How to set up the paradigm for Parallel Macro
First, open the Paradigm Profiles Configurator from the menu of Fiji by selecting Plugins > HPC-ParallelTools > Paradigm Profiles Configurator.
Then fill-out a name for example “cluster” in the text field of the “Create new profile” section.
Select the type of the paradigm by selecting “HPCWorkflowJobManager” from the selection box in the middle of the “Create new profile” section.
Select the option “SSH” this will use SSH to communicate with the remote cluster. The other option uses the HEAppE middleware which can be used if it is installed and configured separately from HPC Workflow Manager and Parallel Macro.
Press the “Create” button found in the “Create new profile” subsection.
A new window will open.
Fill-out the connection details according to the instructions in the table bellow.
ℹ️ If you are using the virtual cluster based on the "Building your own cluster and configuring it" worksheet, then adapt the values from this table.
If you are participating in a workshop organized by IT4Innovations adapt the values from this table.
| Settings | Example Value | Your Action |
|---|---|---|
| Host name | Salomon.it4i.cz | Replace "Salomon.it4i.cz" with the host name of the remote cluster you are connecting to. |
| Port number | 22 | Replace the port number with the one of your remote cluster, usualy it is port number 22. |
| Username | dd-20-36-01 | Replace "dd-20-36-01" with your username for the remote cluster. |
| Authentication method | Key file | Select "Key file" radio button. |
| Key File | C:\Documents\id_rsa-dd-20-36-01 | Select the remote cluster's certificate location in your local computer. |
| Key file password | 123pass | Replace with your password. |
| Password | - | Do nothing. |
| Remote directory with Fiji | /scratch/work/project/dd-20-36/Fiji.app | You can use any Fiji installation in the remote machine that you would normally have all of the access rights to if you connected using SSH normally. One suggestion would be a new directory within your remote cluster home directory. Enter the path to the remote Fiji of your choice. The specified remote working directory will be created automatically on the cluster. |
| Remote working directory | /home/training/dd-20-36-01/WD | Replace dd-20-36-01 with your username. |
| Working directory | C:\Documents\WD | The working directory is local, you need to create one as it is not automatically created. Create a directory in you local machine and browse to it. |
In the example, the settings for a connection to IT4Innovations Salomon supercomputer are given by the user.
Once the information is correct press the "OK" button. The settings will be saved.
Select the paradigm profile you created from the combo box in the “Choose an existing profile” section.
Press the "Select" button.
If correctly selected, the name and type entered will be displayed in the “Currently selected profile” section.
Now the “Paradigm Profiles Configurator” window can be closed by pressing the "OK" button.
If no changes to the settings are needed in the future you only need to create a paradigm profile once. The paradigm profile will be saved for future use.
Try clicking Plugins > HPC-ParallelTools > HPC Workflow Manager. If the connection is successful a new window titled "HPC Workflow Manager" should appear.
⚠️ If the scheduler or Open MPI module is not automatically detected successfully you can specify them manually in the advanced settings.