AW: About NAMD

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Nov 19 2014 - 01:10:11 CST

This CAN be related to using a NFS share which is a samba share at the same
time. This seems to be incompatible in case of file locking and other stuff
and causes problems like this.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Douglas Houston
> Gesendet: Dienstag, 18. November 2014 16:33
> An: NAMD list
> Betreff: Re: namd-l: About NAMD
>
> 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_CollectVectorMsgE
> PvP16CollectionMaster+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_CollectVectorMsgE
> PvP16CollectionMaster+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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