From: Yoav Beck (ucbpybe_at_ucl.ac.uk)
Date: Mon Aug 17 2009 - 05:04:48 CDT
Dear Yingzhe,
If that's the problem then I have no idea how to track down those
errors. The psf file I am using was made during ionization and I did
inspect it, but couldn't find anything peculiar.
Cheers.
Yoav.
yzliu wrote:
> 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 <mailto: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 <mailto:nk.liuyz_at_gmail.com>
> ==============================
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