Re: Colvar on 2.7b2 win vs Linux MPI instalation

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Fri Jan 22 2010 - 15:19:33 CST

Hi Branko,
Was the colvars config file edited under windows, by any chance? If
yes, it might be a DOS/Win-style new line (CR-LF) that is confusing
the Linux version of the parser. You could try treating the file with
dos2unix (either the command-line tool, or online:
http://www.dos2unix.org).
If it is the case, we will look into making the parser more CR-LF resistant.
Cheers,
Jerome

2010/1/22 Branko <bdrakuli_at_chem.bg.ac.yu>:
> We have a problem most probably in colvar module using Linux (self)compiled
> 2.7b2 on MPI.  Linux error is printed bellow; while exactly the same input
> proceeds smoothly under   win dual core processor. Colvar configuration file
> is attached. All suggestions are highly appreciated, thanks a lot in advance
>
> Branko
>
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing the collective variables module, version 20090807.
> colvars: Error: boolean values only are allowed for "analysis".
> colvars: If this error message is unclear, try recompile with
> -DCOLVARS_DEBUG.
> FATAL ERROR: Error in the collective variables module: exiting.
>
> [0] Stack Traceback:
>   [0] CmiAbort+0x25  [0xa605e5]
>   [1] _Z8NAMD_diePKc+0x72  [0x4ea0b2]
>   [2] _ZN16colvarproxy_namd11fatal_errorERKSs+0x70  [0x8574c0]
>   [3] _ZN12colvarmodule11fatal_errorERKSs+0x13  [0x7d4093]
>   [4] _ZN11colvarparse10get_keyvalERKSsPKcRbRKbNS_10Parse_ModeE+0x89e
> [0x7de4de]
>   [5] _ZN12colvarmoduleC1EPKcP11colvarproxy+0x603  [0x7ca823]
>   [6] _ZN16colvarproxy_namdC1Ev+0x364  [0x853484]
>   [7] _ZN10ComputeMgr14createComputesEP10ComputeMap+0x361  [0x55a851]
>   [8] _ZN12CkIndex_Node18_call_startup_voidEPvP4Node+0x269  [0x8cdff9]
>   [9] CkDeliverMessageFree+0x25  [0x9f8945]
>   [10] _Z15_processHandlerPvP11CkCoreState+0x529  [0x9f7f39]
>   [11] CsdScheduleForever+0x48  [0xa63a18]
>   [12] CsdScheduler+0x25  [0xa63ad5]
>   [13] _ZN7BackEnd7suspendEv+0xb  [0x4f493b]
>   [14] _ZN9ScriptTcl3runEPc+0x10e  [0x93ac4e]
>   [15] main+0x26a  [0x4eea6a]
>   [16] __libc_start_main+0xf4  [0x397341d994]
>   [17] _ZNSt8ios_base4InitD1Ev+0x39  [0x4e9829]
> p0_27470:  p4_error: : 1
> p0_27470: (10.734375) net_send: could not write to fd=4, errno = 32
>
> colvarsTrajFrequency    1
> colvarsRestartFrequency 10000
> analysis        on
>
>
> colvar {
>
>   name d
>
>   lowerBoundary  2.98
>   upperBoundary 9.82
>   width 0.01
>
>   distance {
>       group1  {
>          atomnumbers 1 3 5
>       }
>       group2  {
>          atomnumbers 16 17 18
>       }
>   }
> }
>
> colvar {
>   name gyration
>   lowerBoundary  3.90
>   upperBoundary 4.94
>   width 0.01
>
>   gyration {
>       atoms  {
>          atomNumbers 7 8 9 10 11 12 13 14 15 19 20 21 22 23 24 25 26
>       }
>     }
> }
>
> abf {
>   colvars d gyration
>   fullSamples    500
>   hideJacobian    no
>   outputFreq    1000
>   applyBias    yes
> }
>
>

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