Re: FATAL ERROR: Tried to find atom type on node other than node 0

From: yzliu (nk.liuyz_at_gmail.com)
Date: Sat Aug 15 2009 - 11:06:10 CDT

Dear Yoav,

I have met the error because there are some mistakes on the my psf of water.

best wishes,

yingzhe

2009/8/13 Yoav Beck <ucbpybe_at_ucl.ac.uk>

> Dear all,
>
> When running md or minimization on my membrane protein complex on more than
> one processor (it seems to work fine with only one processor) I get this:
>
> Info: Entering startup at 35.8069 s, 14.2221 MB of memory in use
> Info: Startup phase 0 took 0.052151 s, 14.2222 MB of memory in use
> FATAL ERROR: Tried to find atom type on node other than node 0
> ------------- Processor 8 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Tried to find atom type on node other than node 0
>
> FATAL ERROR: Tried to find atom type on node other than node 0
> ------------- Processor 9 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Tried to find atom type on node other than node 0
>
> [8] Stack Traceback:
> [0] CmiAbort+0x5f [0xa4b62f]
> [1] _Z8NAMD_diePKc+0x62 [0x4ffe02]
> [2] _ZN8Molecule17build_atom_statusEv+0x1629 [0x88a8a5]
> [3] _ZN8Molecule16receive_MoleculeEP8MIStream+0xdb3 [0x88380d]
> [4] _ZN4Node11namdOneRecvEv+0x4b7 [0x8a0907]
> [5] _ZN4Node7startupEv+0xebe [0x89fcba]
> [6] _ZN12CkIndex_Node18_call_startup_voidEPvP4Node+0x12 [0x89edf8]
> [7] CkDeliverMessageFree+0x21 [0x9c2af1]
> [8] _Z15_processHandlerPvP11CkCoreState+0x509 [0x9c20e5]
> [9] Stack Traceback:
> [0] CmiAbort+0x5f [0xa4b62f]
> [1] _Z8NAMD_diePKc+0x62 [0x4ffe02]
> [2] _ZN8Molecule17build_atom_statusEv+0x1629 [0x88a8a5]
> [3] _ZN8Molecule16receive_MoleculeEP8MIStream+0xdb3 [0x88380d]
> [4] _ZN4Node11namdOneRecvEv+0x4b7 [0x8a0907]
> [5] _ZN4Node7startupEv+0xebe [0x89fcba]
> [6] _ZN12CkIndex_Node18_call_startup_voidEPvP4Node+0x12 [0x89edf8]
> [7] CkDeliverMessageFree+0x21 [0x9c2af1]
> [8] _Z15_processHandlerPvP11CkCoreState+0x509 [0x9c20e5]
> FATAL ERROR: Tried to find atom type on node other than node 0
> ------------- Processor 2 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Tried to find atom type on node other than node 0
>
> FATAL ERROR: Tried to find atom type on node other than node 0
> ------------- Processor 3 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Tried to find atom type on node other than node 0
>
> [9] CsdScheduleForever+0xa5 [0xa4c42d]
>
> I checked the mailing and saw people with similar problems but no answer. I
> am using 2.7b1 on a linux cluster.
>
> Any help or insight will be greatly appreciate.
>
> Thanks.
>
> Yoav.
>
>

-- 
==============================
Yingzhe Liu
PHD Student of Analytical Chemistry
Chemistry Department
Nankai University
Tianjin, P.R.China,30071
Email: nk.liuyz_at_gmail.com
==============================

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