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Which platform is the fastest with Huygens?

Comparison of deconvolution speed with Huygens on various platforms (Linux, Mac and Windows).

Clearly, the type of processor and its clock speed are very important for system performance. Still, next to the processor and the number of cores, there are many factors affecting system performance: type of memory, chip set which interfaces cpu to memory, speed of cpu interconnect, cache size, number of caches, and also software issues like the Operating System (OS) the system is running on.

Windows vs Linux vs Mac OSX

In recent cases where Windows and Ubuntu were tested on the same hardware Ubuntu Linux outperformed Windows 7 by about 30%, in one case even close to 40%.
We know of just one test in which Windows was run on Apple hardware. In that test Windows outperformed Mac OSX by 5%.

64 bit vs 32 bit

64 bit applications require 2 times more storage for address and size information, which might cause a slow down due to increased memory traffic. For example, on Irix 32 bit applications tend to be 5-10% faster than 64 bit applications.
Still, for many of today's microscopic datasets, the memory limitations imposed by 32bit processing are far too restrictive to consider using it for a small performance gain. For this reason in the tables below you'll find mostly tests of 64 bit binaries, the exception being MacOSX older than 10.6 which has limitations in running 64 bit applications.

Weighted score

The weighted score is a measure of the performance of a machine, relative to a dual AMD Opteron 2.2 GHz computer (which has a weighted score of 1). We achieved the following Huygens Benchmark figures for the speed of deconvolution:

Platform Processor RAM Weighted score Remarks
Apple G5 MacOSX 10.4.2 dual 2 GHz PowerPC cpus 4GB, 512 k L2 0.70
Windows Vista 64 bit 2 x 1.8 GHz Intel Core 4 GB 0.95
Linux-64 laptop Intel Centrino Duo 1.8 GHz 2 GB 0.95
REFERENCE: Linux-64 dual AMD Opteron 2.2 GHz 4 GB 1.00 2003
Apple Quad G5 2.5 GHz PowerPC L2 1MB 2 GB 1.04
Linux-64 CentOS 6.6 Dell T5600, two-socket 8 core Xeon E5-2680 @ 2.70GHz 32 GB 10.16 June 2015 (Huygens 15.05) Synchrotron SOLEIL
Linux-64 2.6 kernel dual core 2.66 GHz Xeon 4 GB 1.32
Apple imac X11 Intel Core2 Duo 2.66 GHz 4 GB 1.38 Oct 2008 J.P. Poindessault, IPBC, U. Poitiers
Win 7 Enterprise, 64-bit Intel Core2 Duo E8400 3 GHz 8 GB 1.51 April 2012 P. Thomas, Henry Wellcome Lab. for Cell Imaging at UEA, UK (Huygens 4.1.1p2)
Apple Mac Pro 2 x dual-core 2 GHz Intel Xeon with MacOSX 10.5 3 GB 1.56
Linux-64 SGI 8 x Itanium2 1.6 Ghz but using 6 processors 2.08
Apple Mac Pro 2 x dual-core 3 GHz Intel Xeon with MacOSX 10.5 4 GB 2.27
Linux-64 2.6 kernel Verari 8-cpu Opteron 850 2.4 GHz 3.11
Linux-64 2.6 kernel dual quad core 2.33GHz Xeon 16 GB 3.35
Apple Mac Pro Intel dual quad-core 2.8 GHz Xeon 14 GB 3.58 nov2008 J.P. Poindessault, IPBC, U. Poitiers
Linux-64 Intel Xeon(R) CPU dual quad core E5440 @ 2.83GHz 16 GB 3.55 Feb2011 (Huygens 3.7.0p3), J. Radinger, University of Innsbruck
Win 7 Enterprise, 64-bit Xeon E5-2609 Quad-Core CPU @ 2.4 GHz 64 GB 3.81 July 2012 (Huygens 4.2.1p4 64), P. Thomas, Henry Wellcome Lab. for Cell Imaging at UEA, UK
Linux-64 Intel Xeon(R) CPU dual quad core E5440 @ 2.83GHz 16 GB 4.05 April2011 (Huygens 3.7.1p4 64), J. Radinger, University of Innsbruck
Linux-64 Two-socket hex core Xeon Linux, Supermicro X8DTL server with 2x Xeon E5645, 2.4-2.67 GHz, 12MB cache. 96 GB 7.82 Jan2012 (Huygens 4.2.0p2 -64)
Mac OS-X 10.6.8 Snow Leopard Mac Pro 2 x3 GHz Quad Core (8 cores total) Intel Xeon (800 MHz DDR2 FB-DIMM) 24 GB 3.88 E. Hartveit, University of Bergen, Feb2012 (HuPro X11, v4.1.1p0 64-bit)
Windows 7 Professional 64-bit Mac Pro 2 x3 GHz Quad Core (8 cores total) Intel Xeon (800 MHz DDR2 FB-DIMM) 24 GB 4.09 E. Hartveit, University of Bergen, Feb2012 (4.1.1p0 64-bit). A remarkable result. Note SVI: Huygens is faster on Apple hardware if it runs Windows instead of OSX.
Windows 7 64bit Win7 Enterprise Intel Z77 quad core i7-3770K Processor (8M Cache, 3.90 GHz) 32 GB 6.40 J.A. Kochan, Jagiellonian University in Krakow, March2014 (Huygens 4.5.1p0)
Linux-64 Ubuntu 11.10 Supermicro 5046A-X desktop with one 6-core Intel i7 990 @ 3.46GHz 8 GB 6.36 SVI, Jan 2012, HuScript 4.1.1p0.
Linux-64 Ubuntu 12.04 Supermicro 5046A-X desktop with one 6-core Intel i7 990 @ 3.46GHz 8 GB 8.68 SVI, June 2012, HuScript 4.2.1p3.
Linux-64 Ubuntu 11.10 Acer laptop dual core Intel i5 2450M CPU @ 2.50GHz 8 GB 3.58 SVI, Mar 2012, HuPro 4.2.0p8. This laptop is 25% faster with Linux than with Windows.
Windows 7 64-bit Acer laptop dual core Intel i5 2450M CPU @ 2.50GHz 8 GB 2.80 SVI, Mar 2012, HuPro 4.2.0p8
Linux-64 Ubuntu 11.10 Supermicro X8DA dual socket, quad core Intel 5620 CPU @ 2.40GHz 96 GB 5.85 SVI, Apr 2012, HuPro 4.1.1p2. This workstation is nearly 40% faster with Linux than with Windows.
Windows server 2008R2 Supermicro X8DA dual socket, quad core Intel 5620 CPU @ 2.40GHz 96 GB 4.21 SVI, Apr 2012, HuPro 4.1.1p2.
Linux-64 Ubuntu 12.04 single socket desktop, quad core Intel i5 3550, 3.3 GHz 8 GB 7.35 SVI, June 2012, HuPro 4.2.1p3
Windows 7 single socket, quad core Intel i7 3610QM, 2,30 / 3,30 Turbo GHz 8GB 5.89 SVI, Aug 2012, HuScript 4.2.1p7, Toshiba Satellite laptop
Linux-64, Ubuntu 12.04 single socket, quad core Intel i7 3610QM, 2,30 / 3,30 Turbo GHz 8GB 7.56 SVI, Aug 2012, HuScript 4.2.1p7, Toshiba Satellite laptop. Notice that this workstation is nearly 30% faster with Linux than with Windows.
Linux-64, Ubuntu 12.04 single socket, 8 core AMD FX-8120 3.10 GHz 8GB 4.39 SVI, Sep 2013, HuScript 4.3.1p0.
Linux-64 Two-socket hex core Xeon Linux, Supermicro X8DTL server with 2x Xeon E5645, 2.4-2.67 GHz, 12MB cache. 96 GB 9.03 Aug2012 (Huygens 4.2.1p7 -64)
Windows Server 2008R2 Enterprise Supermicro Superserver 6016TT-TF with 2x E5520 CPU @ 2.27GHz 48GB 5.10 V. Bindokas, University of Chicago, Aug 2013, HuPro 4.3
Windows Server 2008R2 Enterprise Single quad core E5440 CPU @ 2.83 GHz 48GB 2.66 V. Bindokas, University of Chicago, Aug 2013, HuPro 4.3
Linux-64 CentOs 6.4 Two-socket deca core E5-2680v2 @ 2.80GHz 128GB 16.21 SVI, October 2013, HuScript 4.4.0p9
Linux-64 Red Hat Two-socket 8 core Xeon E5-2670 @ 2.6 Ghz 256GB 13.11 Wolfson Imaging Centre, Weatherall Institute of Molecular Medicine, University of Oxford, HuPro 4.4.0p9
Windows 7, 64-bit Dell T7600, Two-socket 8 core Xeon E5-2680 @ 2.70 Ghz 32GB 9.49 Manchester Collaborative Centre for Inflammation Research, HuPro 4.4.0p8
Linux-64 Ubuntu 13.10 Dell T7600, Two-socket 8 core Xeon E5-2680 @ 2.70 Ghz 32GB 10.39 Manchester Collaborative Centre for Inflammation Research, HuPro 4.4.0p8
Linux-64 Ubuntu 12.04 Dell T5610, Two-socket Intel Xeon E5-2620 (2x6 cores @ 2.1 GHz) 32GB 9.92 Utrecht University, HuScript 4.5.0p9
Linux-64 Ubuntu 13.10 Single socket, dual core Celeron 2955U @ 1.4GHz 2GB 1.82 SVI, December 2013, HuPro 4.5.0p5. Acer C720 Chromebook(!), in developer mode.
Windows Server 2012 R2 standard Intel Xeon CPU E5-1650 v2 @3.50GHz 128GB 8.61 SVI, January 28 2015, ACQUIFER AG Huygens Professional 14.10.1p8. HIVE-11
Linux-64 Scientific7.1 (Nitrogen) One socket 8-core E5-2667v3 @3.20GHz x 16 128GB (1866MHz) 15.27 LIMES Institute University of Bonn (Huygens 14.10.1p4, March2015)
Linux Ubuntu 12.04 Intel 4-core i5-3330 CPU @ 3.00GHz × 4 4 GB 4.84 SVI, April 2015, Huygens Professional 14.10.3p1
Linux Ubuntu 15.04 Intel Core i5-4690T CPU @ 2.50GHz × 4 8 GB 4.18 SVI, May 2015, Huygens Professional 15.05.0p2
Linux CentOS 6.5 2 x Intel Xeon E5-2680v3 @ 2.5GHz 192 GB 20.52 N. Ehrenfeuchter, Biozentrum, University of Basel, November 2015, Huygens Core 15.10.0p6

These figures might work out differently for different image sizes, or different thread counts.

Contact Information

Scientific Volume Imaging B.V.

Laapersveld 63
1213 VB Hilversum
The Netherlands


Phone: +31 (0)35 64216 26
Fax: +31 (0)35 683 7971
E-mail: info at svi.nl

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