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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