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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this version of mesa (which Mac OS X and hence analysis uses to handle the 3D graphics when OpenGl is used) is a bit outdated (version 5.0.1 on my machine, just vi this file and look at the header information).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