option from the "System" menu option. Or by SSHing into
   Sol using the command ssh <asurite>@sol.asu.edu

3. interactive -p htc -c 4 -t 30

4. module load mamba/latest

5. Two options here

   1. If you have an existing env: source activate myENV

   (or create a new on using the mamba create command)

   2. If you want to build a new env:

      Code Block
      mamba create -n myENV -c conda-forge python=3 source activate myENV

6. pip install q2-greengenes2

Step 5 - Jupyter Notebook

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