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Setting up arivis Pro

System requirements

This article explores some of the hardware considerations when configuring a system for use with arivis Pro.

Introduction

arivis Pro has been built from the ground up for the visualization and processing of very large datasets while being RAM independent. This, consequently, has a significant effect on how the software is implemented and affects how we deal with the most common bottlenecks in computing.

CPUs

Because CPUs are generally limited by their clock speeds, a common workaround for this limitation is to use parallelization. Not all processes can be parallelized, but what can be parallelized generally has been in arivis Pro. Therefore, a computer with more cores is generally preferable to a computer with a higher clock rate. Buying computers with 2 or more multi-core CPUs can be a more cost-effective way to increase your core count than buying a single CPU with more cores. However, CPU speed and core count may also be limited by memory usage.

We recommend a minimum of 4 CPU cores (though it will work with fewer if that is what is available), but 8 or more cores are preferable for most image analysis operations.

Memory

Generally speaking, everything that needs to go through the CPU must first be transferred to the RAM. Furthermore, the results of any CPU processing will also typically be stored in RAM, at least temporarily. This means that you generally need twice as much RAM as the data you are trying to process.

arivis Pro has been designed to work around this limitation by using blocking, and temporary documents.

Blocking involves just-in-time loading of portions of the dataset within the available RAM so that it is never necessary to hold the whole dataset in RAM. This means that arivis Pro can process multi-terabyte-sized datasets on a computer with as little as 16GB of RAM or even less.

Having stated this, arivis Pro will use whatever memory is available, and having more RAM may speed up some RAM-intensive processes (e.g. segmentation and processing of very large complex objects).

The other implication is that if we are not holding the whole data in RAM, we need to create temporary documents on the hard disk to store the result of image processing operations which affects how much storage we will need.

Because of this architecture, arivis Pro will allow you to process datasets larger than 500 GB with as little as 4 GB of RAM, but we recommend a minimum of 8 GB while 16 GB is preferable. As RAM gets a lot more expensive the more you add and the Software is not dependent on RAM availability to such an extent, we do not typically recommend that you buy more than 128 GB of RAM, except for systems intended for multi-user concurrent usage. We generally recommend 8 GB of RAM per CPU computing core.

Storage

Local storage is key to arivis Pro's performance. Through extensive use of Just-in-Time loading and temporary documents, arivis Pro relies heavily on local storage. In many ways, more so than it relies on RAM. Therefore, it is important to have plenty of local storage, both to store documents locally while working with them to enable fast just-in-time loading, and to allow for the creation of temporary documents to store the results of any image processing operations.

Using fast solid-state drives (SSDs) can provide marginal gain improvements for many read/write-intensive applications, but generally getting more storage is preferable to buying faster storage. We generally recommend having at least 5x as much free disk space as the documents you are trying to process. Note that both the active and temporary documents can use compression to further increase the size of files that can be processed locally.

Buying RAID storage where multiple relatively slow spinning disk drives run in parallel to increase speed and reliability can be a more cost-effective way to add a lot of fast storage.

Network-based or removable storage is generally not recommended due to the possibility that the connection may be intermittent, and the overheads in data transfer under such conditions can lead to significant slow-downs in performance.

Operating system

arivis Pro is a program for Windows 64-bit operating systems. There is no MacOS or Linux version. Please have a look at this article for more information on Installing arivis Pro on Apple hardware. The minimum requirement for support is Windows 10, but Windows 11 is also supported. The software may work partially on earlier versions, but note that these are not supported configurations.

Also, while the low memory requirements of arivis Pro make it theoretically capable of processing large datasets in 32-bit environments, the high cost of maintenance of two separate builds of the software and the relative scarcity of 32-bit systems means we no longer offer a 32-bit version. 

Conclusions

So, which hardware configuration should you choose?

The computer you already have, as long as it runs Windows 10 or better, has 100GB or more of free hard disk space, and has a dedicated GPU that supports OpenGL 4.3 will probably be fine for most image analysis tasks and visualization. But if you want to buy a new machine dedicated to arivis Pro then the following recommendations are useful guidelines.

Also, please see this article Choosing the right license type for recommendations regarding licensing options.

Installation and configuration

arivis Pro is a Windows OS application for image analysis. It has been designed to make optimal use of computer resources to enable the processing and analysis of data sets that can be much larger than the available computer memory. Several optimizations are dependent on the installation and configuration of the software.

Installing arivis Pro

  1. Download the installer for the latest version of arivis Pro, see https://downloads.zeiss.com/arivis/Pro/latest
  1. To start the installation double click on the installer package.
  2. We recommend to install to the default applications folder.
  3. We recommend installing the GPU acceleration for systems that support it.
  4. Activate your license if needed, see Activating the license.
  5. Once installed, check the directories for temporary documents and change them if needed.
  6. Configure the GPU for optimum use of system resources as needed.

Activating the license

For all new installations you need to activate your license but not for updates to existing installations.

For detailed descriptions of the process of activating, updating or transferring licenses is covered, see this article.

  1. Start the application and, when prompted, open the arivis License Tool.
  2. Select the Online Activation option.
  3. Enter the activation key and activate the license.

GPU configuration

Graphics acceleration

As part of the installation process the software will also detect any GPU present and enable the use of the GPU for graphics acceleration and machine learning data processing if compatible.

The first time we start the 4D Viewer the software will automatically optimize the render settings based on the GPU capabilities:

These settings are optimized so as to balance render quality with interactivity. However, users may prefer to prioritise faster navigation or higher render quality based on their own preferences. These settings can be found in the 4D Viewer pane of the preferences window.

The settings can be reconfigured back to the recommended arivis defaults for your GPU by using the Run Auto-Detection button. Note that laptop systems may not default to using the dedicated GPU. If arivis is installed on a laptop system you should check this article about configuring arivis for laptop GPUs.

ML & DL acceleration

Additionally to using the GPU for graphics acceleration, arivis can also use compatible GPUs to accelerate Machine Learning (ML) and Deep Learning (DL) workflows. To use GPU acceleration for ML & DL tasks arivis Pro needs:

  • NVIDIA GPUs
  • Up to date drivers
  • At least 8 GB of video memory (VRAM)

If these conditions are met and the GPU acceleration was installed as part of the installation the software should automatically use the GPU for ML and DL acceleration. We can check if this is the case within the Machine Learning panel of the Preferences window:

As we can see from the screenshot above, this system uses the GPU for Machine Learning. If the GPU is incompatible the checkbox will be disabled and cannot be checked. If so, first check whether the graphics card should be compatible (NVIDIA chipset and 8GB RAM), then check that the drivers are up to date. Please consult with the system administrator or your IT support team to update the drivers as needed.

Using the GPU package installation

This article provides background, download links and installation instructions for the stand-alone GPU package installation.

Overview

  • If you use ML and have a compatible GPU you should install this and use it
  • The installation is normally part of the standard installation process
  • If you've already installed the software, or you're installing it on an offline workstation, you can download and install this package independently using the instructions below 

Introduction

With the release of Vision4D 3.6, arivis added the ability to use Deep Learning (DL) inference for segmentation of images. This can significantly improve the accuracy of segmentation of complex structures in a range of applications and images.

To optimize the DL operations we use the ONNX runtime libraries. These can be used with both GPU and CPU, but using the GPU to run these operations can dramatically improve the speed of processing. However, the GPU libraries are quite large (600MB) and only compatible with NVIDIA GPUs. Since not all users will require this, either because they have no need for DL or no compatible GPU, we do not include the GPU package as part of the Vision4D installation files and instead download it on request during the installation process. 

Using the GPU for ML Operations

Once the GPU packages have been installed, the option to use the GPU for ML acceleration will appear in the application preferences:

Note that this option may remain greyed out if the GPU drivers that are currently installed are not compatible. In that case, the user should update the drivers and restart the system. Once this option is enabled the software will default to using the GPU for any ML operation.

 

Compatible GPUs

This package makes use of CUDA, a proprietary technology available on NVIDIA GPUs. Please see this Wikipedia article or consult the NVIDIA documentation to find out if your GPU is supported. 

 

Using arivis Pro on laptops with a GPU

Overview

If you have a dedicated GPU. make sure you go into the graphics driver preferences and configure it to use the GPU by default for any arivis application.

  • Win 7-8:
  • Right-click on the desktop and open the graphics card control panel. Select Manage 3D Settings from the tasks on the left, then select the Program Settings tab. Click the Add button and browse to your arivis installation. Then select the option to use the high performance GPU.
  • Win 10 and above:
  • Go to the Start menu and open the Settings app. Go to the System settings and then to Display. Scroll down the panel to find the Graphics settings link. Click the Browse button and navigate to your arivis installation, then select your dedicated GPU.

Note that this needs to be done for all arivis installations on your device, so if you are using arivis Pro and arivis Pro VR you will need to configure both.

Setting default GPU

On systems running Windows version earlier than windows 10

On older systems the default GPU selection is done through the driver interface. We can start by right-clicking on the arivis Pro app icon and then select Run with graphics processor> Change default graphics processor...

On newer systems we need to do this through the graphics control panel. Depending on your installation it can be opened in a variety of ways (e.g. through the Start menu, Taskbar shortcuts, or right-clicking on the desktop). This will open the driver window for the GPU you are using. In this example we are using a NVIDIA GPU and so this opens the NVIDIA Control Panel:

We can then click the Add button to select the path for the arivisPro.exe application and then select which GPU to use by default below.

From then on, the system will default to that GPU when launching the application.

For system running Windows 10 and higher

On newer Windows 10 systems the GPU preference is set through the Settings application. Start by opening the Settings app from the Start menu.

Then, select the Systems Settings, and then the Display options. At the bottom of the display setting options, you will find the Graphics settings:

In the Graphics options you can click the Browse button to find the path to your arivis Pro EXE and then select which GPU to use by default when launching the application:

GPU selection on launch

If you need to preserve battery life, maybe because you are doing image analysis on the go then sacrificing graphics performance for the duration of the session may be an acceptable compromise, but you may also choose to run the application with the dedicated GPU on other occasions. You can specify which GPU to use on launching the application by right-clicking on the application icon and choosing the Run with graphics processor option:

You can then choose with GPU to use as needed and the application will launch.

But it is also possible to permanently set a preference for wich GPU to use that that the application will automatically select a specific GPU on launch unless specified otherwise as above.

Using arivis software and virtual machines

Considerations when installing and using arivis products with virtual machines.

Introduction

Virtual machines are a convenient way to create environments for software utilization that are unmoored from physical hardware and can be easily reset, copied, or transferred to new machines. However, these same abilities affect several aspects of how the software is licensed and operated.

Licensing

arivis software products are protected from unauthorized use by a licensing system provided by a third-party provider. This licensing system allows institutions who purchase licenses to protect their asset, and us as software vendors from the illegal distribution of our products. Licensing works by locking the software to a specific piece of hardware, typically a computer or dongle.

In the case of a hard key, the license is effectively located on a USB dongle, and whichever machine has the key plugged in is able to read the license and make it available to users. 

In the case of soft licenses, the key is activated on a computer by making a digital fingerprint of the machine on which it is activated and locking the activation to this fingerprint.

This is important when using a virtual machine. If you have a dongle, the dongle must be visible to the virtual machine. If you are using a soft key, changes to the virtual machine, such as copying it to a new computer, will change the VM's fingerprint and irreversibly invalidate the license. Therefore, if you activate a soft license on a VM, you MUST deactivate the license prior to making any changes to the VM and reactivate once the changes are completed. Failure to do this will invalidate the license and support related to License invalidation due to VM changes are not covered by warranty or maintenance and may be chargeable.

Please see the article Activating, updating and transferring licenses to find out more about activating and transferring licenses.

Conclusions

VMs are, of course, very handy in a range of scenarios. Indeed, the arivis development team does use VMs extensively for testing in-house for these very reasons. However, users should be aware of the distinct differences in how VMs operate to ensure that they have a great user experience. arivis is keen to support users in whatever environment they find most useful to them, and making users aware of the consequences of running in such an environment is part of what the support team can do to ensure a great user experience. 

The arivis support team will always try to help users if they are experiencing issues linked to VMs, but you should be aware that our ability to support will be limited by your configuration, and issues caused by user error may not be covered by maintenance agreements and may therefore be chargeable.

Using arivis Pro over remote desktop

This article highlights some considerations when using Vision4D from a remote machine over RDP.

Introduction

Generally, it is best to use Vision4D on a system that is local to the data storage. Since data storage of very large datasets can be challenging on standard desktop or laptop systems a common workaround is to use a high-end imaging workstation with lots of storage, and to access this workstation using Remote Desktop Protocol (RDP).  However, these configurations have historically been problematic with regard to GPU utilization. This article aims to clarify some of those issues and provide solutions.

GPUs and RDP

Good graphics cards are essential for good 3D rendering performance. Our system hardware recommendation article goes into more details on this topic, but for now, we'll keep it simple and say that Vision4D needs at least OpenGL 4.3 support or higher to display data in the 4D viewer. 

RDP allows users to remotely access the computing resources of a machine other than the one they are physically in contact with. However, using RDP is in many ways significantly different from directly accessing the machine. One of these differences is how the graphics card uses its resources. Historically, using GPUs over RDP has required professional cards with specific drivers, and this is still a good guideline as server cards are generally tuned for multiple concurrent usage and use with RDP. Gaming cards, which are usually significantly cheaper, have historically not provided good support for use with RDP. However, recent driver updates from NVIDIA have significantly improved the compatibility of their GPUs with RDP. 

The following configurations have been tested internally and confirmed to work:

System

1

2

3

4

5

6

Graphics Card

GeForce RTX2080Ti

GeForce GTX1080

GeForce GTX970

GeForce GTX1080Ti

GeForce GTX1080

GeForce GTX1080Ti

Windows Version

20H2

2004

2004

20H2

1909

2004

Driver Version

456.71

456.71

452.06

461.09

451.67

451.67

These systems have been tested using access from a variety of clients, including Mac and Linux clients.

Licensing

The use of Vision4D over RDP is also limited by the licensing system we use.

As of 2020, soft licenses are delivered with RDP enabled by default.

Licenses purchased earlier may be upgraded to enable RDP under certain circumstances. If you have a soft license but RDP is disabled, please contact support using the link at the top of this page.

If you have a Network license, hard or soft, RDP is on by default.

If you have a hard local license, these licenses can only be configured for RDP for arivis Vision4D 3.4 or above. Older versions of Vision4D do not support RDP with a hard local key. If RDP is necessary, please contact your local sales representative to discuss replacing your hard key for a soft key or any other options that might work for you.

Conclusions

While the configurations tested above work, remote desktop GPU support is mostly outside of arivis' control. However, there are a few things we recommend:

  1. Always make sure you have the most up to date windows version and drivers for your graphics card.
  2. If your GPU doesn't work over RDP, first check that it works when used locally and then contact your IT support team or your GPU manufacturer.
  3. Pro graphics card are generally recommended for server installations and multi-user setups.

Creating a system report

How to create, review and share a system report when troubleshooting software issues.

We build arivis software to be as reliable as possible to ensure that users can always process their data, no matter the size. However, despite our efforts it is possible that some users may experience unexpected behaviors which our engineering team should investigate with a view to constantly improve our products. It is therefore often very useful to be able to collect crucial system information to allow us to quickly focus on the matter at hand. With this in mind, a reporting tool is built into the software to allow us to quickly find out about user's current configuration and issues.

  1. To generate a system report go to the Help menu and select the Run System Check... option.
  2. Wait a few seconds and the system report will be ready. The Send Report tool opens and is automatically configured to send the report to the arivis engineering team.
  3. Type in a valid email address so that we might contact you with additional questions if necessary, or to let you know when the issue is resolved. The system report does include a lot of errors generated by the software and the OS, but a concise description of the steps taken to reproduce the issue are immensely valuable to the engineering team.
  4. To view the report, click View Report prior to sending it if you want to review its content.
  5. Click Save... to save the report in case you will need it at a later date.
  6. Close the Report Viewer and click Send Report to send the report.
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