Re: Colvar on 2.7b2 win vs Linux MPI instalation

From: Branko (bdrakuli_at_chem.bg.ac.yu)
Date: Sat Jan 23 2010 - 05:32:48 CST

Hi Jerome,

Thanks a lot for advice, colvar file was i made under windows (i.e.
notpad :-) ). I'll try with dos2unix and let you know about results.
Kind regards

Branko

Jerome Henin wrote:
> 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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>>

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