Simulations with NAMD

From: Santanu Chatterjee (
Date: Fri Feb 05 2010 - 10:37:44 CST

   I am running a set of few hundred simulations with NAMD. I am running
each of these simulations in parallel
on 4 processors each. These simulations are supposed to be running for few
weeks. I noticed that some of
them died without finishing. At the end of the screen output file, I got the
following error message :

FATAL ERROR: Input/output error
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Input/output error

Stack Traceback:
  [0] CmiAbort+0x4f [0x7eb405]
  [1] _Z8NAMD_diePKc+0x62 [0x4b31e2]
  [2] _Z13write_dcdstepiiPfS_S_Pd+0x650 [0x4b41e0]
  [3] _ZN6Output14output_dcdfileEiiP11FloatVectorPK7Lattice+0x46c
  [4] _ZN6Output10coordinateEiiP6VectorP11FloatVectorR7Lattice+0x9b
  [6] CkDeliverMessageFree+0x21 [0x786a6b]
  [7] _Z15_processHandlerPvP11CkCoreState+0x4a9 [0x7860c9]
  [8] CsdScheduleForever+0xa2 [0x7f18a2]
  [9] CsdScheduler+0x1c [0x7f14a0]
  [10] _ZN7BackEnd7suspendEv+0xb [0x4bab01]
  [11] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x122 [0x6fc260]
  [12] TclInvokeStringCommand+0x91 [0x80cc78]
  [13] /afs/[0x842ac8]
  [14] Tcl_EvalEx+0x176 [0x84310b]
  [15] Tcl_EvalFile+0x134 [0x83ab14]
  [16] _ZN9ScriptTcl3runEPc+0x14 [0x6fb99e]
  [17] main+0x21b [0x4b69c3]
  [18] __libc_start_main+0xf4 [0x307f01d994]
  [19] _ZNSt8ios_base4InitD1Ev+0x3a [0x4b2b5a]
Fatal error on PE 0> FATAL ERROR: Input/output error

I am trying to understand the source of this error. I am sure that this is
not disk space issue. Can someone please help?


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