Thank for you answer. Meanwhile, our user told us that she found the
ideal configuration for running her simulations; nevertheless, i linked
her this discussion in case she can find some interesting suggestion.
Cheers,
Alessandro
Il 16/01/2012 16.05, Matthew Zwier ha scritto:
Ciao,
I've seen this behavior (something running fine on one core but
failing on multiple cores, or certain multiples of cores) frequently.
It's almost always due to an unstable system. Have your user try
equilibrating longer, or minimize with flexible water before trying
equilibration. You can search the GROMACS web site for the phrase
blowing up for more information.
Cheers,
Matt Z.
On Mon, Jan 16, 2012 at 8:37 AM, Marani Alessandroa.mar...@cineca.it wrote:
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'
250 steps, 5000.0 ps.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 83427404711319.468750, max 431899260485632.00 (between atoms 59 and
60)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
37 38 89.60.1530 124222742528. 0.1530
38 41 89.10.1530 104382357504. 0.1530
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 56829711484907.867188, max 212898492186624.00 (between atoms 3 and
4)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
61 62 89.00.1530 1380386603008. 0.1530
58 61 87.60.1530 669758914560. 0.1530
58 59 89.20.1430 1994809540608. 0.1430
59 60 90.00.1000 43189926887424. 0.1000
57 58 88.30.1530 1126801342464. 0.1530
54 57 85.90.1530 198269452288. 0.1530
54 55 89.60.1430 1261346488320. 0.1430
38 39 89.60.1430 156364750848. 0.1430
39 40 90.00.1000 3183089549312. 0.1000
[...]
18 21 89.90.1530 215265542144. 0.1530
18 19 90.00.1430 872386920448. 0.1430
19 20 90.00.1000 6085561286656. 0.1000
95 96 90.00.1000 5006930477056. 0.1000
97 98 89.70.1530 215830478848. 0.1530
98101 90.50.1530 232671739904. 0.1530
98 99 90.00.1430 746076962816. 0.1430
99100 90.00.1000 6068662435840. 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)
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