<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=ISO-8859-15">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Dear users,<br>
I would like to ask your help about understanding a problem i'm not
able to recognize by myself.<br>
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:<br>
<br>
<i>starting mdrun 'PVA head29tail in water'<br>
2500000 steps, 5000.0 ps.<br>
<br>
Step 0, time 0 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 83427404711319.468750, max 431899260485632.000000 (between
atoms 59 and 60)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
37 38 89.6 0.1530 124222742528.0000 0.1530<br>
38 41 89.1 0.1530 104382357504.0000 0.1530<br>
<br>
Step 0, time 0 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 56829711484907.867188, max 212898492186624.000000 (between
atoms 3 and 4)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
61 62 89.0 0.1530 1380386603008.0000 0.1530<br>
58 61 87.6 0.1530 669758914560.0000 0.1530<br>
58 59 89.2 0.1430 1994809540608.0000 0.1430<br>
59 60 90.0 0.1000 43189926887424.0000 0.1000<br>
57 58 88.3 0.1530 1126801342464.0000 0.1530<br>
54 57 85.9 0.1530 198269452288.0000 0.1530<br>
54 55 89.6 0.1430 1261346488320.0000 0.1430<br>
38 39 89.6 0.1430 156364750848.0000 0.1430<br>
39 40 90.0 0.1000 3183089549312.0000 0.1000<br>
</i><i> [...]<br>
18 21 89.9 0.1530 215265542144.0000 0.1530<br>
18 19 90.0 0.1430 872386920448.0000 0.1430<br>
19 20 90.0 0.1000 6085561286656.0000 0.1000<br>
95 96 90.0 0.1000 5006930477056.0000 0.1000<br>
97 98 89.7 0.1530 215830478848.0000 0.1530<br>
98 101 90.5 0.1530 232671739904.0000 0.1530<br>
98 99 90.0 0.1430 746076962816.0000 0.1430<br>
99 100 90.0 0.1000 6068662435840.0000 0.1000<br>
step 0: Water molecule starting at atom 6014 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
<br>
step 0: Water molecule starting at atom 7355 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Wrote pdb files with previous and current coordinates<br>
step 0<br>
Warning: 1-4 interaction between 37 and 40 at distance
3039839053625.364 which is larger than the 1-4 table size 2.200 nm<br>
These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>
if not, you should increase table-extension in your mdp file<br>
or with user tables increase the table size<br>
Warning: 1-4 interaction between 61 and 64 at distance
15924520737123.646 which is larger than the 1-4 table size 2.200
nm<br>
These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>
if not, you should increase table-extension in your mdp file<br>
or with user tables increase the table size<br>
ERROR: 0031-250 task 0: Segmentation fault<br>
ERROR: 0031-250 task 1: Segmentation fault<br>
<br>
</i>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 <i>"There is no domain decomposition for 7 nodes that
is compatible with the given box and a minimum cell size of
0.95625 nm"</i>, but for example 6 or 8 cpus give a successful
run).<br>
<br>
Can anyone understand what is the reason of this strange behaviour?<br>
Thanks,<br>
Marani Alessandro (HPC User support, CINECA - Italy)<br>
</body>
</html>