Re: Re: Colvar on 2.7b2 win vs Linux MPI instalation

From: Branko (bdrakuli_at_chem.bg.ac.yu)
Date: Tue Feb 09 2010 - 15:15:46 CST

Sorry for very late respond, but we have other (subjective :-) )
problems with MPI compilation. I could not guaranteed, but most likely
that conversion tool solve the problem. One more question Are using
of colvars slow down 2.7b2 when job is executing on MPI, is there any
problem with "parallelization"? Any advise is highly appreciated.

Sincerely

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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