From: griadi_at_utalca.cl
Date: Fri Jun 02 2006 - 13:14:01 CDT
I would mv the *.old files to some other folder to start the bug checks, for the
error points that out.
Cheers,
Gonzalo.
Mensaje citado por Morad Alawneh <alawneh_at_chem.byu.edu>:
> *Dear namd users,
>
>
> I am running namd on the following system:
>
> Dell 1855 Linux cluster. Each node is equipped with two Intel Xeon EM64T
> processors (3.6GHz) and 4 GB of memory. The nodes are connected with
> Infiniband, a high-speed, low-latency copper interconnect.
>
>
> After submitting a job for equilibrating a system of 7000 atoms using
> NPAT, I got the following error in the log file:
>
> *WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 2300
> WRITING COORDINATES TO RESTART FILE AT STEP 2300
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 2300
> FINISHED WRITING RESTART VELOCITIES
> WRITING COORDINATES TO RESTART FILE AT STEP 2400
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 2400
> FINISHED WRITING RESTART VELOCITIES
> MOMENTUM: 2400 P: -386.09 -62.6697 31.0121 L: 1650.74 3783.66 -711.548
> PRESSURE: 2400 782.528 560.947 -914.258 603.496 -313.132 248.608
> -1067.54 291.696 -412.739
> GPRESSURE: 2400 849.091 727.376 -769.05 425.045 -520.431 94.9615
> -1312.61 59.3343 -170.688
> PRESSAVG: 2400 221.488 274.83 -182.226 324.747 -195.084 139 -308.64
> 215.067 88.5491
> GPRESSAVG: 2400 242.739 253.611 -172.625 344.895 -204.018 136.809
> -290.813 233.204 75.7252
> TIMING: 2400 CPU: 164.094, 0.0647402/step Wall: 176.866,
> 0.0867005/step, 1.14637 hours remaining, 150134 kB of memory in use.
> ENERGY: 2400 326.5744 1514.7628 608.9915
> 26.3488 -20476.7558 709.6410 35.7148
> 0.0000 4143.6286 -13111.0938 302.0233
> -13085.0334 -13083.1968 300.8514 18.8856
> 52.6571 61979.3625 38.3179 38.1486*
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 2400
> WRITING COORDINATES TO RESTART FILE AT STEP 2500
> FATAL ERROR: Error on renaming file res_sys_equil6.coor to
> res_sys_equil6.coor.old: File exists
> Stack Traceback:
> [0] CmiAbort+0x2b [0x6e6ea9]
> [1] _Z8NAMD_errPKc+0x79 [0x4a2059]
> [2] _Z16NAMD_backup_filePKcS0_+0xd4 [0x4a2204]
> [3] _ZN6Output26output_restart_coordinatesEP6Vectorii+0x104 [0x606b44]
> [4] _ZN6Output10coordinateEiiP6VectorP11FloatVectorR7Lattice+0x2de
> [0x606f0e]
> [5]
> _ZN16CollectionMaster16disposePositionsEPNS_21CollectVectorInstanceE+0x5b
> [0x4aad3b]
> [6] _ZN16CollectionMaster16receivePositionsEP16CollectVectorMsg+0x229
> [0x4aba79]
> [7] CkDeliverMessageFree+0x3a [0x69db98]
> [8] _Z15_processHandlerPvP11CkCoreState+0x213 [0x69f655]
> [9] CmiHandleMessage+0x28 [0x6e7f2f]
> [10] CsdScheduleForever+0x52 [0x6e80ee]
> [11] CsdScheduler+0xd [0x6e8073]
> [12] _ZN9ScriptTcl13runControllerEi+0x48 [0x638ef8]
> [13] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x129 [0x6395e9]
> [14] TclInvokeStringCommand+0x8b [0x70149b]
> [15] TclEvalObjvInternal+0x389 [0x702ca9]
> [16] Tcl_EvalEx+0x1a4 [0x704244]
> [17] Tcl_FSEvalFile+0x122 [0x742482]
> [18] Tcl_EvalFile+0x2e [0x7425be]
> [19] _ZN9ScriptTcl3runEPc+0x12 [0x638f12]
> [20] main+0x25b [0x4a38fb]
> [21] __libc_start_main+0xdb [0x3e5961c4bb]
> [22] fmod+0x9a [0x4a18da]
>
>
>
>
> Does any one have any idea how to solve this problem?
>
>
> Thanks
>
>
>
>
>
>
>
>
>
>
> *
> *--
> *
>
> *
> *
>
> *
> *
>
> */Morad Alawneh/*
>
> *Department of Chemistry and Biochemistry*
>
> *C100 BNSN, BYU*
>
> *Provo, UT 84602*
>
>
-------------------------------------------------
Este mensaje fue enviado por: http://webmail.utalca.cl
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