Browser slow
This page exists to aid IT professionals who may be attempting to investigate an instance of a slow connection to the UCSC Genome Browser (genome.ucsc.edu). The UCSC Genome Browser also has mirrors in Asia (genome-asia.ucsc.edu) and Europe (genome-euro.ucsc.edu) that can be used for comparison performance behavior.
Background of how the Browser accesses data
There are various factors that could make the browser appear to have slow behavior. Below is a listing of how the Browser transmits data, followed by suggested ways to test and troubleshoot performance with various verifying steps.
The function of the browser consists of the following activities:
- your desktop web browser requests the URL e.g.: https://genome.ucsc.edu/cgi-bin/hgTracks?measureTiming=1
- the UCSC Apache WEB server receives the request
- Apache runs the program hgTracks on the UCSC system
- the output of that program is returned via the Apache connection as HTML text to your desktop web browser
- as your desktop web browser receives that HTML text it interprets it to begin displaying the content
- there are a number of URL links in that HTML text (on the order of about 65 links)
- most of those links are static content that your web browser already has in its cache
- there are approximately 5 links that are dynamic content, your web browser requests those files from UCSC
- after all the files are received by your web browser the page display is complete in your web browser
When you use the measureTiming=1 argument in the URL request to UCSC, the hgTracks process will report millisecond timing for the various operations that take place at UCSC. The final measurement reported: Overall total time is the total time spent in processing at UCSC. All operations are complete at UCSC in that time. Any additional time observed beyond that time is due to network transfer timing for the HTML content and additional files specified in the HTML code. The total amount of data transferred is typically less than 2Mb of data, and most of that is static content that does not transfer when it is already in your web browser cache. Typical dynamic content that does transfer is on the order of 300Kb for the HTML text and 300Kb for the graphic images. This depends upon what tracks are set to display in the browser view.
Check network connection
Verify browser address can be found, unix command: host genome.ucsc.edu
$ host genome.ucsc.edu genome.ucsc.edu is an alias for genome.soe.ucsc.edu. genome.soe.ucsc.edu has address 128.114.119.131 genome.soe.ucsc.edu has address 128.114.119.132
Verify network path is available to the browser: ping -c 3 genome.ucsc.edu
$ ping -c 3 genome.ucsc.edu PING genome.soe.ucsc.edu (128.114.119.131) 56(84) bytes of data. 64 bytes from hgw1.soe.ucsc.edu (128.114.119.131): icmp_seq=1 ttl=43 time=170 ms 64 bytes from hgw1.soe.ucsc.edu (128.114.119.131): icmp_seq=2 ttl=43 time=170 ms 64 bytes from hgw1.soe.ucsc.edu (128.114.119.131): icmp_seq=3 ttl=43 time=170 ms --- genome.soe.ucsc.edu ping statistics --- 3 packets transmitted, 3 received, 0% packet loss, time 2000ms rtt min/avg/max/mdev = 170.361/170.370/170.378/0.007 ms
verify browser alive and well
time wget --user-agent=browserAliveTest -O- https://genome.ucsc.edu/cgi-bin/hgTracks?measureTiming=1 2>&1 | grep Overall <span class='timing'>Overall total time: 526 millis<br /></span> real 0m1.245s user 0m0.021s sys 0m0.019s
Note the Overall total time: 526 millis is the total run time of the hgTracks CGI binary
The real 0m1.2345s is the total run time of the wget command including the transmission of the html text from the hgTracks operation. This test can also be used on the http connection to see if it is any different:
time wget --user-agent=browserAliveTest -O- http://genome.ucsc.edu/cgi-bin/hgTracks?measureTiming=1 2>&1 | grep Overall <span class='timing'>Overall total time: 439 millis<br /></span> real 0m0.959s user 0m0.003s sys 0m0.012s
verify browser performance similar to web browser access
The simple wget test above only transmits the single top-level content of the html page returned from hgTracks. Your web browser will use references within that page to request more files from the browser. To simulate a complete, no cache involved, transfer of all files in the browser page, go to a work directory where the wget command can create a hierarchy of files. For example:
$ cd /dev/shm $ time wget --user-agent=browserFullPageTest \ -o browser.wget.log \ --wait=0 \ --execute="robots=off" \ --no-cookies \ --timestamping \ --level=1 \ --convert-links \ --no-parent \ --page-requisites \ --adjust-extension \ --max-redirect=0 \ "https://genome.ucsc.edu/cgi-bin/hgTracks?measureTiming=1" real 0m9.962s user 0m0.074s sys 0m0.040s $ grep Overall genome.ucsc.edu/cgi-bin/*.html <span class='timing'>Overall total time: 463 millis<br /></span>
Again, the Overall total time: 463 millis is the total run time of the hgTracks CGI binary, and the real 0m9.962s is the total time for the wget command to transfer everything. You will find a hierarchy of files in a newly created directory ./genome.ucsc.edu.
If this command is repeated, with the previous result available in ./genome.ucsc.edu, this will simulate (not perfectly) a web browser operation where the static content remains in cache and doesn't need to be transferred again. This isn't a perfect web browser simulation because this command does a HEAD operation on each access that it wants to determine if it can be cached. A web browser has other means of caching to avoid constant HEAD operation. It will occasionally, but not often.
The browser.wget.log file can provide clues of timing for each request to see what may be taking a long time.
