From: Douglas Houston (DouglasR.Houston_at_ed.ac.uk)
Date: Wed Nov 26 2014 - 05:28:39 CST
Hi Norman,
a reasonable hypothesis; unfortunately we don't use samba.
cheers,
Doug
Quoting Norman Geist <norman.geist_at_uni-greifswald.de> on Wed, 19 Nov
2014 08:10:11 +0100:
> 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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_____________________________________________________
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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