Some users have reported problems with PyMOL on SGI hardware, particularly after upgrading IRIX. We now know what it going on:
It seems that SGI broke the critical pthread library in several recent versions of IRIX. In order to get PyMOL and other pthread-dependent programs to run reliably on these versions, you'll need to install IRIX patch 5316 from SGI. http://support.sgi.com/ You will need a supportfolio account to d/l the patch, I think. Cheers, Warren --- Patch 5316 : Pthreads fixes for IRIX 6.5.18 through 6.5.21 [6.5.21f 6.5.21m 6.5.20f 6.5.20m 6.5.19f 6.5.19m 6.5.18f 6.5.18m] ---------------------------------------------------------------------------- ---- Relations This patch replaces the following patches: 5119, 5120 This patch has no known incompatibilities This patch fixes the following bugs: 804314 - MPI: Regression in MPI_Init_thread for -64 compiler option 865969 - #pragma optional in wrong spot in libpthread sources 866686 - Pthreads library tracing options should be documented 877668 - Need pt_t* from Pthread ID for SpeedShop 877670 - Sometimes get PT_SWITCH_IN after PT_DELETE event 878336 - Don't count callout time toward Pthread timeslice 879200 - Remove libc.c from Pthreads source 880842 - Pthreads changes for SpeedShop support 881230 - pthread and irix scheduler race condition 892326 - Need 881230 for 6.5.18-6.5.20 892842 - Pthread debugging broken on 6.5.21 ALPHA 898314 - Pthreads mutex/cv hanging since 6.5.18 899696 - Patch request for bug 898314 (pthreads) ----- > I have had problems running the newer 0.9x releases on > our R10K based SGIs with Irix 6.5.18 for some time now. > Comparing pymol 0.93 to pymol 0.86 I noticed you no longer > have the same contents in the ext directory. On the SGI, > pymol 0.86 had a bin subdirectory with python executables > whereas pymol 0.93 only has a ext/lib subdirectory. Is this > normal as I don't have python installed on the machines. Also > the sgi freeware python is still at 2.1.x whereas pymol 0.93 > expects 2.2. Thanks in advance for any clarifications.
