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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