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

From: Narender Singh Maan (nsmaan_at_gmail.com)
Date: Mon Jul 13 2009 - 10:46:47 CDT

Hello,
This is the reply I got from our cluster maintenance support:
.........................................
The first time we saw the error was with version 2.6 This is our standard
installation, however I'm not sure if this was compiled from source or not.
This version uses mvapich 1

I installed 2.7b1 from the downloaded source distribution, not from the CVS
distribution. I compiled it with gcc 4.1.2 and openmpi 1.2.6. I created my
own "architecture", which was basically Linux-x86_64-g++ where I replaced
the compilers with mpicc and mpic++. I used the included charm-6.1.
............................................

Thank you
narender

On Thu, Jul 9, 2009 at 10:39 AM, Chris Harrison <char_at_ks.uiuc.edu> wrote:

> Singh,
>
> Did you download binaries or compile: a) 2.6, and b) 2.7b1?
> If you compiled did you download the source code from CVS? If so, when?
> What version of charm++ are you using?
>
> 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 Thu, Jul 9, 2009 at 9:00 AM, Narender Singh Maan <nsmaan_at_gmail.com>wrote:
>
>> Hello,
>> I am trying to do simulation of a fairly large system (~300K atoms). The
>> EM runs fine using multiple nodes but not the MD. I am using 2.6 version. I
>> tried doing it on two different clusters (and version 2.7b1 also) but
>> getting the same error each time .
>> ..............................
>> Info: 181713 RIGID BONDS
>> Info: 451053 DEGREES OF FREEDOM
>> Info: 77560 HYDROGEN GROUPS
>> Info: TOTAL MASS = 1.29591e+06 amu
>> Info: TOTAL CHARGE = 5.40633e-05 e
>> Info: *****************************
>> Info: Entering startup phase 0 with 37950 kB of memory in use.
>> Info: Entering startup phase 1 with 37950 kB of memory in use.
>> 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
>> FATAL ERROR: Tried to find atom type on node other than node 0
>> Stack Traceback:
>> FATAL ERROR: Tried to find atom type on node other than node 0
>> Stack Traceback:
>> Stack Traceback:
>> Stack Traceback:
>> Stack Traceback:
>> FATAL ERROR: Tried to find atom type on node other than node 0
>> Stack Traceback:
>> ....................
>> ....................
>> FATAL ERROR: Tried to find atom type on node other than node 0
>> Stack Traceback:
>> FATAL ERROR: Tried to find atom type on node other than node 0
>> Stack Traceback:
>> Stack Traceback:
>> Stack Traceback:
>> Stack Traceback:
>> ....................
>> ...................
>> Stack Traceback:
>> [0] CmiAbort+0x1fffffffff80b470 [0x40000000007495a0]
>> [1] _Z8NAMD_diePKc+0x1fffffffff240f80 [0x400000000017f0c0]
>> [2] _ZN8Molecule17build_atom_statusEv+0x1fffffffff5939e0
>> [0x40000000004d1b30]
>> [3] _ZN8Molecule16receive_MoleculeEP8MIStream+0x1fffffffff59fc60
>> [0x40000000004dddc0]
>> [4] _ZN4Node11namdOneRecvEv+0x1fffffffff5cc000 [0x400000000050a170]
>> [5] _ZN4Node7startupEv+0x1fffffffff5cb6a0 [0x4000000000509820]
>> [6] _ZN12CkIndex_Node18_call_startup_voidEPvP4Node+0x1fffffffff5fdca0
>> [0x4000000000508d40]
>> [7] CkDeliverMessageFree+0x1fffffffff76e6b0 [0x40000000006ac840]
>> [8] _Z15_processHandlerPvP11CkCoreState+0x1fffffffff773110
>> [0x40000000006ac460]
>> [9] CmiHandleMessage+0x1fffffffff80cd80 [0x400000000074af20]
>> ...................
>> ...................
>>
>> Could anyone please help me out on whats going on....
>> Thank you
>> Singh
>>
>>
>

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