From: Narender Singh Maan (nsmaan_at_gmail.com)
Date: Thu Jul 09 2009 - 10:47:11 CDT
Hi,
Like Goutham said, single processor runs fine for me too.
Do you think its because of the system's atom numbering? Since i have ~300K
atoms, after 99999 the numbering has some alphabets also (the system was
built using membrane builder module of charmm-gui..
http://www.charmm-gui.org/?doc=input/membrane ..) ..i.e.
.............
ATOM 99991 H1 TIP3T 766 11.976 31.791 -48.664 1.00 0.00 TIP2
ATOM 99992 H2 TIP3T 766 11.976 31.791 -48.664 1.00 0.00 TIP2
ATOM 99993 OH2 TIP3T 767 6.017 29.320 -54.546 1.00 0.00 TIP2
ATOM 99994 H1 TIP3T 767 5.024 29.223 -54.592 1.00 0.00 TIP2
ATOM 99995 H2 TIP3T 767 5.024 29.223 -54.592 1.00 0.00 TIP2
ATOM 99996 OH2 TIP3T 768 2.133 32.639 -44.707 1.00 0.00 TIP2
ATOM 99997 H1 TIP3T 768 2.158 33.255 -45.491 1.00 0.00 TIP2
ATOM 99998 H2 TIP3T 768 2.158 33.255 -45.491 1.00 0.00 TIP2
ATOM 99999 OH2 TIP3T 769 -1.371 26.075 -54.758 1.00 0.00 TIP2
ATOM 186a0 H1 TIP3T 769 -1.957 26.104 -53.951 1.00 0.00 TIP2
ATOM 186a1 H2 TIP3T 769 -1.957 26.104 -53.951 1.00 0.00 TIP2
ATOM 186a2 OH2 TIP3T 770 6.374 26.444 -46.366 1.00 0.00 TIP2
ATOM 186a3 H1 TIP3T 770 5.553 25.977 -46.684 1.00 0.00 TIP2
ATOM 186a4 H2 TIP3T 770 5.553 25.977 -46.684 1.00 0.00 TIP2
ATOM 186a5 OH2 TIP3T 771 0.744 32.258 -55.487 1.00 0.00 TIP2
ATOM 186a6 H1 TIP3T 771 0.833 32.811 -56.313 1.00 0.00 TIP2
ATOM 186a7 H2 TIP3T 771 0.833 32.811 -56.313 1.00 0.00 TIP2
ATOM 186a8 OH2 TIP3T 772 4.202 25.430 -47.270 1.00 0.00 TIP2
ATOM 186a9 H1 TIP3T 772 3.401 25.120 -47.763 1.00 0.00 TIP2
ATOM 186aa H2 TIP3T 772 3.401 25.120 -47.763 1.00 0.00 TIP2
ATOM 186ab OH2 TIP3T 773 3.085 35.701 -51.197 1.00 0.00 TIP2
ATOM 186ac H1 TIP3T 773 3.689 34.920 -51.092 1.00 0.00 TIP2
ATOM 186ad H2 TIP3T 773 3.689 34.920 -51.092 1.00 0.00 TIP2
ATOM 186ae OH2 TIP3T 774 1.561 31.245 -42.655 1.00 0.00 TIP2
ATOM 186af H1 TIP3T 774 1.826 31.737 -43.482 1.00 0.00 TIP2
ATOM 186b0 H2 TIP3T 774 1.826 31.737 -43.482 1.00 0.00 TIP2
On Thu, Jul 9, 2009 at 10:49 AM, Chris Harrison <char_at_ks.uiuc.edu> wrote:
> Goutham,
>
> Which version of namd are you using; ie, 2.6 vs 2.7b1?
> Was it compiled from source or downloaded as a binary?
> Is it a from the CVS? If so, when?
> Which version of charm++ are you using?
> Are you using MPI ? If so, which flavor and which version?
>
> Chris
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
>
>
>
> On Mon, Jul 6, 2009 at 4:10 PM, Goutham <gouthambs_at_gmail.com> wrote:
>
>> Hey All,
>> When I do a MD run using Charmrun and namd, I get the following error:
>>
>> FATAL ERROR: Tried to find atom type on node other than node 0
>>
>> However, when I do a single processor run, without charmrun, the error
>> doesn't occur. And the program works just fine. Does any one have any idea
>> on what is happening here?
>>
>> Thanks
>> Goutham
>>
>> PS: Stack Trace -
>>
>> FATAL ERROR: Tried to find atom type on node other than node 0
>> [1] 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] CsdScheduleForever+0xa5 [0xa4c42d]
>> [10] CsdScheduler+0x1c [0xa4c02e]
>> [11] _Z11master_initiPPc+0x280 [0x508c20]
>> [12] _ZN7BackEnd4initEiPPc+0x31 [0x508999]
>> [13] main+0x2f [0x50432f]
>> [14] __libc_start_main+0xdb [0x3486b1c3fb]
>> [15] _ZNSt8ios_base4InitD1Ev+0x4a [0x4ff76a]
>>
>>
>
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