GB Performance

[Grivainis, Mark]

Hello,

 

I am trying to improve the performance of our Genome Browser Mirror.

 

When I enable the timing information, the “Time after visibilities” takes a significant amount of time.

Do you have any suggestions on how I could go about debugging why this is the case?

 

Here is the load time output:

 

Startup (bottleneck delay 0 ms, not applied if under 10000) : 6 millis
Get cart of 34 for user:4657_BjqOOrqACLEs4zAzFHnDzMARjZJz session:(null): 0 millis
before chromAliasSetup: 0 millis
after chromAliasSetup: 0 millis
Time before getTrackList: 17 millis
Time after trackDbLoad : 0 millis
Time after visibilities: 10165 millis
parentChildCartCleanup: 283 millis
Waiting for parallel (2 threads for 2 tracks) remote data fetch: 51 millis
Time at start of obtaining trash hgt png image file: 4842 millis
Time completed writing trash hgt png image file: 28 millis
Done with trackForm: 1 millis
Time at end of doMiddle, next up cart write: 1 millis
Time to write and close cart: 0 millis
Overall total time: 15394 millis

 

Many thanks,

Mark Grivainis

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[Maximilian Haeussler]

Hi Mark,

can you tell us a little more how your browser was setup? Did you use the browserSetup.sh script? And are you loading the data from UCSC remotely or have you mirrored your database (I think the latter, given your description).

Are you using a local mariadb database server for the hgcentral database, like the system that browserSetup.sh creates?

best
Max 

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[Grivainis, Mark]

Hi Max,

 

Thank you for getting back to me.

 

browserSetup.sh was used to set up the server.

We have mirrored the database, and MariaDB is running locally on the server.

 

Regards,

Mark

 

 

From: Maximilian Haeussler <mhae...@ucsc.edu>
Date: Tuesday, June 17, 2025 at 17:52
To: Grivainis, Mark <Mark.Gr...@nyulangone.org>
Cc: genome...@soe.ucsc.edu <genome...@soe.ucsc.edu>
Subject: Re: [genome-mirror] GB Performance

[EXTERNAL]

[Maximilian Haeussler]

And there are no "slow-db" statements in your hg.conf file anymore (= they're all commented out) ? 

[Grivainis, Mark]

All three slow-db lines are commented out.

[Maximilian Haeussler]

Great. And also this statement is commented out:

gbdbLoc2=http://hgdownload.soe.ucsc.edu/gbdb/

And you're looking at the default location, single locus, with default tracks? Can we access this server from outside?

[Grivainis, Mark]

Yes, that’s also commented out.

 

Unfortunately, you must be connected to a VPN to access the server.

 

I reset my user settings and loaded hg38.

After doing this, the page sometimes loads quickly, but other times it’s very slow.

 

Time after visibilities is now quick, but the trackDbLoad is slow

This is the timing info when the page loads slowly.

 

Startup (bottleneck delay 0 ms, not applied if under 10000) : 11 millis
Get cart of 24 for user:4657_BjqOOrqACLEs4zAzFHnDzMARjZJz session:3194_WtarNuaVWkIaVncNw8j4AqaZ4jEp: 0 millis
before chromAliasSetup: 0 millis
after chromAliasSetup: 12 millis
Time before getTrackList: 1 millis
Time after trackDbLoad : 11474 millis
Time after visibilities: 7 millis
parentChildCartCleanup: 7 millis
Time at start of obtaining trash hgt png image file: 59 millis
Time completed writing trash hgt png image file: 63 millis
Done with trackForm: 2 millis

Time at end of doMiddle, next up cart write: 1 millis
Time to write and close cart: 0 millis

Overall total time: 11637 millis

[Maximilian Haeussler]

Can you try adding this line to your hg.conf:

cacheTrackDbDir=/dev/shm/trackDbCache

If this helps, then we must make this the default value. 

If not, it's possible that we'll have you run gdb a few times.

[Grivainis, Mark]

Thank you, Max.

 

After that change, I no longer have the occasional long load time.