Verified Commit 29bc2408 authored by Adam Caprez's avatar Adam Caprez
Browse files

Change 'source' to 'conda' and add blurb for job scripts.

parent ee7ed28c
......@@ -89,7 +89,7 @@ If the package is available, this will also display available package
versions and compatible Python versions the package may be installed
under.
### Creating Custom Anaconda Environment
### Creating Custom Anaconda Environments
The `create` command is used to create a new environment.  It requires
at a minimum a name for the environment, and at least one package to
......@@ -113,14 +113,25 @@ To use the environment, we must first *activate* it.
{{% panel theme="info" header="Activate environment" %}}
{{< highlight bash >}}
source activate mynumpy
conda activate mynumpy
{{< /highlight >}}
{{% /panel %}}
Our new environment is now active, and we can use it.  The shell prompt
will change to indicate this as well (this can be disable if desired).
### Creating Custom GPU Anaconda Environment
To use your environment in a job, add the lines
{{% panel theme="info" header="Use your environment in a SLURM job" %}}
{{< highlight bash >}}
module load anaconda
conda activate mynumpy
{{< /highlight >}}
{{% /panel %}}
to the beginning of your submit script (replacing `mynumpy` with your environment's name).
### Creating Custom GPU Anaconda Environments
We provide GPU versions of various frameworks such as `tensorflow`, `keras`, `theano`, via [modules](../module_commands). However, sometimes you may need additional libraries or packages that are not available as part of these modules. In this case, you will need to create your own GPU Anaconda environment.
......@@ -142,7 +153,7 @@ This will create a new `tensorflow-gpu-1.12-custom` environment in your home dir
{{% panel theme="info" header="Install new packages in the currently active environment" %}}
{{< highlight bash >}}
module load anaconda
source activate tensorflow-gpu-1.12-custom
conda activate tensorflow-gpu-1.12-custom
conda install <packages>
{{< /highlight >}}
{{% /panel %}}
......@@ -150,11 +161,11 @@ conda install <packages>
Next, whenever you want to use this custom GPU Anaconda environment, you need to add these two lines in your submit script:
{{< highlight bash >}}
module load anaconda
source activate tensorflow-gpu-1.12-custom
conda activate tensorflow-gpu-1.12-custom
{{< /highlight >}}
{{% notice info %}}
If you have custom GPU Anaconda environment please only use the two lines from above and **DO NOT** load the module you have cloned earlier. Using `module load tensorflow-gpu/py36/1.12` and `source activate tensorflow-gpu-1.12-custom` in the same script is **wrong** and may give you various errors and incorrect results.
If you have custom GPU Anaconda environment please only use the two lines from above and **DO NOT** load the module you have cloned earlier. Using `module load tensorflow-gpu/py36/1.12` and `conda activate tensorflow-gpu-1.12-custom` in the same script is **wrong** and may give you various errors and incorrect results.
{{% /notice %}}
......@@ -236,7 +247,7 @@ Jupyter Notebook. To do so, follow the steps below, replacing
2. Using the command-line environment, load the target conda
environment:
{{< highlight bash >}}source activate myenv{{< /highlight >}}
{{< highlight bash >}}conda activate myenv{{< /highlight >}}
3. Install the Jupyter kernel and add the environment:
......
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