Re: About NAMD

From: Douglas Houston (DouglasR.Houston_at_ed.ac.uk)
Date: Tue Nov 18 2014 - 09:32:59 CST

Hi Dennis,

A late reply I know, but just in case you never were able to solve
this problem I can tell you that I have been encountering the same
error (my output below - I think it's the same error anyway).

I don't know what causes it - I have 6 machines that all read/write
from a NFS drive on a networked machine. An example: I started
separate jobs 4 days ago on all 6 nodes, 4 are still running and 2
failed with this error.

But moving the working directory to the local drives (i.e. inside the
boxes) has fixed the problem.

cheers,
Doug

WRITING COORDINATES TO DCD FILE AT STEP 23547000
WRITING COORDINATES TO RESTART FILE AT STEP 23547000
ERROR: Error on renaming file ionized_1st.restart.coor to
ionized_1st.restart.coor.old: Invalid cross-device link
FATAL ERROR: Unable to open binary file ionized_1st.restart.coor: File exists
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Unable to open binary file
ionized_1st.restart.coor: File exists

[0] Stack Traceback:
   [0:0] CmiAbort+0x7b [0xcbb3b5]
   [0:1] _Z8NAMD_errPKc+0x9d [0x5825bb]
   [0:2] _ZN6Output17write_binary_fileEPciP6Vector+0x19a [0xabcc7e]
   [0:3] _ZN6Output26output_restart_coordinatesEP6Vectorii+0x1b5 [0xabcac7]
   [0:4]
_ZN6Output10coordinateEiiP6VectorP11FloatVectorR7Lattice+0x132
[0xabc706]
   [0:5]
_ZN24CkIndex_CollectionMaster39_call_receivePositions_CollectVectorMsgEPvP16CollectionMaster+0x12b
[0x592e87]
   [0:6] CkDeliverMessageFree+0x21 [0xbf3e71]
   [0:7] _Z15_processHandlerPvP11CkCoreState+0x854 [0xbf2e5c]
   [0:8] CsdScheduleForever+0xa5 [0xcc200d]
   [0:9] CsdScheduler+0x1c [0xcc1c0e]
   [0:10] _ZN7BackEnd7suspendEv+0xb [0x58ac49]
   [0:11] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x1a1 [0xb30247]
   [0:12] TclInvokeStringCommand+0x88 [0xcf1158]
   [0:13] [0xcf3d77]
   [0:14] [0xcf5192]
   [0:15] Tcl_EvalEx+0x16 [0xcf59b6]
   [0:16] Tcl_FSEvalFileEx+0x151 [0xd57b61]
   [0:17] Tcl_EvalFile+0x2e [0xd57d1e]
   [0:18] _ZN9ScriptTcl4loadEPc+0x10 [0xb2f432]
   [0:19] _Z18after_backend_initiPPc+0x448 [0x586530]
   [0:20] main+0x3a [0x5860b2]
   [0:21] __libc_start_main+0xfd [0x3ddf01ee7d]
   [0:22] _ZNSt8ios_base4InitD1Ev+0x4a [0x54112a]
Fatal error on PE 0> FATAL ERROR: Unable to open binary file
ionized_1st.restart.coor: File exists

[douglas_at_itioc4 acetylAAAAAAAAamide_extend]$

On Tue, Jun 25, 2013 at 11:20 AM, Dennis Lam
<Dennis.Lam_at_cix.csi.cuny.edu> wrote:

> Hello,
> I have this problem when I run a job in NAMD using SMD.
> ERROR: Error on renaming file smd_4_2.restart.coor to
> smd_4_2.restart.coor.old: Invalid cross-device link
> FATAL ERROR: Unable to open binary file smd_4_2.restart.coor: File exists
> [0] Stack Traceback:
> [0:0] CmiAbort+0x95 [0xbb9dc5]
> [0:1] _Z8NAMD_errPKc+0x9d [0x582a99]
> [0:2] _ZN6Output17write_binary_fileEPciP6Vector+0x19a [0x9b601a]
> [0:3] _ZN6Output26output_restart_coordinatesEP6Vectorii+0x1a1 [0x9b5e61]
> [0:4]
> _ZN6Output10coordinateEiiP6VectorP11FloatVectorR7Lattice+0x164
> [0x9b5adc]
> [0:5]
> _ZN24CkIndex_CollectionMaster39_call_receivePositions_CollectVectorMsgEPvP16CollectionMaster+0x135
> [0x59359f]
> [0:6] CkDeliverMessageFree+0x21 [0xaee919]
> [0:7] _Z15_processHandlerPvP11CkCoreState+0x7ba [0xaed92a]
> [0:8] CsdScheduleForever+0xb6 [0xbc1196]
> [0:9] CsdScheduler+0x1c [0xbc0d74]
> [0:10] _ZN7BackEnd7suspendEv+0xb [0x58b0a3]
> [0:11] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x19a [0xa2ad68]
> [0:12] TclInvokeStringCommand+0x88 [0xbf8a68]
> [0:13] [0xbfb580]
> [0:14] [0xbfc966]
> [0:15] Tcl_EvalEx+0x16 [0xbfd146]
> [0:16] Tcl_FSEvalFileEx+0x151 [0xc5ef51]
> [0:17] Tcl_EvalFile+0x2e [0xc5f10e]
> [0:18] _ZN9ScriptTcl4loadEPc+0x10 [0xa29f2a]
> [0:19] _Z18after_backend_initiPPc+0x407 [0x586917]
> [0:20] main+0x3a [0x5864da]
> [0:21] __libc_start_main+0xfd [0x2aaaaba1ccdd]
> [0:22] _ZNSt8ios_base4InitD1Ev+0x72 [0x54119a]
> Any suggestions?
> Thanks,
> Dennis

_____________________________________________________
Dr. Douglas R. Houston
Lecturer
Institute of Structural and Molecular Biology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
http://tinyurl.com/douglasrhouston

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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