The Processors command tells YASARA how many processors to use in those parts of the program that support parallel execution. Currently these are:

• Molecular simulations with all force fields except NOVA.
• Molecular graphics and shadows.
• Calculation of numeric molecular surfaces and volumes.

Optimal performance is achieved if the Processors setting matches the number of logical processors in your computer (e.g. for a Pentium D Extreme Edition, with two CPU cores and hyperthreading enabled, you would set Processors to 4).

Here are a few additional hints:

• YASARA does not complain if you set Processors too high (e.g. 6 on a simple 1 CPU machine), but performance will be lower due to the task-switching overhead. Since a simulation is influenced by the number of processors used, this feature allows you to reproduce a simulation run on multiple CPUs also on a single CPU (assuming it's a similar CPU and operating system).

• If you want to run two instances of YASARA in parallel on the same machine, select only half of the available processors for optimal performance.

• When longrange interactions are activated, YASARA currently reaches a performance limit at 3 to 4 CPUs. Providing 5 or more CPUs will thus not speed up simulations any further.

• The parallel MD performance is reduced on old Linux kernels like 2.4.X and before, since these contain an unsolvable problem in the process scheduler. Use kernel 2.6.X or higher.

• If you choose two or more processors, YASARA needs to do its own scheduling for optimal performance and cache usage. As a consequence, the main YASARA process is bound to a certain CPU.

• When running a simulation on more than one processor, the Linux 'top' command usually shows a CPU usage close to 100*N%. In some Linux distributions, there seems to be a bug in 'top' that makes it always show less than 100%. Neverthess, YASARA correctly uses the selected number of CPUs.

Processors 1

Use only one processor.

Processors 4

Use four processors in parallel.

Processors all

Use all available processors.

used,available = Processors

Assign the numbers of used and available processors to variables 'used' and 'available'.