cytoscape is extremely slow
Tim S
It takes literally 4-5 minutes to even boot up cytoscape 3.4 from a normal HDD. I'm running on 8gb of RAM which is all assigned to cytoscape and a i5 4950. Previous versions used to load faster. Waiting for 5 minutes everytime you startup cytoscape it just too long!
Any suggestions on how to make cytoscape load faster?
Tim
Scooter Morris
This is very unusual. Can you try disabling any Apps you have installed to see if that is part of the problem? Also, are you in a Windows environment with a remote user home? Cytoscape writes a lot of data into the CytoscapeConfiguration directory in the user home.
-- scooter
Tim S
Thanks for your response. We have the same problem on all deskptop pc's. It is not related to installed apps. We are running windows 7 enterprise 64x, but everything is locally stored on the harddrive without any remote connections needed. We have the same issue on 4 different kind of windows pc's, varying from i5 6500 pc's with 8gb of ram (all assigned to cytoscape) to Xeon with 64gb RAM and they are all equally slow. Any possible suggestions as to what could cause this. As far as we can recall older versions were not as slow with loading as this version. It takes a very long time loading the "OSGi container" (4 minutes 12 seconds) and loading the rest is 10 seconds and then the org.cytoscape.equations-functions-impl started is an additional 2 minutes. In total it took over 7 minutes to start cytoscape. I really hope this will be better in version 3.5 ( 3.6?)
Tim
edit: with version 3.5.0 RC1 the time is reduced to roughly 4 minutes after having first deleted the cytoscape configurations folder.
Barry Demchak
Hi, Tim and Scooter …
I’m clocking a Cytoscape startup on a Windows 10 VM on Windows 10 host running off SSD and in 6GB RAM and Ivy Bridge (5 year old) processor. I get 45 seconds (timed from launch to Welcome window) with a few apps loaded, independent of whether there’s a fresh reboot. Without the apps, I see 23 seconds, which is well within expectations. This is consistent with our Windows 7 VM experience, too … and on Macs.
When running the same VM off a hard disk, I get 52 seconds for the first startup and 22 seconds for a second startup.
This is with v3.5, but I see no reason for a difference between 3.4 and 3.5. You’re welcome to try 3.5 for yourself … it’s at http://bit.ly/2fPG4R8
I’m puzzled at your timings, too.
Reading your post carefully, it looks like all of your configurations are hard disk based. Are any SSDs, and if so, do they time out the same way??
I wonder if there is any network issue that’s causing timeouts to occur during startup. One network access I’m aware of is connected with the News Feed on the Welcome screen. It fetches http://chianti.ucsd.edu/cytoscape-news/news.html, but does so only in the last 25% of the startup. Does this slowness occur if you completely disable your network?? (… just a test)
Are you using an unusual Java?? … as an experiment, would you mind starting Cytoscape from the Cytoscape.bat file … and beforehand, set the PATH= to *only* C:\Windows\System32?? I’m wondering if there’s something time consuming on your path.
Also, on one of the poorly performing systems, would you mind installing the cy3 Performance Reporter app in Cytoscape?? http://apps.cytoscape.org/apps/cy3performancereporter ... Then shut down Cytoscape, start Cytoscape, and use the Apps | Generate Performance Report menu to bring up the statistics window. The Submit button doesn’t work … if you could put the window contents in the clipboard and paste them in an e-mail to me (idekerlab...@gmail.com), I’d appreciate seeing the numbers.
Thanks for trying so hard to get Cytoscape performance up … we’re as surprised as you, and we’d like to get to the bottom of this.
Thanks!
From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Tim S
Sent: Wednesday, December 07, 2016 6:47 AM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] Re: cytoscape is extremely slow
Hi Scooter,
Thanks for your response. We have the same problem on all deskptop pc's. It is not related to installed apps. We are running windows 7 enterprise 64x, but everything is locally stored on the harddrive without any remote connections needed. We have the same issue on 4 different kind of windows pc's, varying from i5 6500 pc's with 8gb of ram (all assigned to cytoscape) to Xeon with 64gb RAM and they are all equally slow. Any possible suggestions as to what could cause this. As far as we can recall older versions were not as slow with loading as this version. It takes a very long time loading the "OSGi container" (4 minutes 12 seconds) and loading the rest is 10 seconds and then the org.cytoscape.equations-functions-impl started is an additional 2 minutes. In total it took over 7 minutes to start cytoscape. I really hope this will be better in version 3.5 ( 3.6?)
Tim
Op donderdag 1 december 2016 17:16:23 UTC+1 schreef Scooter Morris:
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Tim S
Thanks for your response! Funny thing, yesterday we got 2 new pc's in our office. This carry the same harddrive and specs but have a different (unmonitored and non-ICT controlled) windows 7 system (still windows 7 enterprise). Cytoscape 3.5 starts within 10 seconds!!! on this desktop. So it has to be somehow in the windows 7 version or some regulation that is going on. Regarding my system and the others currently in the office, one has an SSD and the other carry the same SSHD drives as are in the new pc and they are all 5-10 min startup times, this would mean that it has something to do with the windows 7 version.
Removing the network (cable) is not increasing startup times at all it makes no difference. Same thing for moving the whole cytoscape directory to the C:/Windows/system32 drive and running the BAT file, no improvement in the timings. The JAVA version is 1.8.0_11. The diagnostic report is in the attachment!
Thanks again for the help!
Tim
Barry Demchak
Hi, Tim –
Great job making this progress … it sounds like ICT has set a group policy that may be causing this. It would be good to address this with them … it’s quite possible that a rational policy setting is having unintended consequences. I remain interested in what turns up.
To compare your numbers to mine, here’s what I see
Total Launch Duration: yours=153186, mine=14189
Framework Launch Duration: yours=127654, mine=8658
For individual bundle startups (i.e., the last number for each bundle), your numbers are about half mine. This speaks to the much better performance of your CPU … meaning that I really should get a new machine. J
So, whatever is happening, it’s happening very early in the Cytoscape startup … there must be a clue in there … good to take to the ICT people for the group policy sleuthing.
(If the difference is in policies, it could be that enterprise policy is to involve central file servers *much* more than on unmanaged machines. You can see how much code/data Cytoscape is carrying by looking at your CytoscapeConfiguration directory. Not small. If there is major transfer of that directory during startup, we could see times as long as yours if your network is busy, slow or unoptimized. This is a shot in the dark, but we’ve seen odd enterprise / central server configurations in the past.)
Best of luck … please keep us in the loop.
--
Scooter Morris
Do your ICT controlled systems have a anti-virus program running? If so, you may want to try to set CytoscapeConfiguration as exempt from scanning. When Cytoscape starts up, a lot of files are written into that directory, and if the anti-virus program scans each one, it might significantly impact startup.
-- scooter
Tim S
Thanks for your response, I have contacted our ICT department and hope they will look into this! We have had some recent upgrades of HP 800 G2 models which are starting cytoscape in under 10 seconds! Great improvement, sadly I have a a lot of programs installed on my current machine so I cannot really swap them .
@scooter, indeed McAfee is installed, I however, cannot make any changes in settings or policy of the virusscanner, it is externally controlled.
Tim