Hi Nate,
After scramble,py failed, I ran
$ python ./scripts/scramble.py -e bx_python
and bx_python seems to be built without any problem:
...
writing build/bdist.linux-armv7l/egg/EGG-INFO/native_libs.txt
creating dist
creating 'dist/bx_python-0.7.1_7b95ff194725-py2.7-linux-armv7l-ucs4.egg' and
adding 'build/bdist.linux-armv7l/egg' to it
removing 'build/bdist.linux-armv7l/egg' (and everything under it)
scramble(): Copied egg to:
/nfs/users/galaxy_dist/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-armv7l-ucs4.egg
...and I then reran
$ python ./scripts/scramble.py
and it shows all eggs already exist. Then I ran
$ sh run.sh
to launch Galaxy, without making any change to universe_wsgi.ini. The launch of
Galaxy failed with the following error message:
...
galaxy.webapps.galaxy.buildapp DEBUG 2013-02-22 15:14:03,077 Enabling 'Request
ID' middleware
Starting server in PID 19121.
Traceback (most recent call last):
File "./scripts/paster.py", line 33, in <module>
serve.run()
File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line
1056, in run
invoke(command, command_name, options, args[1:])
File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line
1062, in invoke
exit_code = runner.run(args)
File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 227,
in run
result = self.command()
File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 677,
in command
serve()
File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 661,
in serve
server(app)
File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/loadwsgi.py", line
292, in server_wrapper
**context.local_conf)
File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/loadwsgi.py", line
97, in fix_call
val = callable(*args, **kw)
File
"/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line
1342, in server_runner
serve(wsgi_app, **kwargs)
File
"/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line
1291, in serve
request_queue_size=request_queue_size)
File
"/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line
1134, in __init__
request_queue_size=request_queue_size)
File
"/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line
1113, in __init__
request_queue_size=request_queue_size)
File
"/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line
328, in __init__
HTTPServer.__init__(self, server_address, RequestHandlerClass)
File "/usr/lib/python2.7/SocketServer.py", line 408, in __init__
self.server_bind()
File "/usr/lib/python2.7/BaseHTTPServer.py", line 108, in server_bind
SocketServer.TCPServer.server_bind(self)
File "/usr/lib/python2.7/SocketServer.py", line 419, in server_bind
self.socket.bind(self.server_address)
File "/usr/lib/python2.7/socket.py", line 224, in meth
return getattr(self._sock,name)(*args)
socket.error: [Errno 98] Address already in use
galaxy.jobs.manager INFO 2013-02-22 15:14:03,134 sending stop signal to worker
thread
galaxy.jobs.manager INFO 2013-02-22 15:14:03,135 job manager queue stopped
galaxy.jobs.manager INFO 2013-02-22 15:14:03,135 sending stop signal to worker
thread
galaxy.jobs.manager INFO 2013-02-22 15:14:03,135 job manager stop queue stopped
galaxy.jobs.handler INFO 2013-02-22 15:14:03,136 sending stop signal to worker
thread
galaxy.jobs.handler INFO 2013-02-22 15:14:03,136 job handler queue stopped
galaxy.jobs.runners.lwr INFO 2013-02-22 15:14:03,136 sending stop signal to
worker threads
galaxy.jobs.runners.lwr INFO 2013-02-22 15:14:03,137 local job runner stopped
galaxy.jobs.runners.local INFO 2013-02-22 15:14:03,137 sending stop signal to
worker threads
galaxy.jobs.runners.local INFO 2013-02-22 15:14:03,138 local job runner stopped
galaxy.jobs.handler INFO 2013-02-22 15:14:03,139 sending stop signal to worker
thread
galaxy.jobs.handler INFO 2013-02-22 15:14:03,139 job handler stop queue stopped
Exception in thread LWRRunner.monitor_thread (most likely raised during
interpreter shutdown):
I hope you find this information useful. Do you have any idea about what went
wrong?
Many thanks,
Shun
________________________________________
From: Nate Coraor [[email protected]]
Sent: 21 February 2013 16:56
To: Shun Liang
Cc: James Taylor; [email protected]
Subject: Re: [galaxy-dev] Installing Galaxy on ARM Architecture
On Feb 21, 2013, at 11:47 AM, Shun Liang wrote:
> Sorry just forgot to CC the mailing list.
> ________________________________________
>
> Hi James,
>
> I followed the manual installation instruction on
> "https://bitbucket.org/james_taylor/bx-python/wiki/HowToInstall";, and
> surprisingly, bx-python seems to be built on the ARM server without any
> problem:
>
> Installed
> /nfs/users/bx-python/lib/python/bx_python-0.7.1-py2.7-linux-armv7l.egg
> Processing dependencies for bx-python==0.7.1
> Finished processing dependencies for bx-python==0.7.1
Hi Shun.
I'm moving this over to galaxy-dev since it's about a local installation.
Galaxy's eggs lib isn't finding the egg you built because Galaxy adds the
Mercurial revision to the egg version, and then expects the egg to be
physically located in galaxy-dist/eggs/. The library will be looking for:
bx_python-0.7.1_7b95ff194725-py2.7-linux-armv71.egg
If you are able to build it through scramble that would be ideal since it
handles that naming for you, and there will be other C-Extension eggs to build
under similar constraints. There should have been an error earlier in the
scramble output with more details on why building bx-python failed. If you
rerun scramble on just that egg, you should be able to recapture the output:
% python ./scripts/scramble.py -e bx_python
--nate
>
>
>
> Regards,
> Shun
> ________________________________________
> From: [email protected] [[email protected]] on behalf of James Taylor
> [[email protected]]
> Sent: 21 February 2013 16:07
> To: Shun Liang
> Cc: [email protected]
> Subject: Re: [galaxy-user] Installing Galaxy on ARM Architecture
>
> You are definitely in uncharted territory with an arm server. Can you
> try building just bx-python itself and let us know what the errors
> are?
>
> --
> James Taylor, Assistant Professor, Biology/CS, Emory University
>
>
> On Thu, Feb 21, 2013 at 11:03 AM, Shun Liang <[email protected]>
> wrote:
>> Hi,
>>
>> I am trying to install Galaxy on an ARMV7 architecture Linux server. I ran
>> "run.sh" and failed because some of the python eggs could not be fetched. I
>> then have a look at "http://eggs.galaxyproject.org/"; and I have realized
>> there aren't any armv7 builds for those eggs.
>>
>> I then decided to build (or scramble) the eggs on my own. I ran
>> "scripts/scramble.py" and this also failed with the following message (after
>> building a lot of things):
>>
>> scramble(): Copied egg to:
>> /nfs/users/galaxy_dist/eggs/twill-0.9-py2.7.egg
>> Traceback (most recent call last):
>> File "scripts/scramble.py", line 26, in <module>
>> eggs = c.scramble()
>> File "/nfs/users/galaxy_dist/lib/galaxy/eggs/scramble.py", line 242, in
>> scramble
>> raise last_exc # only 1 failure out of the crate, be more informative
>> galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build
>> failed for bx_python 0.7.1
>>
>>
>> May I ask what may cause this problem? Have I done anything wrong? Or, is it
>> even possible to install Galaxy on ARM architecture Linux?
>>
>>
>>
>> Many thanks,
>> Shun
>>
>>
>> ___________________________________________________________
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org. Please keep all replies on the list by
>> using "reply all" in your mail client. For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>>
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>>
>> http://lists.bx.psu.edu/
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
___________________________________________________________
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/
