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CCPNMR  March 2007

CCPNMR March 2007

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Subject:

Re: For the Mac Users

From:

Johnny Eugene Croy <[log in to unmask]>

Reply-To:

CcpNmr software mailing list <[log in to unmask]>

Date:

Wed, 28 Mar 2007 12:07:37 -0600

Content-Type:

text/plain

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text/plain (169 lines)

Wayne,

I get the same thing with my computer as well (using the new mesa libs)

GL_VENDOR = ATI Technologies Inc.
GL_RENDERER = ATI Radeon 9600 XT OpenGL Engine
GL_VERSION = 1.5 ATI-1.4.18

So I assume that Mesa is managing the OpenGL parts of the graphics.   
With this in mind, I thought that it might be better to have OpenGL  
handle its own graphics (cut out the middle man, Mesa) so I  
recompiled using the OpenGL native libraries (using gl.h file, found  
in /System/Libraries/Frameworks/OpenGL.Frameworks/Headers/) and NOT  
the mesa libs.  Again, I used the GLUT libraries that are requested  
from GLUT that was Fink downloaded.  Things appear to be the same  
when compiled using these libs, still a bit quicker but not much  
different from the Mesa compiled version.  Any thoughts?  Should it  
be quicker without using Mesa?

In a side note, it appears that when you compile analysis and use the  
OS X framework of GLUT, it calls the gl.h file that is located in / 
usr/X11R6/include/GL/.  If so, in my case (and I don't know for you)  
that is the header for the Mesa 3D graphics library.  So, I would  
assume that the graphics are being handled by Mesa and not directly  
by OpenGL.

- J

PS:  I hope that this makes sense...I am still a bit wet behind the  
ears when it comes to compiling UNIX stuff.

On Mar 28, 2007, at 10:54 AM, Wayne Boucher wrote:

> Hello,
>
> The one comment I have is on OpenGL/glut.  On my Mac the OpenGL is in
> /usr/X11R6 and the glut is in /System/Library/Frameworks/ 
> GLUT.framework
> and when I start up analysis it claims that these are native OpenGL  
> for
> the graphics card, not Mesa.  I think the latter is no real  
> improvement on
> Tk, generally.  So I get (on my Powerbook G4, so over a year old now,
> perhaps the Intel Macs do things differently):
>
>   GL_VENDOR = ATI Technologies Inc.
>   GL_RENDERER = ATI Radeon 9600 XT OpenGL Engine
>   GL_VERSION = 1.5 ATI-1.4.18
>
> Wayne
>
> On Wed, 28 Mar 2007, Johnny Croy wrote:
>
>> Hello everyone,
>>
>> We had the great opportunity to meet with Tim here in Boulder  
>> yesterday and
>> he gave me some suggestions to get analysis to run a bit more  
>> smoothly on my
>> Powerbook G4 1.5 Mhz machine.  As you all know, the core of  
>> analysis is
>> written and compiled in Python, but the graphics part of things is  
>> all done
>> in C code.  Tim suggested that I mess around with the  
>> environment.txt file
>> that is found in ccpnmr1.0/c.
>>
>> After messing around with this file and recompiling (just the C  
>> code using
>> make clean and make), I finally made some changes to the  
>> installCode.py
>> script (I edited this script so that when the environment.txt file  
>> was
>> generated it always contained these values).
>>
>> 1.  I changed the C complier flags in line 543 from
>>
>> CFLAGS = -O $(MALLOC_FLAG) $(FPIC_FLAG) $(XOR_FLAG)
>> to
>> CFLAGS = -O2 -mcpu=7450 -mtune=7450 $(MALLOC_FLAG) $(FPIC_FLAG) $ 
>> (XOR_FLAG)
>>
>> These changes allow the gcc complier to run in a more optimized  
>> fashion
>> which (I have been told) allows for faster binaries in the end.   
>> The -O2
>> flag sets the gcc complier to run in level 2 optimized mode.  The - 
>> mcpu and
>> -mtune flags are computer specific flags that again optimize gcc  
>> to your
>> specific computer platform.  Here is a bit more on these flags  
>> taken from a
>> thread that I found at
>> http://www.powerdeveloper.org/forums/viewtopic.php? 
>> p=1631&sid=3aac2aad5898ce8ce35c8705a659726a
>>
>>
>> "-mcpu=7450 tells GCC to support all instructions available on the
>> ppc7450-series (the 7447 which you find in the Pegasos is 7450- 
>> compatible,
>> the main difference between the 744x and 745x is that the latter  
>> supports
>> L3-cache).  Alternatively, this flag can be set to powerpc if you  
>> are not
>> sure.  I don't know what the correct setting is for the Intel Mac  
>> people,
>> but I am sure that you can find it on google!
>>
>> -mtune=7450 tells GCC to optimize for the 7450"
>>
>> 2.  Since I have a more than capable Open GL graphics card in my  
>> system, I
>> made some changes to the files that handle the 3D graphics when  
>> Open Gl is
>> used (Mesa and GLUT).
>>
>> I looked into the OS X framework for GLUT that is found in
>> /usr/X11R6/include/GL/gl.h.  According to the header in this file,  
>> this
>> version of mesa (which Mac OS X and hence analysis uses to handle  
>> the 3D
>> graphics when OpenGl is used) is a bit outdated (version 5.0.1 on my
>> machine, just vi this file and look at the header information).  I  
>> then used
>> fink to download and compile the latest version of Mesa (version  
>> 6.5.2, the
>> current version).
>>
>> 3.  With these updated and current files, I then recomplied  
>> analysis using
>> the C-flag optimized python script installCode.py.  Again here I  
>> used Fink
>> installed Tk/Tcl and Python2.5 options.  When asked by the script  
>> if I
>> wanted to use the Mac OS X Framework version of GLUT, I declined.   
>> I then
>> entered in the newly updated libraries from Mesa that I downloaded  
>> from Fink
>> and finished compiling as usual. Didn't have any problems with  
>> compiling
>> analysis and the test ran smoothly.
>>
>> Final thoughts:
>>
>> 1.  Analysis is running pretty smoothly with this new compiling  
>> scheme.  I
>> have a set of 3D assignment spectra (HNCA, HNCACB, HN(CO)CA, etc)  
>> that was
>> running pretty slowly in my analysis which was complied with the  
>> standard C
>> flags and Mac OS X GLUT.  Now, things are a bit more zippy and  
>> redraws
>> appear to be quicker!  Additionally, I can now run in the "on-the- 
>> fly" mode
>> instead of the precontoured mode which helps for looking at the  
>> really weak
>> peaks that are missed in the precontoured mode!  I am in the  
>> process of
>> transferring my data in from ANSIG, so I will give some updates on  
>> how the
>> program is running and the overall speed of things.
>>
>> If anyone has any suggestions to the above changes, please let me  
>> know.  I
>> will post any problems that I run across.  Good luck!
>>
>> - Johnny
>>

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