[gmx-users] Crashes caused by particles communicated to PME node

[Bert]

Hi gmx-users,

My system has a 7*7*22 box and 3dc geometry for PME is applid (large vacuum
space is in the z direction. I found a crash caused by particles
communicated to PME node. Note that this problem had a fix already (
http://www.gromacs.org/component/option,com_wrapper/Itemid,90/), I was
afraid that it would not be fixed in PME3DC, because this problem did not
occur when I shift to geometry=3d. Both 4.0rc1 and the latest CVS version
had this error. Thanks for your suggestions.


-----------------------------------------------------output-------------------------------------------------------------------------
Step 695, time 1.39 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000001, max 0.000003 (between atoms 4610 and 4616)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4570   4576   30.6    0.1000   0.1000      0.1000

Step 696, time 1.392 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000001, max 0.000004 (between atoms 4486 and 4492)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4570   4576   34.3    0.1000   0.1000      0.1000

Step 697, time 1.394 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000002, max 0.000011 (between atoms 464 and 470)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 697, time 1.394 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000001, max 0.000004 (between atoms 6586 and 6592)

Step 697, time 1.394 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000001, max 0.000003 (between atoms 3794 and 3800)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 697, time 1.394 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000001, max 0.000004 (between atoms 5850 and 5856)
   6038   6044   47.9    0.1000   0.1000      0.1000
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4728   4734   30.9    0.1000   0.1000      0.1000
    904    910   58.9    0.1000   0.1000      0.1000
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 697, time 1.394 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.248747, max 2.690606 (between atoms 3676 and 3682)
   4570   4576   30.1    0.1000   0.1000      0.1000
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3676   3682   90.0    0.1000   0.3691      0.1000
Wrote pdb files with previous and current coordinates

-------------------------------------------------------
Program mdrun, VERSION 4.0_rc1
Source code file: pme.c, line: 518

Fatal error:
2 particles communicated to PME node 2 are more than a cell length out of
the domain decomposition cell of their charge group
-------------------------------------------------------

"Wicky-wicky Wa-wild West" (Will Smith)

Error on node 2, will try to stop all the nodes
Halting parallel program mdrun on CPU 2 out of 8

gcq#263: "Wicky-wicky Wa-wild West" (Will Smith)

-----------------------------------------------------------------------------
One of the processes started by mpirun has exited with a nonzero exit
code.  This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.

PID 15418 failed on node n0 (127.0.0.1) with exit status 1.
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