Would you like to help us benchmark servers?
We are gathering data on the performance of DISCOVAR on different servers and under different configurations, and we are looking to you to help. We would like to generate a table comparing performance statistics, based on a benchmarking test we have designed. This will help us, and hopefully you too, when deciding on future hardware purchases or determining if existing servers are running efficiently.
If you would like to participate, please follow the instructions given below. In the meantime, here is the table so far.
|5.8 (0.12)||SGI UV2||64 (4x8x2) Intel Xeon E5-4640 2.7 GHz||CentOS 6.4|
|6.4 (0.04)||Dell R820||32 (4×8) Intel Xeon E5 4650 2.7 GHz||CentOS 6.3|
|6.5 (0.04)||Supermicro X9DRW||32 (2x8x2) Intel Xeon E5-2687W 3.1 GHz||CentOS 6.3|
|8.2 (0.04)||BioTeam Slipstream Appliance||32 (2x8x2) Intel Xeon E5 2660 2.2 GHz||CentOS 6.4|
|8.3 (0.06)||Dell C6145||64 (4×16) AMD Opteron 6276 2.3 GHz||CentOS 6.4|
|8.3 (1.27)||Dell R920||96 (4x12x2) Intel Xeon E7-4850 2.3 GHz||CentOS 6.6|
|8.4 (0.06)||Unknown Dell||16 (2×8) AMD Opteron 6276 2.3 GHz||Scientific Linux 6.4|
|8.6 (0.42)||Dell 820||64 (4x8x2) Intel Xeon E5-4620 2.2 GHz||CentOS 6.4|
|8.7 (0.26)||IBM X3550 M4||32 (2x8x2) Intel Xeon E5-2665 2.4 GHz||CentOS 6.3|
|9.2 (0.06)||Dell C8220||16 (1x8x2) Intel Xeon E5-2680 2.7 GHz||CentOS 6.5|
|9.7 (0.09)||Supermicro||64 (4×16) AMD Opteron 6274 2.2 GHz||CentOS 5.9|
|9.7 (0.10)||Dell R815||48 (4×12) AMD Opteron 6174 2.2 GHz||CentOS 5.5|
|10.2 (0.02)||Supermicro H8QG6||48 (4×12) AMD Opteron 6168 1.9 GHz||CentOS 6.3|
|10.2 (0.10)||HP BL406 G6||24 (2x6x2) Intel Xeon 5670 2.9 GHz||CentOS 5.8|
|10.4 (0.04)||Dell R510||24 (2x6x2) Intel Xeon 5660 2.8GHz||CentOS 6.3|
|10.4 (0.07)||Thinkmate||32 (4×8) AMD Opteron 6132HE 2.2 GHz||CentOS 5.9|
|12.6 (0.04)||Fujitsu RX600 S4||24 (6×4) Intel Xeon X7460 2.66 GHz||RedHat 5.9|
|12.7 (1.6)||Dell R910||80 (4x10x2) Intel Xeon E7 4850 2.0 GHz||CentOS 5.8|
|12.9 (0.11)||Thinkmate||48 (4×12) AMD Opteron 6174 2.2 GHz||CentOS 5.9|
|13.0 (0.07)||Dell M610||12 (1x6x2) Intel Xeon 5680 3.3 GHz||CentOS 5.10|
|28.3 (4.2)||Dell R910||80 (4x10x2) Intel Xeon E7 4850 2.0 GHz||Ubuntu|
|113.3 (0.7)||Unknown desktop||2 (2×1) AMD Athlon 64 X2 1.0 GHz||Fedora 20|
* mean (standard deviation) in minutes
† total cores (processors x physical cores x logical cores) chipset clockspeed
We will update this table when we obtain new information. Note that we cannot include prices as they are generally confidential.
Running the benchmark test
Download the benchmarking test and run it on your hardware. For your convenience we have provided statically compiled binaries, but also the source code if you wish to build it yourself.
The benchmark test needs to be done on a server that has essentially no other user processes running during the duration of the test. The runtime will depend on your hardware, but we estimate it should take around 2 hours. The heart of the test is a short DISCOVAR example, which is run 10 times in order to compute a mean and standard deviation. The test does not require large amounts of memory or produce a heavy IO burden.
Send us the result by posting the LOGFILE.txt file produced by the test to this thread on the forum. Please also include a description of your hardware.
What information is collected?
Note that no information about users or jobs running on the system is collected, and nothing is transmitted back to us – other than the contents of the LOGFILE.txt file that you send us. This file contains the runtime benchmarking information, plus the following:
/proc/cpuinfo – information about the microprocessors in the system
/proc/loadavg – information about the load average
/proc/version – kernel version number, build name, etc.
Difficulties running the Benchmark?
We recommend you try running the binary test first – it is statically linked with all the required dependencies, and also includes SAMtools. If you encounter problems please let us know via the user forum. In addition to the binaries you can also download the DISCOVAR source code for the benchmark test release.