| Hi Edward,
Thanks for asking. It worked on my iMac running Mac OS X Lion 10.7.3 (11D50b). Installation went well, double clicking the icon opened the GUI interface without any problem. I just run R1 calculation to test the program after your E-mail. It worked fine and created all the output files, but I felt it was slower than Linux version. Thanks for making it working on the Mac OS. Hope this information is useful!
regards, Dhanas
On May 9, 2012, at 12:31 AM, Edward d'Auvergne wrote: Hi Dhanas, I was wondering if you have tried the relax-1.3.15 Mac OS X DMG file ( http://download.gna.org/relax/relax-1.3.15.Darwin.dmg)? Does this work on your system? Cheers, Edward On 5 April 2012 19:55, Muthu, Dhanasekaran - (dhanas) < dhanas@xxxxxxxxxxxxxxxxx> wrote: Edward,
I used relax-1.3_tickcount_fix.Darwin.dmg.
I really appreciate you are working on this.
Thanks,
Dhanas
On Apr 5, 2012, at 10:49 AM, Edward d'Auvergne wrote:
Hi Dhanas,
Could you say which DMG file you are using? I'm currently building an
entirely new Mac 'Framework' for Python/numpy/scipy/wxPython, and
hopefully I can use this to produce a working relax app for Lion
users.
Cheers,
Edward
On 5 April 2012 19:41, Muthu, Dhanasekaran - (dhanas)
<dhanas@xxxxxxxxxxxxxxxxx> wrote:
Hi Edward,
It is not working on my Mac machine running Lion. The icon bounces few times after double clicking. But do nothing.
-Dhanas Muthu
On Apr 5, 2012, at 8:32 AM, <relax-users-request@xxxxxxx> wrote:
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Today's Topics:
1. Re: Temperature calibration & relax @ Mac OS X 10.7.3 ?Lion?
(Edward d'Auvergne)
2. Re: Temperature calibration & relax @ Mac OS X 10.7.3 ?Lion?
(Martin Ballaschk)
3. Re: Temperature calibration & relax @ Mac OS X 10.7.3 ?Lion?
(Ben Eisenbraun)
4. Re: Temperature calibration & relax @ Mac OS X 10.7.3 ?Lion?
(Edward d'Auvergne)
5. Re: Temperature calibration & relax @ Mac OS X 10.7.3 ?Lion?
(Edward d'Auvergne)
6. Re: Temperature calibration & relax @ Mac OS X 10.7.3 ?Lion?
(Ben Eisenbraun)
----------------------------------------------------------------------
Message: 1
Date: Thu, 5 Apr 2012 15:31:53 +0200
From: "Edward d'Auvergne" <edward@xxxxxxxxxxxxx>
To: Ben Eisenbraun <bene@xxxxxxxxxxxxxxxxxxx>
Cc: "relax-users@xxxxxxx" <relax-users@xxxxxxx>
Subject: Re: Temperature calibration & relax @ Mac OS X 10.7.3 ?Lion?
Message-ID:
<CAED9pY_8JZLPeCxbwKdRDQaZrd6scOqW0dXG5Sk51=Fdoper0g@xxxxxxxxxxxxxx>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
I have now created a little ugly hack in the relax main 1.3 line to
work around the Mac Application problem with the missing
Carbon.Evt.TickCount error message (due to Python version issues).
This is as I described at
https://mail.gna.org/public/relax-users/2012-04/msg00021.html, the
command line argument emulation has been turned off relax now works
around this. I have created a special relax application DMG file for
testing at http://download.gna.org/relax/. The temporary file is
called relax-1.3_tickcount_fix.Darwin.dmg (with a md5sum of
d2b2c4455ea9783023d81e096e22072f). Could I ask anyone who is
suffering from, or who can trigger, this TickCount problem if you
could check and see if the problem is now eliminated?
Cheers,
Edward
On 5 April 2012 10:33, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
Hi Ben,
Thank you for that info, that will really help in solving some of
these problems! ?I never though that one of the issues is that of the
machine architecture. ?This is obviously a multi-layer, i.e. not just
one failure point, problem with the py2app script for converting
Python programs/scripts into full Mac Applications
(http://wiki.python.org/moin/MacPython/py2app,
http://svn.pythonmac.org/py2app/py2app/trunk/doc/index.html). ?I might
have to approach this in a number of ways, some fixes will probably
allow relax to run for some Mac users while others will not be so
lucky. ?In the first attack, I will try to eliminate this TickCount
problem. ?This seams to be a problem with program argument emulation
on the Mac with certain Python versions. ?A solution is posted at
http://stackoverflow.com/questions/3461983/evt-tickcount-not-found-with-python2-6-on-osx-10-6-3,
where the suggested code is:
APP = ['MyApp.py']
OPTIONS = {
? 'argv_emulation': False,
? ...
}
setup(
? ?app=APP,
? ?options={'py2app': OPTIONS},
? ?setup_requires=['py2app'],
)
In relax's py2app setup.py script, the 'argv_emulation' is currently
set to True (see
http://svn.gna.org/viewcvs/*checkout*/relax/1.3/setup.py?revision=15481&content-type=text%2Fplain).
?relax currently requires arguments, but maybe I can hack the code to
catch this and skip the argument processing. ?But only for this
situation as the prompt/scripting UI modes will be important for some
users.
This fix doesn't solve the problem of the py2app created relax app not
using the bundled Python version and internal Python modules, so some
users will still be affected by that. ?For some people this is not an
issue while for others it causes relax to fail.
A third problem might be in the wxPython code, as was seen and
reported by Jack Howarth when creating the Fink distribution of relax
(see the threads starting at
https://mail.gna.org/public/relax-users/2012-03/msg00053.html and
https://mail.gna.org/public/relax-users/2012-04/msg00003.html, and
http://pdb.finkproject.org/pdb/browse.php?name=relax). ?This will
probably also affect those who install relax from the sources
distribution file
(http://www.nmr-relax.com/download.html#Source_code_release). ?The
problem might require a workaround inside the relax GUI code. ?I will
try to tackle each problem one by one, and hopefully as each is solved
more and more users will have luck in running relax in GUI mode on the
Mac.
Cheers,
Edward
P. S. ?For those users who can currently run the relax application in
GUI mode from the DMG file, these fixes should not affect you.
On 4 April 2012 18:58, Ben Eisenbraun <bene@xxxxxxxxxxxxxxxxxxx> wrote:
Hi Edward,
I am seeing the same issues reported by others.
?$ open /programs/i386-mac/relax/1.3.14/relax.app
Output in Console.app:
4/4/12 12:15:26.639 PM [0x0-0x18a28a1].com.nmr-relax.relax: Traceback (most recent call last):
4/4/12 12:15:26.639 PM [0x0-0x18a28a1].com.nmr-relax.relax: ? File "/nfs/programs/i386-mac/relax/1.3.14/relax.app/Contents/Resources/__boot__.py", line 126, in <module>
4/4/12 12:15:26.640 PM [0x0-0x18a28a1].com.nmr-relax.relax: ? ? _argv_emulation()
4/4/12 12:15:26.640 PM [0x0-0x18a28a1].com.nmr-relax.relax: ? File "/nfs/programs/i386-mac/relax/1.3.14/relax.app/Contents/Resources/__boot__.py", line 124, in _argv_emulation
4/4/12 12:15:26.640 PM [0x0-0x18a28a1].com.nmr-relax.relax: ? ? _get_argvemulator().mainloop()
4/4/12 12:15:26.640 PM [0x0-0x18a28a1].com.nmr-relax.relax: ? File "/nfs/programs/i386-mac/relax/1.3.14/relax.app/Contents/Resources/__boot__.py", line 63, in mainloop
4/4/12 12:15:26.640 PM [0x0-0x18a28a1].com.nmr-relax.relax: ? ? stoptime = Evt.TickCount() + timeout
4/4/12 12:15:26.640 PM [0x0-0x18a28a1].com.nmr-relax.relax: AttributeError: 'module' object has no attribute 'TickCount'
4/4/12 12:15:26.715 PM relax: relax Error
This is a problem related to Carbon support in 32-bit vs 64-bit Python. I
can reproduce this on the command line in 10.6 and 10.7 like so:
?$ type python
python is hashed (/usr/bin/python)
?$ python
Python 2.7.1 (r271:86832, Jun 16 2011, 16:59:05)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
from Carbon import Evt
Evt.TickCount()
Traceback (most recent call last):
?File "<stdin>", line 1, in <module>
AttributeError: 'module' object has no attribute 'TickCount'
And it's because the 64-bit Python doesn't have full Carbon support:
?$ export VERSIONER_PYTHON_PREFER_32_BIT=true
?$ python
Python 2.7.1 (r271:86832, Jun 16 2011, 16:59:06)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
from Carbon import Evt
Evt.TickCount()
278493166
Similar thread here:
http://stackoverflow.com/questions/3461983/evt-tickcount-not-found-with-python2-6-on-osx-10-6-3
I can run the relax binary directly if I force 32-bit:
?$ arch -i386 relax.app/Contents/MacOS/relax
And I can get the relax.app bundle to work if I lipo the relax binary:
?$ mv relax relax.orig
?$ lipo -thin i386 -output relax relax.orig
I tried various other ways of forcing 32-bitness for Python: lipo'ing the
python binaries, export VERISONER_PYTHON_PREFER_32_BIT=true,
LSArchitecturePriority in the Info.plist without effect.
-ben
--
| Ben Eisenbraun
| SBGrid Consortium ? ? ? ? ? ? ? ? ? ? ? ? ?| http://sbgrid.org ? ? ? |
| Harvard Medical School ? ? ? ? ? ? ? ? ? ? | http://hms.harvard.edu ?|
------------------------------
Message: 2
Date: Thu, 5 Apr 2012 15:47:47 +0200
From: Martin Ballaschk <ballaschk@xxxxxxxxxxxxx>
To: "Edward d'Auvergne" <edward@xxxxxxxxxxxxx>
Cc: "relax-users@xxxxxxx" <relax-users@xxxxxxx>
Subject: Re: Temperature calibration & relax @ Mac OS X 10.7.3 ?Lion?
Message-ID: <64F7FCE8-479D-4EDB-ABCB-082234D076A8@xxxxxxxxxxxxx>
Content-Type: text/plain; charset=iso-8859-1
Hi Edward,
On 05.04.2012, at 15:31, Edward d'Auvergne wrote:
Could I ask anyone who is
suffering from, or who can trigger, this TickCount problem if you
could check and see if the problem is now eliminated?
Still failing here:
$ open relax.app
Console errors:
05.04.12 15:42:38,708 [0x0-0x625625].com.nmr-relax.relax: Please install the wx Python module to access the relax GUI.
$ cd /Applications/relax.app/Contents/MacOS/
$ ./relax
Please install the wx Python module to access the relax GUI.
$ ./python
python: posix_spawn: /Applications/relax.app/Contents/MacOS/python2.6: No such file or directory
But when forcing 32bit/i386 by using "arch" it works.
Cheers
Martin
--
Martin Ballaschk
AG Schmieder
Leibniz-Institut f?r Molekulare Pharmakologie
Robert-R?ssle-Str. 10
13125 Berlin
ballaschk@xxxxxxxxxxxxx
Tel.: +49-30-94793-234/315
B?ro: A 1.26
Labor: C 1.10
------------------------------
Message: 3
Date: Thu, 5 Apr 2012 10:20:54 -0400
From: Ben Eisenbraun <bene@xxxxxxxxxxxxxxxxxxx>
To: "Edward d'Auvergne" <edward@xxxxxxxxxxxxx>
Cc: "relax-users@xxxxxxx" <relax-users@xxxxxxx>
Subject: Re: Temperature calibration & relax @ Mac OS X 10.7.3 ?Lion?
Message-ID: <20120405142054.GA3371@xxxxxxxxxxxxxxxxxxx>
Content-Type: text/plain; charset=us-ascii
Hi Edward,
A solution is posted at
http://stackoverflow.com/questions/3461983/evt-tickcount-not-found-with-python2-6-on-osx-10-6-3,
I saw that suggestion when I read the thread yesterday. If you're willing
to give up the 64-bit version, this thread might also be useful:
http://stackoverflow.com/questions/7472301/how-to-force-py2app-to-run-app-in-32-bit-mode
This fix doesn't solve the problem of the py2app created relax app not
using the bundled Python version and internal Python modules, so some
users will still be affected by that.
Yesterday when I was looking at this, I added a 'print sys.executable' to
__boot__.py and got:
4/4/12 12:40:10.353 PM [0x0-0x18ac8ab].com.nmr-relax.relax: /nfs/programs/i386-mac/relax/1.3.14/relax.app/Contents/MacOS/python
And it doesn't change regardless of what PythonExecutable or
PyRunTimeLocation is set to in the Info.plist. So it appears that it is
calling the correct binary, but the Contents/MacOS/python is just a binary
wrapper for some other python? I suppose I should read the py2app docs at
some point.
-ben
--
| Ben Eisenbraun
| SBGrid Consortium | http://sbgrid.org |
| Harvard Medical School | http://hms.harvard.edu |
------------------------------
Message: 4
Date: Thu, 5 Apr 2012 16:49:08 +0200
From: "Edward d'Auvergne" <edward@xxxxxxxxxxxxx>
To: Ben Eisenbraun <bene@xxxxxxxxxxxxxxxxxxx>
Cc: "relax-users@xxxxxxx" <relax-users@xxxxxxx>
Subject: Re: Temperature calibration & relax @ Mac OS X 10.7.3 ?Lion?
Message-ID:
<CAED9pY-023FUeuHGVpDvwdk7R3RWxYbN_kLyV+YOoM5WZWASTw@xxxxxxxxxxxxxx>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
A solution is posted at
http://stackoverflow.com/questions/3461983/evt-tickcount-not-found-with-python2-6-on-osx-10-6-3,
I saw that suggestion when I read the thread yesterday. If you're willing
to give up the 64-bit version, this thread might also be useful:
http://stackoverflow.com/questions/7472301/how-to-force-py2app-to-run-app-in-32-bit-mode
Is it worth having a 64-bit x86 version? Would any Mac users need or
use this? I was hoping to distribute a working Universal binary.
Forcing the i386 architecture may cause problems for people on old ppc
machines, so I would like to find a more elegant solution than forcing
i386 on all Mac users. I could set the LSArchitecturePriority
Info.plist value to i386 and ppc in the py2app 'setup.py' script and
then recreate the app, then maybe this would be a solution. But there
must be a better way.
This fix doesn't solve the problem of the py2app created relax app not
using the bundled Python version and internal Python modules, so some
users will still be affected by that.
Yesterday when I was looking at this, I added a 'print sys.executable' to
__boot__.py and got:
4/4/12 12:40:10.353 PM [0x0-0x18ac8ab].com.nmr-relax.relax: /nfs/programs/i386-mac/relax/1.3.14/relax.app/Contents/MacOS/python
And it doesn't change regardless of what PythonExecutable or
PyRunTimeLocation is set to in the Info.plist. So it appears that it is
calling the correct binary, but the Contents/MacOS/python is just a binary
wrapper for some other python? I suppose I should read the py2app docs at
some point.
The Contents/MacOS/python file is strange. It is not python, but a
wrapper to the real Python binary (with a capital P) located somewhere
else in the relax.app file hierarchy. From memory (I cannot find the
docs at the moment), this is a special file which suppresses the
prompt mode of Python and allows it interact properly as a Mac
application (with the menus, dock, etc.).
I could be wrong, but the Mac Info.plist files seem to only be a front
to what is actually inside the app, so changing it does nothing. I
don't know why it is pointing to the wrong Python version, but this is
clearly a problem with the py2app script (or the relax setup.py
configuration file). The sys.executable print outs in the Mac Console
app should be correct though. I think I might now go and investigate
the wxPython install that comes with Xcode 3.2.6 using the 'file'
program. I wonder if these binaries are truly 'Universal'?
Cheers,
Edward
------------------------------
Message: 5
Date: Thu, 5 Apr 2012 17:15:59 +0200
From: "Edward d'Auvergne" <edward@xxxxxxxxxxxxx>
To: Martin Ballaschk <ballaschk@xxxxxxxxxxxxx>
Cc: "relax-users@xxxxxxx" <relax-users@xxxxxxx>
Subject: Re: Temperature calibration & relax @ Mac OS X 10.7.3 ?Lion?
Message-ID:
<CAED9pY_Q1kaOtN+sTDzPJpD7haGjE5TokUBRjV8KoQcs5W6sUQ@xxxxxxxxxxxxxx>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
Ok, that's great news. Using the 'open' command and forcing i386 will
allow the Python and Python modules bundled with the relax app to be
used rather than the system installed versions. I now know that I
have to go hunt down an Universal binary architecture problem. I have
a feeling that something that comes with Xcode 3.2.6 is not properly
set up as a Universal binary. But at least you can run relax by
forcing the machine architecture!
Cheers,
Edward
On 5 April 2012 15:47, Martin Ballaschk <ballaschk@xxxxxxxxxxxxx> wrote:
Hi Edward,
On 05.04.2012, at 15:31, Edward d'Auvergne wrote:
Could I ask anyone who is
suffering from, or who can trigger, this TickCount problem if you
could check and see if the problem is now eliminated?
Still failing here:
$ open relax.app
Console errors:
05.04.12 15:42:38,708 [0x0-0x625625].com.nmr-relax.relax: Please install the wx Python module to access the relax GUI.
$ cd /Applications/relax.app/Contents/MacOS/
$ ./relax
Please install the wx Python module to access the relax GUI.
$ ./python
python: posix_spawn: /Applications/relax.app/Contents/MacOS/python2.6: No such file or directory
But when forcing 32bit/i386 by using "arch" it works.
Cheers
Martin
--
Martin Ballaschk
AG Schmieder
Leibniz-Institut f?r Molekulare Pharmakologie
Robert-R?ssle-Str. 10
13125 Berlin
ballaschk@xxxxxxxxxxxxx
Tel.: +49-30-94793-234/315
B?ro: A 1.26
Labor: C 1.10
------------------------------
Message: 6
Date: Thu, 5 Apr 2012 11:31:51 -0400
From: Ben Eisenbraun <bene@xxxxxxxxxxxxxxxxxxx>
To: "Edward d'Auvergne" <edward@xxxxxxxxxxxxx>
Cc: "relax-users@xxxxxxx" <relax-users@xxxxxxx>
Subject: Re: Temperature calibration & relax @ Mac OS X 10.7.3 ?Lion?
Message-ID: <20120405153151.GA5314@xxxxxxxxxxxxxxxxxxx>
Content-Type: text/plain; charset=us-ascii
Hi Edward,
Is it worth having a 64-bit x86 version?
Does relax need to access more than 4 GB of RAM per process/thread? I think
that's still the main deciding factor in the 32/64-bit choice. Apple claims
that 64-bit apps can see a 5-15% performance increase depending on workload
due to the extra general purpose CPU registers available in 64-bit mode.
*shrug*
Among my user population, we have very few PPC users left. The stats from
our ~425 OS X users in March:
https://developer.sbgrid.org/~bene/consortium-stats/four.html
https://developer.sbgrid.org/~bene/consortium-stats/five.html
Given the current difficulties, my suggestion would be to simplify,
simplify, simplify. :-) Once you have a stable package that is working for
the most common platforms, i.e. OS X Intel 10.6/7, then add more options as
necessary to satisfy the corner cases.
As an aside, the linux packages work great on every distro I've tested:
Red Hat/CentOS 5 and 6, Ubuntu 10.10 and 11.10, Debian 6, 32 and 64-bit for
all of them.
-ben
--
| Ben Eisenbraun
| SBGrid Consortium | http://sbgrid.org |
| Harvard Medical School | http://hms.harvard.edu |
------------------------------
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Re: relax-users Digest, Vol 69, Issue 12