LINCS errors, segfault on step 0 with cmake build but not autoconf
Created an attachment (id=423)
On my OS/X 10.4 build system using gcc, fftw3, and threads but no other options (defaults to 32-bit build), I get multiple LINCS errors and a segfault on step 0 with my cmake build but not with a build using autoconf. This is the git master as of Feb 8, 2010. The system is charmm/CMAP/vsites/GBSA. Sander reported seeing a similar issue for particular systems on a windows cmake build but not linux builds (that was an explicit-solvent system using AMBER03).
PS when there are constraints other than the vsites, mdrun will terminate with a fatal error. When no other constraints (different tpr), mdrun will segfault.
#3 Updated by Erik Lindahl over 10 years ago
This system seems to be using almost every single new feature in git-head in combination, and also using an old Mac architecture we no longer build for.
Could you try to isolate which new feature is causing it by selectively disabling threads, Cmake, GBSA, vsites?
#4 Updated by Peter Kasson over 10 years ago
Update: it fails on current git master autoconf build on merlot with mpi np 8 (system default mpicc) but runs in single-processor. Will test with gbsa off and update. Is there a clean way to strip vsites from a gro/top pair? (could manually delete and rerun pdb2gmx)
#7 Updated by Berk Hess over 10 years ago
I experienced crashes as well and I have found a fixed a bug.
There could be too little memory allocated with DD with a
twin-range cut-off setup combined with constraints or vsites.
I guess this also caused you problems.
Please check if the latest git version fixed it.