Dear Paul & William,
thanks for the quick replies! Hopefully the upcoming upgrade will sort
things out ...
Alex
MRC-LMB
[EMAIL PROTECTED]
> Phenix uses its own internal python so nothing to worry about there.
> The cause of the problem Alex is seeing stems from the way Mac OSX
> deals with sockets. We have a fix for this and will be releasing a
> new Phenix version imminently. Why the problem should appear after an
> update through fink is not clear.
>
> On Jul 26, 2008, at 5:18 AM, William G. Scott wrote:
>
>> Alex:
>>
>> try moving /sw out of the way or not sourcing the /sw/bin/init.(c)
>> sh script when you start a new shell and see if that makes a
>> difference. My guess is phenix is using the wrong python (i.e., one
>> in /sw). Fink won't touch anything outside of /sw (apart from your
>> shell's environment, if you run the initialization script).
>>
>> If that solves the problem, just ensure phenix sees /usr/bin/python
>> first.
>>
>> Having said that, I use phenix every day, update fink every day,
>> and have /sw/bin and the head of my path and have not experienced
>> any problems...
>>
>> Bill
>>
>> PS: There is a phenix bb.
>>
>>
>> On Jul 26, 2008, at 4:50 AM, [EMAIL PROTECTED] wrote:
>>
>>> Dear Phenix Programmers/Users,
>>>
>>> after running a 'fink selfupdate' on OS X 10.5.2 (Xquartz 2.2.3) I
>>> am no
>>> longer able to use my Phenix Suite (Ver 1.3 of 26-05-2008) . It
>>> crashes
>>> everytime with obscure (at least to me) error messages (see below).
>>>
>>> Does anyone have a clue as to how to proceed and maybe fix it?
>>>
>>> Thanks very much in advance!
>>>
>>> Alex Berndt
>>> MRC-LMB
>>> [EMAIL PROTECTED]
>>>
>>>
>>> Python(78825,0xb0185000) malloc: *** mmap(size=4083712) failed (error
>>> code=12)
>>> *** error: can't allocate region
>>> *** set a breakpoint in malloc_error_break to debug
>>> set meta data failed
>>> Traceback (most recent call last):
>>> File "/usr/local/phenix-1.3-rc2/phenix/wxGUI/wxtask.py", line
>>> 522, in
>>> OnGoButton
>>> try: self.parent.OnGo()
>>> File "/usr/local/phenix-1.3-rc2/phenix/wxGUI/Dialogs.py", line
>>> 470, in OnGo
>>> gp.RunStrategy()
>>> File "/usr/local/phenix-1.3-rc2/phenix/wxGUI/BMPTaskCanvas.py", line
>>> 1170, in RunStrategy
>>> self.RunRemotely()
>>> File "/usr/local/phenix-1.3-rc2/phenix/wxGUI/BMPTaskCanvas.py", line
>>> 1293, in RunRemotely
>>> prefs = PDSServerClient.GetPreferences()
>>> File "/usr/local/phenix-1.3-rc2/phenix/phenix/server/
>>> PhenixClient.py",
>>> line 201, in GetPreferences
>>> return self._remote_call('GetPreferences',arg,kw)
>>> File "/usr/local/phenix-1.3-rc2/phenix/phenix/server/
>>> PhenixClient.py",
>>> line 449, in _remote_call
>>> cPickle.dump(all,self.send,1)
>>> File
>>> "/usr/local/phenix-1.3-rc2/build/mac-intel-osx/base/
>>> Python.framework/Versions/2.5/lib/python2.5/socket.py",
>>> line 262, in write
>>> self.flush()
>>> File
>>> "/usr/local/phenix-1.3-rc2/build/mac-intel-osx/base/
>>> Python.framework/Versions/2.5/lib/python2.5/socket.py",
>>> line 249, in flush
>>> self._sock.sendall(buffer)
>>> socket.error: (32, 'Broken pipe'
>
> --
> Paul Adams
> Deputy Division Director, Physical Biosciences Division, Lawrence
> Berkeley Lab
> Adjunct Professor, Department of Bioengineering, U.C. Berkeley
> Vice President for Technology, the Joint BioEnergy Institute
> Head, Berkeley Center for Structural Biology
>
> Building 64, Room 248
> Tel: 510-486-4225, Fax: 510-486-5909
> http://cci.lbl.gov/paul
>
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 64R0121
> Berkeley, CA 94720, USA.
>
> Administrator: Delia Clark [ [EMAIL PROTECTED] ][ 1-510-486-6331 ]
> --
>
