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Web server mode and MySQL PGDBs

asked 2020-07-17 06:57:29 -0500

mdubois gravatar image

updated 2020-07-17 06:58:32 -0500

Dear forum,

We would like some advice on the use of pathway-tools in web server mode.

First, we are currently using PGDBs stored on the filesystem and we have noticed that it uses a lot of memory (several dozen gigabytes for a few hundreds genomes). We were wondering if storing the PGDBs in a MySQL database could help reduce this.

Also, as advised in the doc, the PGDBs used by the web server are copies of the editable PGDBs. When using MySQL PGDBs, is it possible to modify the PGDBs from another computer without restarting the web server ?

Thanks in advance, Mathieu Dubois

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answered 2020-07-18 12:55:09 -0500

Suzanne Paley gravatar image

Hi Mathieu,

I do not think that using a MySQL database instead of files would decrease the memory requirements -- the pgdbs would still all end up being loaded into memory. Instead, I would recommend using the -auto-close command line argument that sets a maximum number of pgdbs that can be open at a time by closing the least-recently accessed ones. A reasonable number to set it to is 100, so you would specify the -auto-close 100 as part of your pathway-tools invocation. BTW, I'm not sure how compatible this setting is with MySQL PGDBs -- we use it with files, and I don't know if it has been sufficiently tested with MySQL PGDBs.

As to your second question, when running with MySQL PGDBs, Pathway Tools attempts to refresh each PGDB (i.e. load in the latest updates) once a night. So in that respect, your server would get the updates. However, image files are generated once and then cached, so unless you also added a script to delete them all each night, they might get out of sync with the contents of the PGDB.

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Thanks for you detaillled advice. We will think about the best option.

mdubois gravatar imagemdubois ( 2020-07-19 15:26:59 -0500 )edit

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Asked: 2020-07-17 06:57:29 -0500

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Last updated: Jul 18 '20