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Article ID: 1460 - Last Modified: June 13, 2014

What kind of computer system do I need to run Schrödinger software?

The minimum hardware requirements are listed in the Installation Guide, but this is not necessarily the optimum hardware configuration, particularly if you are planning to run large modeling jobs. The list below gives some guidelines and recommendations for the choice of hardware.

  • A multi-core CPU. Most jobs (Glide, LigPrep, Phase, for example) can be distributed over multiple processors, so the use of a multi-core CPU or a cluster of CPUs is recommended to increase throughput. Desmond and Jaguar use MPI parallel processing. An 8-core CPU is a good choice for Desmond jobs on a single CPU and is large enough for parallel Jaguar (and QSite) jobs. Note that the number of processors you can actually use is limited by the number of licenses (tokens) that you purchase for the software.
  • A faster CPU will give more throughput.
  • More memory. 4GB per core with 2 cores is the minimum recommended configuration.
  • Larger CPU cache is recommended, especially for jobs that process large amounts of data, such as Jaguar and QSite. Increasing the L2 or L3 cache size for these jobs is more important than a small increase in CPU speed.
  • Faster local disk access is important for jobs that read a lot of data. For example, using SSD, a disk with a higher speed (e.g. 10000 rpm), or a disk array that uses multiple controllers and striping can be beneficial. Distributed Phase database searches are particularly limited by contention for disk access. Jaguar and QSite jobs also perform a lot of IO, so faster disk access is important. Local disks are preferred over networked disks for temporary storage (or for data that is used often) because networked disks are affected by network access, bandwidth, and network traffic.
  • Adequate cooling and power supply. Laptops or notebooks are not usually a good choice for large jobs because the cooling and power supply can be inadequate. If you run jobs for a long time, you should consider a power supply with backup, in case of outages.

The following recommendations might also apply, depending on how you are planning to run jobs.

  • Desmond can use CUDA-based GPGPU computing on Tesla graphics cards from NVIDIA, under Linux.
  • For Maestro, a dedicated graphics card that supports hardware Open GL, with 1GB on-board memory is recommended. Our testing shows that NVIDIA Quadro and GeForce cards and higher-end ATI Radeon HD cards are capable of displaying Maestro, with the appropriate proprietary drivers. The more recent integrated Intel HD Graphics cards are also capable of displaying Maestro. Consumer-grade laptops often do not have adequate graphics cards or dedicated graphics memory.
  • If you want to run Maestro using hardware stereo, a stereo-capable graphics card (quad-buffered stereo) and monitor is required.

If you want to use a laptop, you should ensure that you buy a commercial-grade laptop that meets the requirements above. Consumer-grade laptops often do not have enough memory or adequate graphics cards.

Once you have the hardware, you should install one of the supported operating systems, which are listed in the Installation Guide and on the Download Center. You might also have to install additional libraries, which are listed in the Installation Guide. You should also ensure that the proprietary graphics driver is installed, in a recent version.

Keywords: configuration, system, OS

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