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
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BLDG 64R0121
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