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

From: Narender Singh Maan (nsmaan_at_gmail.com)
Date: Mon Aug 17 2009 - 08:43:41 CDT

Yes the same with me (as Yingzhe). Once i corrected psf it was fine. For me
i actually built the system through charm-gui. And somehow the psf part for
waters was not right. So i deleted all the hydrogens of waters and
reconstructed with psfgen and it was fine after that.
-NS

On Mon, Aug 17, 2009 at 6:04 AM, Yoav Beck <ucbpybe_at_ucl.ac.uk> wrote:

> 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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