Error on closing binary file

From: Seren Soner (seren.soner_at_gmail.com)
Date: Thu Jan 13 2011 - 06:42:50 CST

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Dear all,

I have NAMD_2.7_Linux-x86_64-ibverbs installed on our cluster, but during a
25,000,000 step run; after the coordinate file has been written for
20,410,500th step, an error has occured, and the simulation has stopped.

The error on the coordinate file is;

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 20410500
WRITING COORDINATES TO DCD FILE AT STEP 20410500
WRITING COORDINATES TO RESTART FILE AT STEP 20410500
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 20411000
FATAL ERROR: Error on closing binary file
m01_2kn6_wb_ion_0_50ns.restart.vel: No space left on device
[0] Stack Traceback:
  [0:0] CmiAbort+0x5c [0xb43c72]
  [0:1] _Z8NAMD_errPKc+0x9d [0x520de5]
  [0:2] _ZN6Output17write_binary_fileEPciP6Vector+0x137 [0x9863c3]
  [0:3] _ZN6Output25output_restart_velocitiesEiiP6Vector+0x249 [0x9883f5]
  [0:4] _ZN6Output8velocityEiiP6Vector+0xdb [0x9880b5]
  [0:5]
_ZN24CkIndex_CollectionMaster40_call_receiveVelocities_CollectVectorMsgEPvP16CollectionMaster+0x16c
 [0x533acc]
  [0:6] CkDeliverMessageFree+0x21 [0xa81da5]
  [0:7] _Z15_processHandlerPvP11CkCoreState+0x788 [0xa80df2]
  [0:8] CsdScheduleForever+0xa5 [0xb44c1f]
  [0:9] CsdScheduler+0x1c [0xb44820]
  [0:10] _ZN7BackEnd7suspendEv+0xb [0x5293b1]
  [0:11] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x140 [0x9e62e4]
  [0:12] TclInvokeStringCommand+0x91 [0xb6c0a8]
  [0:13] /share/apps/NAMD_2.7_Linux-x86_64-ibverbs/namd2 [0xba1ef8]
  [0:14] Tcl_EvalEx+0x176 [0xba253b]
  [0:15] Tcl_EvalFile+0x134 [0xb99f44]
  [0:16] _ZN9ScriptTcl3runEPc+0x14 [0x9e59e2]
  [0:17] _Z18after_backend_initiPPc+0x22b [0x524eb3]
  [0:18] main+0x3a [0x524c52]
  [0:19] __libc_start_main+0xf4 [0x39bfe1d994]
  [0:20] _ZNSt8ios_base4InitD1Ev+0x52 [0x51ff6a]

The error which SGE master tells me is,

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error on closing binary file
m01_2kn6_wb_ion_0_50ns.restart.vel: No space left on device

Fatal error on PE 0> FATAL ERROR: Error on closing binary file
m01_2kn6_wb_ion_0_50ns.restart.vel: No space left on device

However, I have around 700 GB's of space still left on the disk, and the
velocity file is around 900kb's of space.

Any ideas what the problem may be ?

Thanks,
Seren

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