Lumerical

Description

Dependencies for ANSYS Lumerical

Available Versions of Lumerical

Version	Module	Available on

Version	Module	Available on
deps_for_2025R2	phys/Lumerical/deps_for_2025R2	Noctua 2, Otus
deps_for_2024R1	phys/Lumerical/deps_for_2024R1	Noctua 2

This table is generated automatically. If you need other versions please click pc2-support@uni-paderborn.de.

Usage Hints for Lumerical

If you need support in using this software or example job scripts please click pc2-support@uni-paderborn.de.

1 Available Versions of Lumerical
2 Usage Hints for Lumerical
- 2.1 Prerequisites
- 2.2 One-time Setup for Compute Projects
- 2.3 One-time Setup for Users
  - 2.3.1 SSH Access to the HPC Systems for Windows
  - 2.3.2 SSH Access to the HPC Systems for Linux
  - 2.3.3 Test SSH Access to the HPC Systems
  - 2.3.4 One-time Setup for Lumerical
- 2.4 Usage
- 2.5 Common Issues
- 2.6 Slides from Lumerical Tutorial on 2025-07-07:

Please don't hesitate to contact us in case of questions or problems. See https://pc2.uni-paderborn.de/go/support and https://pc2.uni-paderborn.de/go/consultationhour for details.

There are three ways to use Lumerical on PC2 Cluster systems:

Directly run Lumerical simulations via job scripts
Run Lumerical GUI on your Computer
Run Lumerical GUI via Remote Desktop in a Web Browser

Prerequisites

To use Lumerical on PC2 cluster systems, you need the following prerequisites:

You need a compute project (abbreviations start with hpc-prf-…) at PC2:
- Often, a work group already has a running compute time project. Please inquire with your group leader. If no existing project is available, you can also apply for a new project. You can find all information regarding compute time proposals at https://pc2.uni-paderborn.de/go/access.
For access to PC2 cluster systems, you need a user account:
- If you are a member of Paderborn University, you can just use your IMT/ZIM account
  - The principal investigator of a compute project can add you to his/her existing compute project as described at https://pc2.uni-paderborn.de/go/useraccount
  - Please note that user addition needs 2-3 hours to become active, i.e., till you can log in
- If you are not a member of Paderborn University: please register for a user account as described at https://pc2.uni-paderborn.de/go/useraccount
You can use our HPC-portal (https://portal.pc2.uni-paderborn.de/dashboard) to check your project memberships and project details.
Be connected to the university network or use the VPN to be able to access systems
- You can check via https://portal.pc2.uni-paderborn.de/vpnconfig
SSH access to the HPC system: You need to be able to log in to the HPC system via SSH. Please refer to section Lumerical
The url of the license server where the floating licenses are hosted. For users from Paderborn University, these licenses are hosted by the ZIM/IMT (see https://imt.uni-paderborn.de/en/license-server), and you can get the required information from your local infrastructure team.
If you want to run the Lumerical GUI on your laptop/Desktop, then a local installation of Lumerical is needed. Simply use the installer for your operating system and enter the license information at the first start of Lumerical.
In case Lumerical is not yet installed for your compute project on the cluster, then you need the Lumerical installation file for Linux (rpm file). See One-time Setup for Compute Projects

One-time Setup for Compute Projects

The following steps only have to be performed once per compute time project:

First, check if Lumerical is already installed for your compute project by checking your projects group directory /pc2/groups/hpc-prf-[abbreviation of compute project]/ or simply ask the person managing the compute time project:
1. If it is installed, they will give you the path to the Lumiercal installation.
2. If it is not installed, please follow the next steps, ask the person managing your compute project to install the version you need, or contact us so that we can install it for you.
If you want to install it yourself, follow the steps (see also the external documentation of Lumerical at https://optics.ansys.com/hc/en-us/articles/360043320733-Installing-on-a-shared-filesystem-on-Linux-without-root-access ):
1. Log in to the HPC system with ssh as shown in Lumerical .
2. Copy the tar.gz-file file to /pc2/groups/hpc-prf-[abbreviation of compute project]/.
3. Change to /pc2/groups/hpc-prf-[abbreviation of compute project]/ and unpack the tar.gz-file with
  tar -zxf Lumerical-<version>.tar.gz
4. Unpack the rpm file:
  rpm2cpio < Lumerical-2025R1-{number}.rpm | cpio -i -d
5. Run
  mv opt/lumerical . rm -rf opt
6. Get the installation path: The installation path required later is
  /pc2/groups/hpc-prf-[abbreviation of compute project]/lumerical/[lumerical version]/
  where [lumerical version] is, for example v241, which you can get with the command
  ls lumerical
7. Check in the list above if a dependency module for your Lumerical version is already available. If it is not yet available, please contact pc2-support@uni-paderborn.de with the name of your compute project and the path to your Lumerical installation so that they can create a suitable one for your version.

One-time Setup for Users

SSH Access to the HPC Systems for Windows

Although SSH access to our compute systems is documented at Access with SSH, we describe here a step-by-step guide for Windows users, including aspects needed specifically for Lumerical. Typically used graphical SSH clients like PuTTY are not sufficient for Lumerical on Windows.

Be connected to the university network or use the VPN to be able to access systems
- You can check via https://portal.pc2.uni-paderborn.de/vpnconfig, it should show on top:
- If it shows something else, please set up/start the VPN. You can find a guide at VPN.
Make sure OpenSSH client is installed in Windows: Settings > System > optional features, then search for OpenSSH
Activate OpenSSH agent in Windows
1. Open a terminal as admin and run:
  Get-Service ssh-agent | Set-Service -StartupType Automatic
2. Open a terminal and run:
  Start-Service ssh-agent
Create ssh key for Lumerical
1. Open a terminal and run (DON’T leave the password empty!!!):
  ssh-keygen -t ed25519 -C "pc2-cluster-access" ssh-add
Configure ssh key on cluster
1. Copy the public key:
  - During the creation of the key in the previous step, you got the output starting with “Your public key has been saved in …“ followed by a path. This is the path to your public key. Open it in a text editor and copy the line.
2. Upload the public key:
  - If you are a member of Paderborn University:
    - As a member of Paderborn University, you can log in to the cluster using your username and password:
      1. Open a terminal and run:
        ssh -t [your user name]@fe.noctua2.pc2.uni-paderborn.de
      2. Enter your password, and you should now see “[your user name]@jura:~$“. That means that you are logged in.
      3. Run the commands
        mkdir .ssh nano .ssh/authorized_keys #paste the copied public key by pressing the right mouse button #press Ctrl+x #press y #press enter exit
  - If you are NOT a member of Paderborn University:
    - Visit https://portal.pc2.uni-paderborn.de/settings#sshkey to upload the public key.

SSH Access to the HPC Systems for Linux

Be connected to the university network or use the VPN to be able to access systems
- You can check via https://portal.pc2.uni-paderborn.de/vpnconfig , it should show on top:
- If it shows something else, please set up/start the VPN. You can find a guide at VPN.
Consult our guide for ssh login and ssh key creation.

Test SSH Access to the HPC Systems

If you open a terminal and try to log in to fe.noctua2.pc2.uni-paderborn.de with
ssh [your user name]@n2login1.ab2021.pc2.uni-paderborn.de
the login should work without having to enter a password. (You might be asked to verify the host key of the login nodes once by typing “yes”.)
To log in not only to the jump host, but also to the login nodes, please test:
ssh [your user name]@fe.noctua2.pc2.uni-paderborn.de -t ssh noctua2
You might be asked to verify the host key of the login nodes once by typing “yes” and enter your user password. You should now see [your user name]@n2loginX, where X is a number between 1 and 6.

One-time Setup for Lumerical

Install Lumerical and open it at least once on your laptop/desktop computer.
Lumerical needs to be told how to access the cluster. For this purpose, there is a configuration file at
- Linux: ~/.config/Lumerical/job_scheduler_input.json
- Windows: %APPDATA%\Lumerical\job_scheduler_input.json (The easiest way to get to %APPDATA% in Windows is to enter %appdata% in the windows search or adress bar in the windows explorer.)
Open a text editor and save the following file at the above-given path:
{ "user_name":"[your user name]", "use_ssh":1, "use_scp":1, "cluster_cwd":"[temporary directory on the cluster]", "master_node_ip":"n2login1.ab2021.pc2.uni-paderborn.de", "ssh_key":"", "path_translation": ["",""] }
Please replace the content in brackets with:
1. [your user name]: the user name that you use to log in to the PC2 cluster systems. If you are a member of Paderborn University this is your IMT/ZIM user name.
2. [temporary directory on the cluster]: Please create a directory for the calculations on the parallel file system, i.e., under /scratch/hpc-prf-[abbreviation of compute project]. We recommend something like /scratch/hpc-prf-[abbreviation of compute project]/[your user name]/lumerical_tmp/. This directory is used by Lumerical during the calculations. It is very important to end the string with a “/”.
Configure Lumerical to submit to the cluster:
1. Open the compute resource configuration in Lumerical via the menu Simulation->Configure resources.
2. Deactivate the usage of “Local Host” by double-clicking “true” in the corresponding row and selecting “false”.
3. Create a new resource by clicking “Add” on the right side.
4. Rename the new resource from “Local Host” to “Noctua 2“ and set capacity 0 (Inf).
5. Edit the new Resource by selecting the corresponding row in the table and clicking “Edit” on the Right:
  1. Job launching Preset: Job Scheduler: Slurm
  2. command: sbatch -N 1 --ntasks-per-node=64 --cpus-per-task=1 -p normal -t 30:00 -A hpc-prf-[abbreviation of compute project]
  3. Submission script:
    #!/bin/bash module reset module load phys/Lumerical/deps_for_2024R1 export LM_LICENSE_FILE=[license sever] export ANSYSLMD_LICENSE_FILE=$LM_LICENSE_FILE export LUMERICAL_DIR="[directory of your Lumerical installation]" export LUMERICAL_BIN=$LUMERICAL_DIR/bin export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK export OMP_PLACES=cores export OMP_PROC_BIND=true srun $LUMERICAL_BIN/fdtd-engine-ompi-lcl -logall -remote {PROJECT_FILE_PATH}
    Please replace:
    - [directory of your Lumerical installation] with the path to your Lumerical installation on the cluster. The path will likely start with /pc2/groups/hpc-prf-[abbreviation of compute project]/
    - [license server]: with the URL to the license server that hosts the Lumerical licenses, i.e., [port]@[hostname]

Usage

After the above one-time setup you can use the cluster to run your Lumiercal calculations by simply clicking “Run” in the graphical interface. The Job Manager will open to monitor your job and see progress.

The resources (number of compute nodes, type of compute nodes,…) can be set in the resource configuration manager by changing the command from the above sbatch -N 1 --ntasks-per-node=64 --cpus-per-task=1 -p normal -t 30:00 -A hpc-prf-[abbreviation of compute project].

You can find all possible settings in our guide on running compute jobs. Here is a list of the most important ones:

number of nodes: -N [number]
number of mpi ranks per node: --ntasks-per-node=[number]
number of OpenMP threads per MPI rank: --cpus-per-task=[number] (should be 1 for FDTD but can be different for FDE, HEAT, CHARGE, FEEM, DGTD and others)
partition: -p [parition name], e.g. normal, largemem,…
time limit of the computation: -t [time limit], e.g, 30:00 for 30 minutes, 1-0 for one day

Common Issues

I am starting a simulation in Lumerical, but it stays in the status “Initializing“:
The typical reason for this problem is that Lumerical can’t submit the simulation as a compute job to the cluster. Most likely, there is a problem with the ssh login to the cluster. Please check:
- Have you logged in with (see Lumerical )
  ssh [your user name]@n2login1.ab2021.pc2.uni-paderborn.de
  at least once? (If it asks you to accept the fingerprint, then you are doing it the first time, enter “yes”, and retry with Lumerical.)
- Can you log in without being asked for a password with
  ssh [your user name]@n2login1.ab2021.pc2.uni-paderborn.de
  If not, then check the configuration of the ssh agent and ssh key above.
You get a “Job Error” in the Job Manager:
- Right-click on the row in the Job Manager and click “View job details”
- Typical issues arise from a job/node specification that is not allowed or not available. You can see this in the lines starting with “sbatch: error:“
- Typical issues are:
  - “sbatch: error: Batch job submission failed: Requested time limit is invalid (missing or exceeds limit): You probably forgot to specify the time limit with -t in the command line in the resource dialog or you requested a time limit that exceeds the maximal time limit (see timelimits).
  - “sbatch: error: Batch job submission failed: Requested node configuration is not available”: You have requested a job with resources that are not available, e.g., too much memory, too many cpu cores,…
    See Node Types and Partitions for details on available nodes.
The job stays in the status “Queued” for a long time:
- Please first check if the cluster is in maintenance or if there is some other issue affecting the execution of jobs via our status dashboard at https://portal.pc2.uni-paderborn.de/
- Long waiting times for jobs are usually the consequence of a low priority of a compute time project. The priority of a compute time project is determined from the relation of the recent usage to the granted resources. Details can be found at Quality-of-Service (QoS) and Job Priorities . The easiest way to increase the priority is to get a higher compute time quota granted for your compute time project. Details on the possibilities to increase the quota for the different project types can be found at https://pc2.uni-paderborn.de/system-access/existing-compute-time-project/step-2-manage-running-project .
Lumerical has lost track of a job but it is still pending or running on the cluster:
- You can monitor and modify your job on the cluster by logging in with ssh (ssh [your user name]@fe.noctua2.pc2.uni-paderborn.de -t ssh noctua2)
  - monitoring jobs: squeue
  - cancelling jobs: scancel [jobid] (You can get the jobid from the output of squeue.)
  - job details: scontrol show job [jobid]