submit() gets blocked when running workflows via API
Hi All, I am using the API (posting to 'http://localhost:8080/api/workflows' ) and running 8 workflows in a row. I use submit function imported from common. First call to submit takes few seconds to return from submit() second takes a few more seconds, but in the fifth submit it gets hanged. However if I start stopping all workflows via the web interface fifth submit() ends goes on with 6th 7th and 8th. I am not sure if there is a limit of workflows running in parallel but if a run them manually through the GUI they work fine (the eight) does anyone know why API calls get blocked? Is it maybe something to do with the Paste HTTP server used by galaxy? Best, C
Hey Carlos, Have you made any progress on this, I have never heard of this behavior but at the same time it does not surprise tremendously either. How large is the workflow? If large - you will almost certainly want to make sure you are using a Postgres database server instead of sqlite. Likewise if you don't have a proxy like nginx or Apache setup that might help. You can checkout the following page for more information on scaling up Galaxy: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer What version of Galaxy are you using? Thanks for using Galaxy and good luck, -John On Wed, Jun 18, 2014 at 11:33 AM, Carlos del Ojo <deepbit@gmail.com> wrote:
Hi All,
I am using the API (posting to 'http://localhost:8080/api/workflows' ) and running 8 workflows in a row.
I use submit function imported from common.
First call to submit takes few seconds to return from submit() second takes a few more seconds, but in the fifth submit it gets hanged.
However if I start stopping all workflows via the web interface fifth submit() ends goes on with 6th 7th and 8th.
I am not sure if there is a limit of workflows running in parallel but if a run them manually through the GUI they work fine (the eight)
does anyone know why API calls get blocked? Is it maybe something to do with the Paste HTTP server used by galaxy?
Best, C
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Hi, We had this behavior when we used the default SQLite. Since we switched on MySQL, it fixed this :P Maybe a clue for you ? Gildas Le 18/06/2014 18:33, Carlos del Ojo a écrit :
Hi All,
I am using the API (posting to 'http://localhost:8080/api/workflows' ) and running 8 workflows in a row.
I use submit function imported from common.
First call to submit takes few seconds to return from submit() second takes a few more seconds, but in the fifth submit it gets hanged.
However if I start stopping all workflows via the web interface fifth submit() ends goes on with 6th 7th and 8th.
I am not sure if there is a limit of workflows running in parallel but if a run them manually through the GUI they work fine (the eight)
does anyone know why API calls get blocked? Is it maybe something to do with the Paste HTTP server used by galaxy?
Best, C
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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Hi, Yes I found a workaround. Initially I had problems because I was using SQLite and I had lock problems that led to ugly SQLAlchemy errors. After changing to Postgres SQL I got rid of lock errors but I had same issue. So I tried to create a simple script (my workflow has 14 processes) from common import submit submit(... submit(... submit(... ... x8 times and same issue, after the 4th or 5th submit call, the HTTP response of of the call to the api takes ages (minutes) to return (or never returns) However, if I run separate threads each calling submit, everything works fine :S... I know it does not make much sense but before implementing threads I did first experiments in serial and it was failing so I did not even try in parallel... but it works. I've been doing some debugging and API seems to work fine, and I think this is some issue with Paste HTTP server but I couldn't be bothered investigating further. Best, C On Mon, Jun 23, 2014 at 8:43 AM, Gildas Le Corguille < lecorguille@sb-roscoff.fr> wrote:
Hi,
We had this behavior when we used the default SQLite. Since we switched on MySQL, it fixed this :P
Maybe a clue for you ?
Gildas
Le 18/06/2014 18:33, Carlos del Ojo a écrit :
Hi All,
I am using the API (posting to 'http://localhost:8080/api/workflows' ) and running 8 workflows in a row.
I use submit function imported from common.
First call to submit takes few seconds to return from submit() second takes a few more seconds, but in the fifth submit it gets hanged.
However if I start stopping all workflows via the web interface fifth submit() ends goes on with 6th 7th and 8th.
I am not sure if there is a limit of workflows running in parallel but if a run them manually through the GUI they work fine (the eight)
does anyone know why API calls get blocked? Is it maybe something to do with the Paste HTTP server used by galaxy?
Best, C
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
-
Carlos del Ojo -
Gildas Le Corguille -
John Chilton