Amira-Avizo Software

Introduction

This content is intended to give recommendations about choosing a suitable workstation to run Amira-Avizo Software.

The four most important components that need to be considered are the graphics card (GPU), the CPU, the RAM and the hard drive.

The performance of direct volume rendering of large volumetric data or large triangulated surface visualization extracted from the data depends heavily on the GPU capability. The performance of image processing algorithms depends heavily on the performance of the CPU. The ability to quickly load or save large data depends heavily on the hard drive performance. And, of course, the amount of available memory in the system will be the main limitation on the size of the data that can be loaded and processed.

Because the hardware requirements will widely vary according to the size of your data and your workflow, we strongly suggest that you take advantage of our supported evaluation version to try working with one of your typical data sets.

In this document, the term “Amira” refers to all Amira Software editions and extensions and the term “Avizo” refers to all Avizo software editions (including Avizo ToGo) and all Avizo Software extensions.

Operating systems

  • Microsoft Windows 7/8/10 (64-bit). Amira-Avizo Software 2019.3 is the last version to support Windows 7.
  • Linux x86_64 (64-bit). Supported 64-bit architecture is Intel64/AMD64 architecture. Supported Linux distribution is CentOS 7.
  • Mac OS X High Sierra (10.13) and Mac OS X Mojave 10.14.

Some of the editions, extensions or functionalities are limited to some platforms:

  • Avizo for Industrial Inspection and Avizo XInline extensions are supported only on Microsoft Windows (64-bit).
  • XWind Extension: support of the ABAQUS reader (.odb format) and STAR-CCM reader are available only on Microsoft Windows and Linux, not on Mac OS X. The Meshing workroom and Generate Tetra Mesh module are supported only on Microsoft Windows, not on Linux or Mac OS X.
  • XScreen is supported only on Microsoft Windows and Linux, not Mac OS X.
  • Avizo XReadIGES Extension, Avizo XReadSTEP Extension, Avizo XReadCATIA5 Extension, Avizo XReadCATIA6 Extension, Avizo XReadJT Extension, Avizo XReadXMT Extension, Avizo XReadPROE Extension, Avizo XReadSOLIDEDGE Extension, Avizo XReadSOLIDWORKS Extension, Avizo XReadUG Extension, Avizo XReadVDA Extension are supported only on Microsoft Windows, not on Linux or Mac OS X,
  • XDigitalVolumeCorrelation is supported only on Microsoft Windows and Linux, not Mac OS X.
  • Avizo XLabSuite molecular diffusivity, formation factor and thermal conductivity computation are supported only on Microsoft Windows, not on Linux or Mac OS X.
  • Amira XObjectTracking is supported only on Microsoft Windows, not on Linux or Mac OS X.
  • The Recipe workroom and Recipe Player module are supported only on Microsoft Windows and Linux, not Mac OS X.
  • Embossed Slice visualization module is supported only on Microsoft Windows and Linux, not Mac OS X.
  • Olympus and TXM file formats are supported only on Microsoft Windows, not on Linux or Mac OS X.
  • GATAN reader (Avizo Software) is supported only on Microsoft Windows and Linux, not Mac OS X.
  • Deep Learning Prediction and Deep Learning Training modules are supported only on Microsoft Windows, not on Linux or Mac OS X. A NVIDIA GPU supporting CUDA Compute Capability 3.5 or higher is also required, with up-to-date drivers.
  • Mac® OS X Mojave (10.14) does not provide any CUDA compatible driver. As a consequence, modules of Avizo offering GPU compute capabilities will be restricted to CPU mode. Cylinder Correlation module (Avizo XFiber and Amira XTracing) , which requires CUDA support, will not be able to run.

Prioritizing hardware for Amira-Avizo Software

Graphics Cards

The single most important determinant of Amira-Avizo Software performance for visualization is the graphics card.

Amira-Avizo Software should run on any graphics system (this includes GPU and its driver) that provides a complete implementation of OpenGL 2.1 or higher (certain features may not be available depending on the OpenGL version and extensions supported).

However, graphics board and driver bugs are not unusual.

The amount of GPU memory needed depends on the size of the data. We recommend a minimum of 1 GB on the card. Some visualization modules may require having graphics memory large enough to hold the actual data. High-end graphics cards have 16 to 32 GB of memory. Optimal performance volumetric visualization at full resolution requires that data fit in graphics memory (some volume rendering modules of Amira-Avizo are able to go around this limitation).

Amira-Avizo Software will not benefit from multiple graphics boards for the purpose of visualization on a single monitor. However, some of the image processing algorithms rely on CUDA for computation, and while the computation can run on the single CUDA-enabled graphics board, this computation can also run on a second CUDA-enabled graphics card installed on the system. A multiple graphics board configuration can be useful to drive many screens or in immersive environments.

When comparing graphics boards, there are many different criteria and performance numbers to consider. Some are more important than others, and some are more important for certain kinds of rendering. Thus, it’s important to consider your specific visualization requirements. Integrated graphics boards are not recommended for graphics-intensive applications such as Amira-Avizo software except for basic visualization.

Wikipedia articles on NVIDIA GeForce/Quadro and AMD Radeon/FirePro cards will detail specific performance metrics:

  • Memory size: This is very important for volume visualization (both volume rendering and slices) to maximize image quality and performance because volume data is stored in the GPU’s texture memory for rendering. It is also important for geometry rendering if the geometry is very large (large number of triangles).
  • Memory interface / Bandwidth: This is important for volume rendering because large amounts of texture data need to be moved from the system to the GPU during rendering. The PCI Express 3 buses are the fastest interfaces available today.
  • Number of cores (also known as stream processors): This is very important for volume rendering because every high- quality rendering feature you enable requires additional code to be executed on the GPU during rendering.
  • Triangles per second: This is very important for geometry rendering (surfaces, meshes).
  • Texels per second / Fill rate: This is very important for volume visualization (especially for volume rendering), because a large number of textures will be rendered and pixels will be “filled” multiple times to blend the final image.

Professional graphics boards

Vendor Family Series
NVIDIA Quadro Maxwell, Kepler, Pascal
AMD FirePro W, V

All driver bugs are submitted to the vendors. A fix may be expected in a future driver release.

Standard graphics boards

Vendor Family Series
NVIDIA GeForce Maxwell, Kepler, Pascal
AMD Radeon since GCN 1.1
Intel HD Graphics Broadwell, Skylake

Due to vendor support policies, on standard graphics boards we are not able to commit to providing a fix for bugs caused by the driver.

  • A professional graphics boards will benefit from the professional support offered by the vendors (driver bug fixes).
  • Always use a recent driver version for your graphics board.
  • With an NVIDIA Quadro board we recommend to use the driver profile “3D App – Visual Simulation”. In case of rendering or performance issues you may want to experiment with different “3D App” profiles.
  • Turning off the Vertical sync feature improves frame rate.
  • Visit http://en.wikipedia.org/wiki/List_of_Nvidia_graphics_processing_units for a complete list of NVIDIA boards and comparisons.
  • Visit http://en.wikipedia.org/wiki/List_of_AMD_graphics_processing_units for a complete list of AMD boards and comparisons.
  • Some visualization modules like Volume Rendering may not support Intel graphic cards.

System Memory

System memory is the second most important determinant for Amira-Avizo Software users who need to process large data.

You may need much more memory than the actual size of the data you want to load within Amira-Avizo Software. Some processing may require several times the memory required by the original data set. If you want to load, for instance, a 4 GB data set in memory and apply a non-local means filter to the original data and then compute a distance map, you may need up to 16 or 20 GB of additional memory for the intermediate results of your processing. Commonly you will need 2 or 3 times the memory footprint of the data being processed for basic operations. For more complex workflows you may need up to 6 or 8 times amount of memory, so 32 GB may be required for a 4 GB dataset. Due to the potentially high memory requirement we highly recommend running on 64-bit computer and operating systems.

Also notice that size of the data on disk may be much smaller than memory needed to load the data as the file format may have compressed the data (for instance, loading a stack of JPEG files).

Amira-Avizo’s Large Data Access (LDA) technology will enable you to work with data sizes exceeding your system’s physical memory. LDA is an excellent way to stretch the performance, but it is not a direct substitute for having more physical memory.

The best performance and optimal resolution will be achieved by using Amira-Avizo’s LDA technology in combination with a large amount of system memory. LDA provides a very convenient way to quickly load and browse your whole dataset. Note that LDA data will not work with most compute modules, which require the full resolution data to be loaded in memory.

Avizo Software and Amira Software XImagePAQ provide another loading option to support 2D and 3D image processing from disk to disk, without requiring loading the entire data into memory; modules then operate per data slab. This enables processing and quantification of large image data even with limited hardware memory. Since processing of each slab requires loading data and saving results from/to the hard drive, it dramatically increases processing time. Thus, processing data fully loaded in memory is always preferred for best performance.

Hard Drives

When working with large files, reading data from the disk can slow down your productivity. A standard hard drive (HDD) (e.g., 7200rpm SATA disk) can only stream data to your application at a sustained rate of about 60 MB/second. That is the theoretical limit; your actual experience is likely to be closer to 40 MB/second. When you want to read a 1 GB file from the disk, you will likely have to wait 25 seconds. For a 10 GB file, the wait is 250 seconds, over 4 minutes. LDA technology will greatly reduce wait time for data visualization, but disk access will still be a limiting factor when you want to read data files at full resolution for data processing. Compared to traditional HDDs, solid state drives (SSD) can improve read and write speeds.

For best performance, the recommended solution is to configure multiple hard drives (3 or more HDD or SSD) in RAID5 mode; note that RAID configurations may require substantially more system administration. For performance only, RAID 0 could be used, but be warned of risk of data loss upon hard-drive failure. If you want performance and data redundancy then RAID 5 is recommended.
Reading data across the network, for example from a file server, will normally be much slower than reading from a local disk. The performance of your network depends on the network technology (100 Mb, 1 Gb, etc.), the amount of other traffic on the network, and number/size of other requests to the file server. Remember, you are (usually) sharing the network and server and will not get the theoretical bandwidth. LDA technology may also facilitate visualization of volume data through the network, but if data loading is a bottleneck for your workflow, we recommend making a local copy of your data.

CPU

While Amira-Avizo Software mostly relies on GPU performance for visualization, many modules are computational intensive and their performance will be strongly affected by CPU performance.
More and more modules inside Amira-Avizo Software are multi-threaded and thus can take advantage of multiple CPUs or multiple CPU cores available on your system. This is the case for most of the quantification modules provided with Amira Software XImagePAQ and Avizo Software, a number of modules of the XLabSuite Extension, and also various computation modules.

Fast CPU clock, number of cores, and memory cache are the three most important factors affecting Amira-Avizo Software performance. While most multi-threaded modules will scale up nicely according to the number of cores, the scaling bottleneck may come from memory access. From experience, up to 8 cores show almost linear scalability while more than 8 cores do not show much gain in performance. A larger memory cache improves performance.

Special considerations regarding Avizo ToGo

All hardware recommendations listed above are also relevant for Avizo ToGo when loading a .togo file generated by Avizo Software.

The amount of memory needed will be greater than the total memory footprint of the data stored in the .togo file plus the memory footprint of the application itself. Note, since data are compressed when stored in the .togo file and the compression rate varies hugely depending on the data, there is no way to predict from the file size the amount of memory needed to load a . togo file.
Graphics recommendations are the same as above, and will vary depending on the complexity of the geometry to be displayed and the size of the data to be rendered with volume rendering.
The CPU recommendations are less demanding than above, as .togo only stores the result of computation and does not run the computation itself.

It is highly recommended before exporting a .togo file from Avizo to remove all unnecessary data and modules in order to minimize the size of the file and also the amount of memory that will be needed by Avizo ToGo. In order to get an estimate of the required system memory for the workstation where the Avizo ToGo file will be loaded, you can use the Task Manager or other system utilities to look at the current Avizo memory usage at the time of export. You may want to provide this information to the recipient of the .togo file so he or she can provide appropriate hardware resources.

How hardware can help optimizing

Here is a summary of hardware characteristics to consider for optimizing particular tasks.

Visualizing large data (LDA):

  • Fast hard drive
  • System memory
  • GPU memory
  • Memory to GPU/CPU bandwidth

Basic volume rendering:

  • GPU fill rate (texels per second)

Advanced volume rendering (Volume Rendering module):

  • Heavy use of pixel shaders
  • GPU clock frequency, number of GPU cores

Large geometry rendering such as large surfaces from Isosurface or Generate Surface, large point clusters, large numerical simulation meshes, etc.:

  • GPU clock frequency, number of triangles per second

Image processing and quantification (Amira Software XImagePAQ, Avizo Software):

  • Multiple CPU cores (for many modules, including most image processing modules)
  • CPU clock frequency

Anisotropic Diffusion, Non-Local Means Filter (high-performance smoothing and noise reduction image filters), XLabSuite (absolute permeability computation):

  • GPU speed, number of GPU cores (stream processors), CUDA-compatible (NVIDIA)

Other compute modules, display module data extraction:

  • CPU clock frequency
  • Multiple CPU cores (for a number of multi-threaded modules, such as Generate Surface, Register Images, Resample, Arithmetic)

Multi-display systems with Amira-Avizo XScreen: tiled displays, immersive displays, virtual reality:

  • Multi-GPU systems such as PC clusters, etc.

GPU computing using custom module programmed using Amira-Avizo XPand and GPU API:

  • GPU clock frequency, number of GPU cores (stream processors)
  • Multi-GPU systems such as NVIDIA Tesla
  • CUDA support

Amira-Avizo2D Software

Introduction

The following recommendations are intended to help you choose a suitable workstation to run the application.

Analyzer runs on Microsoft™ Windows 10 (64-bit). Other than the operating system requirement, the most important components to consider are the graphics card (GPU), the CPU, the RAM, and the hard drive.

The performance of image processing algorithms depends heavily on the performance of the CPU, the GPU, or both. The GPU performance is important for CUDA®-optimized algorithms. Loading or saving large amounts of data depends on the hard drive performance. The amount of system RAM is the main limitation on the size of the data that can be loaded and processed.

Graphic Cards

Analyzer is a 2D application; therefore, it does not require a high-end graphics card for visualization. Any graphics system (GPU+driver) that provides a complete implementation of OpenGL 2.1 or higher is sufficient. However, some algorithms are optimized with a CUDA implementation. The amount of GPU memory required depends mainly on the use of CUDA-optimized algorithms. The minimum recommendation is 1 GB of GPU memory if your sole use of Analyzer is for visualization. For CUDA usage, we highly recommend either 16 or 32 GB of GPU memory. When choosing the graphics card for your workstation, consider whether you require CUDA support. The CUDA technology is available only on NVIDIA graphics cards.

Analyzer does not benefit from multiple graphics boards for visualization on a single monitor. However, some of the image processing algorithms rely on CUDA for computation, and while the computation can run on the single CUDA-enabled graphics card, this computation can also run on a second CUDA-enabled graphics card installed on the system.

System Memory

If you need to process a large amount of data, system memory is an important consideration. At a minimum, you need at least the size of your complete tile set. In practice, you are likely to need much more memory than the actual size of the data being loaded. Some processing can require several times the memory required by the original data set. For example, if you load a 4 GB data set in memory, apply a non-local means filter to it and then compute a distance map, you might need as much as 16 to 20 GB of additional memory for the intermediate results.

Workflow processing occurs separately for each tile of the tile set; therefore, when computation is performed only a single tile is loaded in memory at a time. For a basic workflow, you need, in addition of the size of the input data set, 2 or 3 times the memory footprint of a single tile in the tile set. For a complex workflow, you need up to 6 or 8 times the size of a tile.

Also keep in mind that certain file formats might compress the data so that the disk size of the data is significantly smaller than the memory required to load it.

Hard Drives

When working with large files, reading data from the disk can slow productivity. A standard hard disk drive (for example, a 7200 rpm SATA disk) can only stream data to your application at a sustained rate of about 60 MB/second. That is the theoretical limit; the actual performance is likely to be closer to 40 MB/second. Therefore, reading a 1 GB file from disk typically takes 25 seconds. For a 10 GB file, the wait is over 4 minutes. Compared to traditional HDDs, solid state drives (SSD) can improve read and write speeds.

For best performance, the recommended solution is to configure multiple hard drives (3 or more HDD or SSD) in RAID 5 mode; however, be aware that RAID configurations might require substantially more system administration. For performance only, you could use RAID 0, but at the risk of data loss upon a hard-drive failure. If you want both performance and data redundancy, then RAID 5 is recommended.

CPU

A fast CPU clock, the number of cores, and the memory cache are the most important factors affecting performance. While most multi-threaded modules scale up nicely according to the number of cores, a scaling bottleneck might come from memory access. From experience, up to 8 cores show almost linear scalability while more than 8 cores do not show much gain in performance. A larger memory cache improves performance.

Network

Internet access is necessary to activate the product; however, your firewall might prevent the connection to the license server. For more information, refer to activation documentation. Also be aware that reading data across the network (a file server, for example) is normally much slower than reading from a local disk. The performance of your network depends on the network technology (100 Mb, 1 Gb, etc.), the amount of other traffic on the network, and the number and size of other requests to the file server, so in practice you are unlikely to achieve the theoretical bandwidth.