Hi Nate,
So I went ahead and set `static_enabled = False` in universe_wsgi.ini,
restarted uWSGI, and browsed to localhost. I'm including the results
of each step below:
After restarting uWSGI, the last few lines of uwsgi.log looked like this:
WSGI app 0 (mountpoint='') ready in 11 seconds on interpreter
0xa934c0 pid: 3561 (default app)
*** uWSGI is running in multiple interpreter mode ***
spawned uWSGI master process (pid: 3561)
spawned uWSGI worker 1 (pid: 3575, cores: 4)
spawned uWSGI worker 2 (pid: 3576, cores: 4)
spawned uWSGI worker 3 (pid: 3583, cores: 4)
spawned uWSGI worker 4 (pid: 3587, cores: 4)
spawned uWSGI worker 5 (pid: 3591, cores: 4)
spawned uWSGI worker 6 (pid: 3595, cores: 4)
spawned uWSGI worker 7 (pid: 3599, cores: 4)
spawned uWSGI worker 8 (pid: 3603, cores: 4)
spawned uWSGI worker 9 (pid: 3607, cores: 4)
spawned uWSGI worker 10 (pid: 3611, cores: 4)
*** Stats server enabled on 127.0.0.1:9191 fd: 30 ***
...so no traceback this time!
Then, browsing to localhost redirects to https://localhost and finally returns:
"Internal Server Error
Galaxy was unable to successfully complete your request
An error occurred.
This may be an intermittent problem due to load or other
unpredictable factors, reloading the page may address the problem.
The error has been logged to our team."
That request was logged to uwsgi.log:
127.0.0.1 - - [03/Feb/2015:14:51:01 -0400] "GET / HTTP/1.1" 500 -
"-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:35.0) Gecko/20100101
Firefox/35.0"
Error - <type 'exceptions.KeyError'>: 'SCRIPT_NAME'
URL: https://localhost/
File 'lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
app_iter = self.application(environ, sr_checker)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__
return self.application(environ, start_response)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File 'lib/galaxy/web/framework/base.py', line 132 in __call__
return self.handle_request( environ, start_response )
File 'lib/galaxy/web/framework/base.py', line 159 in handle_request
trans = self.transaction_factory( environ )
File 'lib/galaxy/web/framework/webapp.py', line 71 in <lambda>
self.set_transaction_factory( lambda e:
self.transaction_chooser( e, galaxy_app, session_cookie ) )
File 'lib/galaxy/web/framework/webapp.py', line 102 in transaction_chooser
return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie )
File 'lib/galaxy/web/framework/webapp.py', line 207 in __init__
self._ensure_logged_in_user( environ, session_cookie )
File 'lib/galaxy/web/framework/webapp.py', line 441 in
_ensure_logged_in_user
if self.request.path.startswith( external_display_path ):
File 'lib/galaxy/web/framework/base.py', line 258 in __get__
value = self.func( obj )
File 'lib/galaxy/web/framework/base.py', line 341 in path
return self.environ['SCRIPT_NAME'] + self.environ['PATH_INFO']
KeyError: 'SCRIPT_NAME'
CGI Variables
-------------
DOCUMENT_ROOT: '/usr/share/nginx/html'
HTTP_ACCEPT:
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
HTTP_ACCEPT_ENCODING: 'gzip, deflate'
HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5'
HTTP_CONNECTION: 'keep-alive'
HTTP_HOST: 'localhost'
HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:35.0) Gecko/20100101 Firefox/35.0'
PATH_INFO: '/'
REMOTE_ADDR: '127.0.0.1'
REMOTE_PORT: '50064'
REQUEST_METHOD: 'GET'
REQUEST_URI: '/'
SERVER_NAME: 'localhost'
SERVER_PORT: '443'
SERVER_PROTOCOL: 'HTTP/1.1'
UWSGI_SCHEME: 'https'
WSGI Variables
--------------
application: <paste.recursive.RecursiveMiddleware object at
0x7f2ec2f32290>
is_api_request: False
paste.cookies: (<SimpleCookie: >, '')
paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
object at 0x7f2ec2f32210>
paste.recursive.forward: <paste.recursive.Forwarder from />
paste.recursive.include: <paste.recursive.Includer from />
paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
paste.recursive.script_name: ''
paste.throw_errors: True
request_id: 'fadecee2abdd11e4bfb614feb5e02dd6'
uwsgi.core: 0
uwsgi.node: 'i changed this string to hide the server name'
uwsgi.version: '2.0.9'
wsgi process: 'Multi process AND threads (?)'
wsgi.file_wrapper: <built-in function uwsgi_sendfile>
------------------------------------------------------------
[pid: 3607|app: 0|req: 1/1] 127.0.0.1 () {40 vars in 593 bytes}
[Tue Feb 3 14:51:01 2015] GET / => generated 777 bytes in 230 msecs
(HTTP/1.1 500) 1 headers in 63 bytes (1 switches on core 0)
I thought I would include some pieces of universe_wsgi.ini to help
with troubleshooting:
# ---- HTTP Server
----------------------------------------------------------
# Configuration of the internal HTTP server.
[server:main]
# The internal HTTP server to use. Currently only Paste is provided. This
# option is required.
use = egg:Paste#http
# The port on which to listen.
#port = 8080
# The address on which to listen. By default, only listen to
localhost (Galaxy
# will not be accessible over the network). Use '0.0.0.0' to listen on all
# available network interfaces.
host = 0.0.0.0
# Use a threadpool for the web server instead of creating a thread for each
# request.
use_threadpool = True
# Number of threads in the web server thread pool.
threadpool_workers = 10
# Set the number of seconds a thread can work before you should
kill it (assuming it will never finish) to 3 hours.
threadpool_kill_thread_limit = 10800
# ---- uwsgi ----------------------------------------------------------
[uwsgi]
processes = 10
stats = 127.0.0.1:9191
socket = 127.0.0.1:4001
pythonpath = lib
threads = 4
logto = /home/galaxy/galaxy-dist/uwsgi.log
master = True
Also, we are using a self-signed certificate as a temporary solution,
so not sure if that matters.
Thanks!
On Mon, Feb 2, 2015 at 11:32 AM, Nate Coraor <n...@bx.psu.edu> wrote:
> Hi Nicholas,
>
> Set `static_enabled = False` in universe_wsgi.ini and restart uWSGI, and see
> if that makes a difference.
>
> Thanks,
> --nate
>
> On Mon, Feb 2, 2015 at 11:26 AM, Nicholas Kline <nx...@case.edu> wrote:
>>
>> Hi Nate. Thanks a lot for all the help so far. So, I started uWSGI like
>> so:
>>
>> - activate virtual env
>> - cd ~/galaxy-dist
>> - PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste
>> universe_wsgi.ini
>>
>> Then browsed to localhost, which redirected to https://localhost/ as
>> expected since I want all traffic to be over HTTPS, and finally
>> returned:
>>
>> 502 Bad Gateway
>>
>> I checked uwsgi.log and it's quite large, almost 3,000 lines. Should I
>> post it to this list for review? I've included the last few lines
>> below:
>>
>> *** uWSGI is running in multiple interpreter mode ***
>> spawned uWSGI master process (pid: 4083)
>> spawned uWSGI worker 1 (pid: 4195, cores: 4)
>> spawned uWSGI worker 2 (pid: 4199, cores: 4)
>> spawned uWSGI worker 3 (pid: 4203, cores: 4)
>> spawned uWSGI worker 4 (pid: 4207, cores: 4)
>> spawned uWSGI worker 5 (pid: 4211, cores: 4)
>> spawned uWSGI worker 6 (pid: 4215, cores: 4)
>> spawned uWSGI worker 7 (pid: 4219, cores: 4)
>> spawned uWSGI worker 8 (pid: 4223, cores: 4)
>> spawned uWSGI worker 9 (pid: 4224, cores: 4)
>> spawned uWSGI worker 10 (pid: 4225, cores: 4)
>> *** Stats server enabled on 127.0.0.1:9191 fd: 30 ***
>> Traceback (most recent call last):
>> File
>> "/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/urlmap.py",
>> line 201, in __call__
>> environ['SCRIPT_NAME'] += app_url
>> KeyError: 'SCRIPT_NAME'
>> [pid: 4219|app: 0|req: 1/1] 127.0.0.1 () {40 vars in 593 bytes} [Fri
>> Jan 30 15:15:10 2015] GET / => generated 0 bytes in 18 msecs (HTTP/1.1
>> 500) 0 headers in 0 bytes (0 switches on core 0)
>>
>> If you need me to post my Nginx config too, just let me know. Thanks!
>>
>>
>>
>> On Wed, Jan 28, 2015 at 2:53 PM, Nate Coraor <n...@bx.psu.edu> wrote:
>> > On Wed, Jan 28, 2015 at 11:55 AM, Nicholas Kline <nx...@case.edu> wrote:
>> >>
>> >> Hi Nate. Thank you for the reply. So I installed uWSGI inside my
>> >> Python virtual environment since that was one of the options listed in
>> >> the documentation, like so:
>> >>
>> >> cd ~/galaxy_env/
>> >> source bin/activate
>> >> pip install uwsgi
>> >>
>> >> It looks like uWSGI was successfully installed. I then
>> >> exited/deactivated the virtual environment via 'deactivate'.
>> >>
>> >> Next, I tried to start uWSGI:
>> >>
>> >> ~/galaxy-dist$ PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi
>> >> --ini-paste config/galaxy.ini
>> >
>> >
>> > Calling uwsgi after deactivating the virtualenv means it'd be running
>> > from
>> > wherever it's found on $PATH, which is probably not the one you just
>> > installed into the virtualenv. But if it works, it may not matter.
>> >
>> >>
>> >>
>> >> ... but it returned this:
>> >>
>> >>
>> >> realpath() of config/galaxy.ini failed: No such file or directory
>> >> [core/utils.c line 3607]
>> >>
>> >> So, I pointed it to universe_wsgi.ini instead, like so:
>> >>
>> >> ~/galaxy-dist$ PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi
>> >> --ini-paste universe_wsgi.ini
>> >
>> >
>> > universe_wsgi.ini was renamed to config/galaxy.ini late last year.
>> > However,
>> > if you still have it, it's perfectly fine to leave it there and continue
>> > using it.
>> >
>> >>
>> >>
>> >> ...and this was returned:
>> >>
>> >> [uWSGI] getting INI configuration from universe_wsgi.ini
>> >>
>> >> At that point, Terminal just kinda sits there and does not display any
>> >> output, error messages, etc.
>> >
>> >
>> > If uwsgi is running, this suggests it's working. If you have set up the
>> > uwsgi proxy in nginx you should be able to try to access Galaxy via the
>> > web
>> > at this point. More detail may be available in the uwsgi log file - did
>> > you
>> > set `logto` in the `[uwsgi]` section of universe_wsgi.ini?
>> >
>> >>
>> >> Questions:
>> >>
>> >> 1. Was I correct in specifying universe_wsgi.ini ?
>> >
>> >
>> > The location of the config file is up to you. universe_wsgi.ini in the
>> > root
>> > of the Galaxy directory was the old default.
>> >
>> >>
>> >> 2. Nothing is returned after "[uWSGI] getting INI configuration from
>> >> universe_wsgi.ini". Is that normal?
>> >
>> >
>> > Yes. You probably want to set `logto` as described above and start uwsgi
>> > in
>> > the background, e.g. with the `-d` command line option.
>> >
>> >> 3. Should I activate the Python virtual environment first (via "source
>> >> bin/activate") before executing "~/galaxy-dist$
>> >> PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste
>> >> universe_wsgi.ini" ?
>> >
>> >
>> > Yes, I would do this.
>> >
>> >>
>> >> 4. Is the next step to start Galaxy, like so?
>> >>
>> >> cd galaxy-dist
>> >> GALAXY_RUN_ALL=1 sh run.sh --daemon
>> >
>> >
>> > uwsgi is running your Galaxy web processes, so I would check to ensure
>> > they
>> > are working first. Once you've verified that, you can use the command
>> > above
>> > to start any job handlers you have configured.
>> >
>> > --nate
>> >
>> >>
>> >>
>> >> I appreciate your help.
>> >>
>> >>
>> >>
>> >>
>> >> On Mon, Jan 26, 2015 at 5:22 PM, Nate Coraor <n...@bx.psu.edu> wrote:
>> >> > Hi Nicholas,
>> >> >
>> >> > Sorry for the somewhat misleading text in the documentation. The part
>> >> > about
>> >> > "no extra modules or recompiling" refers to nginx itself - uWSGI
>> >> > protocol
>> >> > support is built in to the core functionality of nginx. This does not
>> >> > mean
>> >> > that uWSGI itself is installed. Installing uWSGI is addressed a bit
>> >> > further
>> >> > up:
>> >> >
>> >> >> You will also need to have uWSGI installed. There are a variety of
>> >> >> ways
>> >> >> to
>> >> >> do this. It can be installed system-wide by installing from your
>> >> >> system's
>> >> >> package manager (on Debian and Ubuntu systems, the uwsgi and
>> >> >> uwsgi-plugin-python provide the necessary components), or with
>> >> >> theeasy_install or pip commands (which will install it to the
>> >> >> system's
>> >> >> Python site-packages directory). Alternatively, if you are already
>> >> >> running
>> >> >> Galaxy from a Python virtualenv, you can use pip install uwsgi with
>> >> >> that
>> >> >> virtualenv's copy of pip to install to that virtualenv as your
>> >> >> unprivileged
>> >> >> Galaxy user.
>> >> >
>> >> >
>> >> > In the case of Ubuntu sudo apt-get install uwsgi uwsgi-plugin-python
>> >> > should
>> >> > provide the necessary components.
>> >> >
>> >> > --nate
>> >> >
>> >> > On Mon, Jan 26, 2015 at 2:46 PM, Nicholas Kline <nx...@case.edu>
>> >> > wrote:
>> >> >>
>> >> >> Hello,
>> >> >>
>> >> >> I am trying to setup a local production Galaxy server for our
>> >> >> department. Our Galaxy server environment is as follows:
>> >> >>
>> >> >> - Ubuntu 14.04 64-bit
>> >> >> - 94 GB Memory
>> >> >> - Intel Xeon
>> >> >> - Python virtual environment
>> >> >> - Nginx
>> >> >> - PostgreSQL
>> >> >> - ProFTPd
>> >> >>
>> >> >> Today I tried starting the Galaxy server for the first time. I think
>> >> >> the first step in that process is starting uWSGI, correct? To do so,
>> >> >> I
>> >> >> executed these commands:
>> >> >>
>> >> >> cd ~/galaxy-dist/
>> >> >> PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste
>> >> >> config/galaxy.ini
>> >> >>
>> >> >> However, it appears something failed. This information is returned:
>> >> >>
>> >> >> The program 'uwsgi' can be found in the following packages:
>> >> >> * uwsgi-core
>> >> >> * uwsgi-plugin-alarm-curl
>> >> >> * uwsgi-plugin-alarm-xmpp
>> >> >> * uwsgi-plugin-curl-cron
>> >> >> * uwsgi-plugin-emperor-pg
>> >> >> * uwsgi-plugin-erlang
>> >> >> * uwsgi-plugin-geoip
>> >> >> * uwsgi-plugin-graylog2
>> >> >> * uwsgi-plugin-jvm-openjdk-6
>> >> >> * uwsgi-plugin-jvm-openjdk-7
>> >> >> * uwsgi-plugin-ldap
>> >> >> * uwsgi-plugin-lua5.1
>> >> >> * uwsgi-plugin-lua5.2
>> >> >> * uwsgi-plugin-php
>> >> >> * uwsgi-plugin-psgi
>> >> >> * uwsgi-plugin-python
>> >> >> * uwsgi-plugin-python3
>> >> >> * uwsgi-plugin-rack-ruby1.9.1
>> >> >> * uwsgi-plugin-router-access
>> >> >> * uwsgi-plugin-sqlite3
>> >> >> * uwsgi-plugin-v8
>> >> >> * uwsgi-plugin-xslt
>> >> >> Ask your administrator to install one of them
>> >> >>
>> >> >> According to the galaxy documentation at
>> >> >> https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling ,
>> >> >> "uWSGI support is built in to nginx, so no extra modules or
>> >> >> recompiling should be required".
>> >> >>
>> >> >> Also, should '--ini-paste config/galaxy.ini' really be configured
>> >> >> like
>> >> >> this instead: --ini-paste universe_wsgi.ini ?
>> >> >>
>> >> >> Thank you
>> >> >> ___________________________________________________________
>> >> >> 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/
