Re: [ccp4bb] PHENIX question

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: offtopic-"colorful tag"
From: Nazzareno Dimasi ndimasi {- at -} GMAIL {- dot -} COM
Date: 2008-07-26

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Subject: Re: PHENIX question
From: aberndt {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK aberndt {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2008-07-26

Subject: Re: PHENIX question
From: Paul Adams PDAdams {- at -} LBL {- dot -} GOV
Date: 2008-07-26

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, aberndt@MRC-LMB.CAM.AC.UK 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
>> aberndt@mrc-lmb.cam.ac.uk
>>
>>
>> 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

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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: offtopic-"colorful tag"
From: Nazzareno Dimasi ndimasi {- at -} GMAIL {- dot -} COM
Date: 2008-07-26