3DNA Forum

Welcome => Bug reports => Topic started by: sharvey7 on October 14, 2016, 02:00:49 pm

Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · Reproduce DSSR · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Title: Trouble running 3DNA on a Macintosh
Post by: sharvey7 on October 14, 2016, 02:00:49 pm
I'm having trouble running 3DNA on my Mac.  I followed the installation instructions exactly, and all the files are in the appropriate directory, but when I run the "find_pair" command, it doesn't work.  Here's a log of my commands and the system's response:

Steve-Harveys-MacBook-Pro-2:bin steveharvey$ pwd

Steve-Harveys-MacBook-Pro-2:bin steveharvey$ ls
alc2img      blocview   ex_str      frame_mol   o1p_o2p      rebuild      stack2img   x3dna_ensemble
analyze      cehs      fiber      get_part   pdb2img      regular_dna   std_base   x3dna_setup
anyhelix   comb_str   find_pair   mutate_bases   r3d_atom   rotate_mol   step_hel   x3dna_utils

Steve-Harveys-MacBook-Pro-2:bin steveharvey$ ./find_pair -h
Illegal instruction: 4

Steve-Harveys-MacBook-Pro-2:bin steveharvey$ find_pair -h
-bash: find_pair: command not found

Title: Re: Trouble running 3DNA on a Macintosh
Post by: xiangjun on October 14, 2016, 02:46:41 pm
Hi Steve,

Thanks for posting the difficulty you experienced when trying to run 3DNA on Mac. A quick Google search with "Illegal instruction: 4 Mac" leads to the following link:

What version of Mac OS X are you using? Click the Apple icon on the upper-left corner, and then click "About This Mac" to get the info. As I am posting this message, my MacBook Air has "Version 10.11.6". Please post your info back.

The distributed version of 3DNA v2.3 for Mac was compiled with Mac OS 10.8 on SBGrid (https://sbgrid.org), which is more than 3 years old now. Since newer Mac OS X are free, so virtually all Mac users should be using newer versions than 10.8. I suspect yours may be older (10.6?). Certainly, you're the first one who's reported such an error message.

Alternatively, since 3DNA v2.3 is now distributed with source code, you could easily go to the src/ directory and type 'make'. Assuming you've the builder tools (Xcode/gcc) available on your Mac (which can compile the classic "Hello, World" C program), then everything should be alright. Have a try and let me know how it goes.


Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.