Scientific Volume Imaging

Read our extended explanation on how to run Huygens remotely at RemoteDisplay.

The performance of Huygens is by the CPU(s), the GPU card(s), and the amount of RAM. Since Huygens does most of its processing on floating point data and needs to store several intermediate images during deconvolution, large amounts of RAM are welcome. The amount of RAM should preferably be 6-10 times the size of your image file. Since RAM is cheap nowadays, we recommend to include enough and to keep the option open for adding more RAM in the near future. Since computations in Huygens can be distributed over many CPU and GPU processor cores, having more cores in both the CPU and GPU is helpful. For advise on GPU cards, we can refer to our specific websites on GPU cards and GPU acceleration. You can also look into the option of having multiple GPU cards in your hardware as we are supporting this now.

As for the hardware brand, any of the well known suppliers like HP/Compaq, IBM, Supermicro, Dell, will suffice.

The performance is largely determined by the processor, the memory bandwidth and latency, and the operating system. Currently, Linux offers the best performance. Recommendations for single socket computers: fastest Intel i7 available. For two or more socket systems we recommend an Intel CPU. Model numbers and prices change rapidly in that field, please take up contact with us for up to date advice.

See our benchmark results for CPU based systems and benchmark results of GPU cards.

First, it is a good idea to check how much swap space is already available with the command:The -m switch tells free to report the space in megabytes. To increase the amount of swap space you can either allocate 1) a dedicated swap partition on disk, or 2) a swap file. Both procedures must be executed from the root account.

1) Dedicated swap partition

For this you need a dedicated free partition. This partition can be at most 2 GB in size. Suppose this partition is /dev/hdg7 then initialize the swapspace with:

Edit the file /etc/fstab and add a new entry for this swap partition:

/dev/hdg7 swap swap defaults 0 0

Enable the new swap partition with:

2) Adding a new swap file This procedure is more complex, but the advantage is that you don't need to repartition or add disks for it. First locate which of your currently mounted partitions has enough free disk space available by using the df command. Suppose you find that the filesystem which is mounted as the /mydata directory has sufficient free disk space available to hold a 2 GB swap file. Use the following commands to create it:

on one line:

The dd command may take some time to complete. After the mkswap command has completed edit the file /etc/fstab and a new single line entry for the swap file: Lastly enable the new swap file with the swapon command:

In a default Linux installation the maximum size of sections of shared memory is too small to be of use for deconvolution. To view the current maximum size of shared memory segments run: To increase this value add the following line to /etc/sysctl.conf: and then to activate this new value run this command: To have this command run during system startup on SuSE add it to the file /etc/init.d/boot.local. RedHat systems should already look at /etc/sysctl.conf at startup. If it exists sysctl is automatically run.

First of all you need sufficient RAM and swap space. To add swap space see:

• How to add swap space on Linux?

See also:

• How do I enable the use of shared memory on Linux?

Open a unix shell (terminal), become root, and issue the following commands:

While installing a new version of Huygens Essential on my Windows machine, I got the message "Error opening file for writing: c:\Program Files\Svi\bin\essential.exe". What is wrong?
Huygens essential is already running either by your self or by someone else who was running essential before you logged him or her off in order to install the new version in your own environment.