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 >