Client Installation

Downloading the SimStack client

If you do not have a working conda or mamba installation, please install mambaforge for your architecture from github.com/conda-forge/miniforge.

After installing, make sure you have the mamba command available in your shell and call:

# Create a new environment for simstack client:
mamba create --name=simstack simstack -c https://mamba.nanomatch-distribution.de/mamba-repo -c conda-forge
# Activate the environment
conda activate simstack
# and run simstack:
simstack

If you want to use your installed simstack client, just open a shell and type:

conda activate simstack
# and run simstack:
simstack

Finally, if you want to update an existing simstack install:

conda activate simstack
mamba update simstack -c https://mamba.nanomatch-distribution.de/mamba-repo -c conda-forge
# Or if you need a specific version, example 1.2.5:
mamba install simstack=1.2.5 -c https://mamba.nanomatch-distribution.de/mamba-repo -c conda-forge

The client version requires passwordless via ssh access to communicate with the HPC. If you do not have passwordless via ssh access to the HPC resources already preconfigured, you need to generate a ssh keypair and transfer it to your authorized_keys file of your user account on the available HPC resource. You achieve this with two simple commands, as shown below.

Warning

Please run the below commands on the same local machine, where the SimStack client will be installed.

Installation on Linux and OSX (Arm and x64)

If you don’t have the ssh keys, use the steps below to generate them.

ssh key generation, just press enter for the passphrase option.
ssh-keygen -t rsa
The ssh-key command above generated two keys in the ~/.ssh directory. Now you have to copy the key to your user account in one of the available HPC resources.
id_rsa
id_rsa.pub
Please choose the HPC where you want to have passwordless access.
ssh-copy-id user@int.bionano.int.kit.edu
ssh-copy-id user@int-nano.int.kit.edu
Test the connectivity of your passwordless ssh by running one of the commands below in the Powershell prompt.
ssh user@int-nano.int.kit.edu
ssh user@int.bionano.int.kit.edu
After completing, the above steps runs the below commands.
cd  simstack_linux
./run_simstack.sh

Installation on Windows

You have two options on Windows: You can install either the native Windows version, or (in an updated WSL2 environment) the Linux version. WSL2 comes with all client tools required, so this is the recommended approach. If you want to use the Windows version, continue this tutorial.

If you don’t have the ssh keys, use the steps below to generate them.

Make sure that the ssh is enabled on your Windows system.

Check if Powershell is installed on your Windows system, if not you can install it from the Microsoft Store.
To generate a public/private rsa key pair on Windows, open the Powershell prompt run the below command, and just press enter for the passphrase option.
ssh-keygen
To copy the ssh key to your user account on the HPC resource, choose and run one of the commands below in the Powershell prompt. Literally copy the command changing only the user.
type $env:USERPROFILE\.ssh\id_rsa.pub | ssh user@int-nano.int.kit.edu "cat >> .ssh/authorized_keys"
type $env:USERPROFILE\.ssh\id_rsa.pub | ssh user@int.bionano.int.kit.edu "cat >> .ssh/authorized_keys"
After completing, the above steps, double click on run-simstack and be happy.

Testing the connectivity

You can test the connectivity of your passwordless ssh in both systems by running one of the commands below. You successfully transferred the key if you establish the ssh connectivity to your HPC without entering your user password.

ssh user@int-nano.int.kit.edu
ssh user@int.bionano.int.kit.edu

Warning

The HPC resource considered here for this tutorial are the int-nano (first line) and bionano (second line) clusters. Please note that you must replace the user with your user account characters in the above lines, and here we are considering that you named your public ssh key as id_rsa.pub located in the .ssh\ directory. This website has a detailed explanation of how to generate ssh keys on Windows and copy it to your HPC resource.

Simstack Server Configuration

Setup the server by opening the configuration menu: Configuration -> Servers

You must replace the characters xxxxxx with your proper setup as highlighted in the figure above, and don’t forget to load (SSH Private Key) your ssh key.

Registry Name: accepts any name.

Base URI: can accepts any HPC IP, but here we will limit ourselves with one of the below options.

int-bionano.int.kit.edu

int-nano.int.kit.edu

Username: enter with the user account according to your available HPC resource.

If ssh key is setup correctly, you should now be able to connect by clicking the Connect button at the top right of SimStack. The green button means you successfully connect to the server.

Warning

If you get an error message during your try, double-check the field on the server setup.

Simstack Overview

Using the SimStack client (picture above), simulation workflows are constructed by dragging and dropping various (already incorporated modules) from the window on the left side area (Available WaNos) into the Workflow canvas area. Double click each module to modify module-specific parameters (see input file field) and allocate resources in the Requested computational resources field for each module. To save and reuse your workflow lately, press ` Crtl+S` or `File -> Save`. It will then appear in the left panel Saved Workflows and can be re-loaded by double-clicking. To submit your workflow, connect to the computational resource (the connect button as shown in the last figure of Simstack Server Configuration section) and click `Run -> Run` on the menu bar, or `Crtl + r`. All required input files are uploaded automatically to the HPC resource, and workflow modules may run serially or in parallel, depending on if your workflow uses or not some of the Loop controls features. As shown in the figure above, the SimStack client will display a yellow folder while be running. When successfully finished, the client will exhibit a green folder, and you will be able to retrieve all the relevant data from your simulations. If the simulation presents a computational issue during the execution, SimStack returns a red folder, which we can be inspected to fix the problem.