Re: [modeller_usage] Re: when does MODELLER hang

There is also the problem that windows text editors appear to put unreadable 
characters into, particularly, ali files meaning that modeller doeasn't read 
them in the way you intended. Thus they look alright but are not. This has been 
reported to this list before. It would also suggest using Linux.

Nigel

Quoting Antoine Leimgruber <>:

> >
> 
> Dear Jaimin,
> 
> although I would be very carefull in saying that a top file and an ali 
> file are "alright", the problem might be somewhere else.
> 
> I recall from you numerous emails that you are running under windows. I 
> did it once. From my experience, this is the time equation I get when 
> running on various platforms:
> 
> 2.2Ghz linux athlon = 1
> powermac G5 = 1.3
> windows2000 700Ghz Athlon = 10++
> 
> I agree with you that this list is not a complete benchmark, put there 
> are two points:
> 
> 1. I'm disappointed by the G5's performance, but this is not the 
> problem you are interested in.
> 2. Windows was slow, i.e. more than 10 times slower than my mac 
> notebook G4 800GHz. Actually, it was so slow, that 10 times does not 
> mean anything at all.
> 
> In conclusion, if you get stuck when generating the restraints (which 
> is a costly step anyway), it might actually work, but being so slow 
> you'd think it is stuck. At least if stuck does not mean "crashed". 
> Maybe RAM is the problem ? Is it swapping ?
> I recall that you said it was working on a linux PC, but that you were 
> not very fond of using linux. Maybe you will loose less time learning 
> this very usefull OS rather than fighting against your windows PC ? ;-)
> I strongly advise you to switch to linux.
> 
> 
> BR
> Antoine
> 
> >
> >
> >
> > Dear MODELLER users,
> >
> > Thank you for ur help so far.
> > One problem still persists. MODELLER hangs at one point after some 
> > time:
> >
> > Dynamically allocated memory at        amprmcns [B,kB,MB]:     17981749
> > 17560.
> > 301    17.149
> > openf5__224_> Open       11  OLD  SEQUENTIAL  galk.rsr
> > openf5__224_> Open       11  OLD  SEQUENTIAL  galk.rsr
> >
> > The TOP and ALI files are alright.
> > Please solve my problem.
> 
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> 
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> 


Dr. Nigel Lindsey
Senior Lecturer in Biomedical Sciences
Department of Biomedical Sciences
University of Bradford
Bradford
W.Yorks

Tel +44 01274 233567


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