> > Dear users, > I would like to ask your help about understanding a problem i'm not able > to recognize by myself. > Basically, a user of our sistem (IBM SP6, power6 architecture) is trying > to run a simulation of a very simple sistem, a polymer chain in a lot of > water molecules. While the simulation works perfectly in serial on her > local pc, when she tries to run it in SP6 using 2 cpus in parallel, the > simulation doesn't even start due of these errors: > > /starting mdrun 'PVA head29tail in water' > 2500000 steps, 5000.0 ps. > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 83427404711319.468750, max 431899260485632.000000 (between atoms 59 > and 60) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 37 38 89.6 0.1530 124222742528.0000 0.1530 > 38 41 89.1 0.1530 104382357504.0000 0.1530 > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 56829711484907.867188, max 212898492186624.000000 (between atoms 3 > and 4) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 61 62 89.0 0.1530 1380386603008.0000 0.1530 > 58 61 87.6 0.1530 669758914560.0000 0.1530 > 58 59 89.2 0.1430 1994809540608.0000 0.1430 > 59 60 90.0 0.1000 43189926887424.0000 0.1000 > 57 58 88.3 0.1530 1126801342464.0000 0.1530 > 54 57 85.9 0.1530 198269452288.0000 0.1530 > 54 55 89.6 0.1430 1261346488320.0000 0.1430 > 38 39 89.6 0.1430 156364750848.0000 0.1430 > 39 40 90.0 0.1000 3183089549312.0000 0.1000 > // [...] > 18 21 89.9 0.1530 215265542144.0000 0.1530 > 18 19 90.0 0.1430 872386920448.0000 0.1430 > 19 20 90.0 0.1000 6085561286656.0000 0.1000 > 95 96 90.0 0.1000 5006930477056.0000 0.1000 > 97 98 89.7 0.1530 215830478848.0000 0.1530 > 98 101 90.5 0.1530 232671739904.0000 0.1530 > 98 99 90.0 0.1430 746076962816.0000 0.1430 > 99 100 90.0 0.1000 6068662435840.0000 0.1000 > step 0: Water molecule starting at atom 6014 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > step 0: Water molecule starting at atom 7355 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > Wrote pdb files with previous and current coordinates > Wrote pdb files with previous and current coordinates > step 0 > Warning: 1-4 interaction between 37 and 40 at distance 3039839053625.364 > which is larger than the 1-4 table size 2.200 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > Warning: 1-4 interaction between 61 and 64 at distance > 15924520737123.646 which is larger than the 1-4 table size 2.200 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > ERROR: 0031-250 task 0: Segmentation fault > ERROR: 0031-250 task 1: Segmentation fault > > /The same errors occur when trying the simulation up to 4 cpus, but (and > that's the strange thing), everything works fine with 6+ cpus (actually, > there are some numbers giving an incompatibility error, like /"There is > no domain decomposition for 7 nodes that is compatible with the given > box and a minimum cell size of 0.95625 nm"/, but for example 6 or 8 cpus > give a successful run). > > Can anyone understand what is the reason of this strange behaviour? > Thanks, > Marani Alessandro (HPC User support, CINECA - Italy)
Hmm... Try "mdrun -pd %NUMPROC" -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
