Hi Christian, I'd suggest creating a virtualenv and starting Galaxy from that.
--nate On Wed, Aug 12, 2015 at 8:24 AM, Christian Schudoma (TSL) < christian.schud...@sainsbury-laboratory.ac.uk> wrote: > Hi Guys, > > I started pulling in the patches named below. After applying patch 345 > (curl ... | patch -p1), all new job submissions and finishing jobs fail > with > > /tsl/services/galaxy/dist/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning: > Module simplejson was already imported from > /tsl/services/galaxy/dist/lib/python2.6/site-packages/simplejson-3.6.5-py2.6-linux-x86_64.egg/simplejson/__init__.pyc, > but > /tsl/services/galaxy/dist/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg > is being added to sys.path self.check_version_conflict() > > > Any ideas? > > > Thanks > Christian > > > > On 16/07/15 19:36, Poole, Richard wrote: > > Hi Nate, > > Problem solved (with one small exception) with much help from Marius. I > followed his instructions to apply the three patches via mercurial: > > You can get the diff of a pull request by adding .diff, like so: > > > https://patch-diff.githubusercontent.com/raw/galaxyproject/galaxy/pull/345.diff > > https://patch-diff.githubusercontent.com/raw/galaxyproject/galaxy/pull/416.diff > > https://patch-diff.githubusercontent.com/raw/galaxyproject/galaxy/pull/466.diff > > These should be the 3 pull requests for the issue you referenced. > So you should be able to do curl > https://patch-diff.githubusercontent.com/raw/galaxyproject/galaxy/pull/345.diff > |patch > -p1 > > and then the other 2. > It's probably a good idea to do another branch for testing this, > e.g. > hg branch fix_metadata > hg commit -m "branch to test metadatafix" > > I had to manually resolve one of the patches in > lib/galaxy/tools/actions/metadata > > > I also had to manually resolve that one as the patch for that file didn’t > apply properly. > > I was then able to reset all metadata for the BAMs listed following the > SQL search and hey presto history display back to normal speed :) > > The one issue I still have is that 9 of the offending BAMs are actually in > a history that I deleted permanently by accident during the UI > slow-response. So they are still listed in the SQL search. This doesn’t > seem to be adversely affecting the speed but obviously I can’t reset their > metadata now. Is this a problem? > > Thanks for the help, > Rich > > > On 16 Jul 2015, at 11:45, Poole, Richard <r.po...@ucl.ac.uk> wrote: > > Hi Nate, > > I have managed to update to the latest version of the default branch but I > do not see the ‘max_metadate_value_size’ in my universe_wsgi.ini (this file > was not changed during the update). Same thing if I use hg pull && hg > update stable or hg pull && hg update release_15.05. > > Does this mean this change is not yet on mercurial and if so how can I > pull this specific change (using curl?) to generate my own branch specific > for the patch? > > Thanks, > Richard > > On 15 Jul 2015, at 20:59, Richard Poole <ucga...@live.ucl.ac.uk> wrote: > > Just a little update - executed the SQL query and luckily only returned 20 > BAM files - the most recently generated ones of course. Now makes sense > this could well be the cause of the UI problem as my account became more > and more unresponsive the more of these 20 BAM files I generated over the > last week……….. > > Rich > > On 15 Jul 2015, at 20:38, Richard Poole <ucga...@live.ucl.ac.uk> wrote: > > Hi Nate, > > Ok - I can try this but I’m not an SQL database expert - far from it in > fact. That query will just list ‘problematic’ datasets? I have a lot of > histories with BAM files ;) > > Resetting the metadata needs to be done before this fix works? I ask > because my history is so slow now as to be unusable…….or setting the cutoff > allows Galaxy to be usable but it wipes out the metadata (which then needs > resetting). > > I am still using universe_wsgi.ini not galaxy.ini and I don’t see the > 'max_metadata_value_size’ in any section of my universe_wsgi_ini file - I > guess because I’m not on latest update. I am actually not sure what version > I am on as to fix an earlier issue with shared datasets (that wasn’t yet on > mercurial) on the advice of a few folks I generated a branch specific for > the patch using: > > hg branch fix_history_sharing > > curl > https://github.com/galaxyproject/galaxy/commit/62772bc86e2504982f207a982542cbcc3faf0c65.diff|patch > -p1 > > Also not being a huge mecurial expert I am a little unsure now how to > switch back to stable branch correctly and pull the latest updates. Could > you advise (sorry to be a noob)? > > Rich > > > > On 15 Jul 2015, at 20:22, Nate Coraor <n...@bx.psu.edu> wrote: > > Hi Richard, > > Unfortunately, you will need to reset metadata for any problematic > datasets once you have updated to the latest version of 15.05 and set a > cutoff value. You can find the datasets with the following SQL query in > your database: > > select hda.id, u.email, h.name, hda.hid, hda.name, length(hda.metadata) > from history_dataset_association hda > join history h on hda.history_id=h.id > join galaxy_user u on h.user_id=u.id > where length(hda.metadata) > 1048576 order by length(hda.metadata) desc; > > And you can reset metadata by clicking on the dataset's pencil icon in > your history and clicking "auto-detect". > > --nate > > On Wed, Jul 15, 2015 at 3:16 PM, Poole, Richard <r.po...@ucl.ac.uk> wrote: > >> Hi Nate, >> >> I am indeed using later than 15.05………so I will try this fix next time I >> can restart the server and let you know. >> >> Richard >> >> On 15 Jul 2015, at 19:32, Nate Coraor <n...@bx.psu.edu> wrote: >> >> Hi Richard, >> >> By any chance, are you running Galaxy 15.05 or later? 15.05 includes new >> metadata for bam files that can cause UI performance problems with certain >> types of bam files. This can be limited with the new >> `max_metadata_value_size` in galaxy.ini (on usegalaxy.org we've set it >> to 1000000). >> >> I've also created a pull request to make this limiting the default: >> https://github.com/galaxyproject/galaxy/pull/466 >> >> However, if you are using an older version of Galaxy, this issue is not >> related to the problem you're experiencing. >> >> --nate >> >> On Wed, Jul 15, 2015 at 2:16 PM, Poole, Richard <r.po...@ucl.ac.uk> >> wrote: >> >>> Hi Christian and Carl, >>> >>> Thanks both for the replies. >>> >>> To answer your questions in reverse order. I have about XX histories in >>> my account each with an average of about XX datasets. Total data in my >>> account is about 1TB. >>> >>> It is indeed an admin account and other users with close to 1TB of data >>> do not have a similar slow down. Although their data is spread over far >>> fewer histories. Is there a way then to prevent the file_name attribute >>> being requested for admin accounts so I can see if this speeds things back >>> up again? >>> >>> Although the Galaxy server is running on my iMac the data is stored >>> external on a large directly attached NAS. I think I first noticed this >>> slow down after deleting and purging a bunch of older histories to free >>> space on the NAS. I have tried running some of the cleanup_datasets scripts >>> but they are actually returning errors and not running right now (can give >>> you the error messages if necessary). >>> >>> The slowdown is actually getting worse now and it is even slow to >>> display tool pages, as well as often getting this error if it is really >>> slow: >>> Proxy Error >>> >>> The proxy server received an invalid response from an upstream server. >>> The proxy server could not handle the request *GET /history/list >>> <http://iworm.anat.ucl.ac.uk:8080/history/list>*. >>> >>> Reason: *Error reading from remote server* >>> I am running through an apache proxy - perhaps the apache settings need >>> tweaking too? (I forget right now where I set these up!). >>> >>> As for the database itself, I am running PostgreSQL 9.3 and I tweaked >>> the settings in my universe_wsgi.ini as per the instructions on >>> https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Advanced_configuration >>> >>> So my settings are: >>> >>> # -- Database >>> >>> # By default, Galaxy uses a SQLite database at >>> 'database/universe.sqlite'. You >>> # may use a SQLAlchemy connection string to specify an external database >>> # instead. This string takes many options which are explained in detail >>> in the >>> # config file documentation. >>> database_connection = >>> postgresql://*******:*******@localhost:5432/galaxy_prod >>> >>> # If the server logs errors about not having enough database pool >>> connections, >>> # you will want to increase these values, or consider running more Galaxy >>> # processes. >>> database_engine_option_pool_size = 10 >>> database_engine_option_max_overflow = 20 >>> >>> # If using MySQL and the server logs the error "MySQL server has gone >>> away", >>> # you will want to set this to some positive value (7200 should work). >>> #database_engine_option_pool_recycle = -1 >>> >>> # If large database query results are causing memory or response time >>> issues in >>> # the Galaxy process, leave the result on the server instead. This >>> option is >>> # only available for PostgreSQL and is highly recommended. >>> database_engine_option_server_side_cursors = True >>> >>> # Create only one connection to the database per thread, to reduce the >>> # connection overhead. Recommended when not using SQLite: >>> database_engine_option_strategy = threadlocal >>> >>> # Log all database transactions, can be useful for debugging and >>> performance >>> # profiling. Logging is done via Python's 'logging' module under the >>> qualname >>> # 'galaxy.model.orm.logging_connection_proxy' >>> database_query_profiling_proxy = False >>> >>> # -- Files and directories >>> >>> Let me know if you think these settings are appropriate or need further >>> tweaks. >>> >>> Thanks again for your responses so far, >>> >>> Richard >>> >>> >>> >>> On 13 Jul 2015, at 16:31, Carl Eberhard <carlfeberh...@gmail.com> wrote: >>> >>> Hi, Richard >>> >>> How many histories are on your account? How many datasets (roughly)? >>> >>> Are you using an Admin account to view the histories and does the slow >>> down still occur for regular users with large amounts of data? >>> >>> One of the exposed attributes of datasets (for admins - not other users >>> generally) is the file_name. I've noticed that retrieving this attribute >>> from the file system can be slow. >>> >>> Christian also provides good advice. >>> >>> On Thu, Jul 9, 2015 at 4:12 AM, Christian Brenninkmeijer < >>> christian.brenninkmei...@manchester.ac.uk> wrote: >>> >>>> Hi Richard, >>>> >>>> I am relatively new to galaxy so if you get a different response from >>>> one of the core team ignore this. >>>> >>>> One thing I would check is the underlying database. >>>> What do you have set for "database_connection" in your galaxy.ini file. >>>> >>>> Especially if you are using the default sqlite this could be the issue. >>>> As that is store in a single file on disk. >>>> >>>> Whichever database you have make sure it has enough resources to handle >>>> what will now be a large size. >>>> >>>> Christian >>>> ------------------------------ >>>> *From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on >>>> behalf of Poole, Richard [r.po...@ucl.ac.uk] >>>> *Sent:* Wednesday, July 08, 2015 9:04 PM >>>> *To:* email@example.com >>>> *Subject:* [galaxy-dev] Slow repsonses viewing histories >>>> >>>> Hi all, >>>> >>>> I am having trouble right now with my own personal account on my >>>> production server. Grid refreshes are taking a huge amount of time (e.g. >>>> when viewing ‘saved histories’ or even generating the dataset list for a >>>> single history). My account is very full of data (1TB), could it be this? >>>> >>>> There are no obvious messages in the logs though so I am a bit stumped >>>> as to why.I do not have the same trouble when impersonating other users >>>> with fairly full accounts. Perhaps a database issue (I do not know how to >>>> ‘cleanup’ the database or indeed Galaxy user accounts). Any thoughts? >>>> >>>> Thanks, >>>> Richard >>>> >>>> *Richard J Poole PhD* >>>> Wellcome Trust Fellow >>>> Department of Cell and Developmental Biology >>>> University College London >>>> 21 University Street, London WC1E 6DE >>>> Office (518 Rockefeller): +44 20 7679 6577 (int. 46577) >>>> Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133) >>>> >>>> >>>> ___________________________________________________________ >>>> 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: >>>> https://lists.galaxyproject.org/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>>> >>> >>> >>> >>> ___________________________________________________________ >>> 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: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> >> > > > > > >
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