If you can consistently cause the problem I wonder if it is worth
trying this 
(http://serverfault.com/questions/528653/how-can-i-stop-nginx-from-retrying-put-or-post-requests-on-upstream-server-timeo)
advice out - it would be good to know if it helps. There is a gist
here - https://gist.github.com/wojons/6154645.

I don't think any POST in Galaxy should be retries instead of errored
on so I don't see any downside of adding this to the nginx
configuration.

-John


On Mon, Sep 21, 2015 at 10:27 AM, Martin Vickers <mj...@aber.ac.uk> wrote:
>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi John,
>
> Thanks for taking the time to reply. I never thought to look at the
> proxy settings but I think you're right, the behaviour seems to match
> what you've described.
>
> Like you I'm not really an expert on proxies and have no idea what would
> be mis-configured that would cause this.
>
> I'm using nginx and the configuration is as described in the wiki. I've
> not loaded any special extensions.
>
> nginx is configured like this;
>
> upstream galaxy_app {
>     server localhost:8090;
>     server localhost:8091;
>     server localhost:8092;
>     server localhost:8093;
>     server localhost:8094;
>     server localhost:8095;
> }
>
> server {
>     # pass to uWSGI by default
>     location / {
>         proxy_pass http://galaxy_app;
>         proxy_set_header X-Forwarded-Host $host;
>         proxy_set_header X-Forwarded-For  $proxy_add_x_forwarded_for;
>         proxy_set_header X-URL-SCHEME https;
>     }
>
> ....static content
>
> }
>
> and in galaxy.ini I have a bunch of handlers, e.g.
>
>
> [server:handler0]
> use = egg:Paste#http
> port = 8090
> host = 127.0.0.1
> use_threadpool = true
> threadpool_workers = 5
>
> I thought that maybe the issue was to do with the 'job admin
> complication' very briefly mentioned here;
>
> https://production-galaxy-instances-with-cloudman-and-cloudbiolinux.readthedocs.org/en/latest/
>
> so I added this to my nginx conf
>
>     location /admin/jobs {
>         proxy_pass  http://localhost:8090;
>     }
>
>
> so this complication is not the one I'm having here.
>
> Are any of the people John mentioned having this issue here on the dev
> board?
>
> Cheers,
>
> Martin
>
> On 09/14/2015 03:11 PM, John Chilton wrote:
>> If I had to guess, I would guess this is caused by a mis-configured
>> proxy (nginx or Apache) that is resubmitting a POST request that is
>> taking Galaxy to long to respond to. Order of events being something
>> like:
>>
>> - User clicks to upload library items.
>> - Proxy gets requests and passes to Galaxy
>> - Galaxy takes a long time to process request and doesn't respond
>> within a timeout.
>> - Proxy resends POST request to Galaxy.
>> - Galaxy takes a long time to process request and doesn't respond
>> within a timeout.
>> ...
>>
>> Proxies should never resend POST requests to Galaxy as far a I can
>> imagine, but we have seen this for instance when submitting workflows.
>> Some people have had their proxy retry that request repeatedly.
>>
>> I don't really know if this is a problem with the default proxy
>> configurations we list on the wiki or if it comes down to
>> customizations or special loaded extensions at various sites that have
>> encountered this.
>>
>> Is this enough to help debug the problem? I'm not really an expert on
>> specific proxies, etc... and you have it there and seem to be able to
>> reproduce the problem. If you do want further help I would post the
>> proxy you are using, the extensions, the configuration, and the Galaxy
>> logs corresponding to this incident to see if we can see the repeated
>> posts and the route that is being posted to.
>>
>> If you are not using a proxy, then I am stumped :(.
>>
>> -John
>>
>>
>> On Fri, Sep 4, 2015 at 12:04 PM, Martin Vickers <mj...@aber.ac.uk> wrote:
>>> Hi All,
>>>
>>> I've noticed an issue a couple of times now where I've added a directory
>>> of fastq's from an NFS mounted filesystem (reference only rather than
>>> copying into galaxy) and then galaxy times out. Load average begins to
>>> get really high and then consumes all the RAM and sometimes crashes.
>>> These are the same symptom as I had before with this issue that was
>>> never resolved;
>>>
>>> http://dev.list.galaxyproject.org/run-sh-segfault-td4667549.html#a4667553
>>>
>>> What I've noticed is that in the dataset I'm uploading to galaxy, there
>>> are suddenly many duplicates. In this example that's just happened,
>>> there are 288 fastq.gz files in the physical folder, but galaxy has
>>> created 6 references to each file resulting in 1728 datasets in the
>>> folder (see attached images).
>>>
>>> When this happened before and crashed the galaxy application, whenever
>>> it restarted it'd try to resume what it was doing which created an
>>> endless loop of retrying and crashing until the job was removed.
>>>
>>> Does anyone know what may be causing this?
>>>
>>> Cheers,
>>>
>>> Martin
>>>
>>> --
>>>
>>> --
>>> Dr. Martin Vickers
>>>
>>> Data Manager/HPC Systems Administrator
>>> Institute of Biological, Environmental and Rural Sciences
>>> IBERS New Building
>>> Aberystwyth University
>>>
>>> w: http://www.martin-vickers.co.uk/
>>> e: mj...@aber.ac.uk
>>> t: 01970 62 2807
>>>
>>>
>>> ___________________________________________________________
>>> 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/
>
> - --
>
> - --
> Dr. Martin Vickers
>
> Data Manager/HPC Systems Administrator
> Institute of Biological, Environmental and Rural Sciences
> IBERS New Building
> Aberystwyth University
> SY23 3FG
>
> w: http://www.martin-vickers.co.uk/
> e: mj...@aber.ac.uk
> t: 01970 62 2807
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>
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