AMBER Archive (2009)

Subject: Re: [AMBER] Installation on MacOSX

From: Alan (alanwilter_at_gmail.com)
Date: Tue Dec 15 2009 - 10:11:20 CST

Thanks David W. It's reassuring.

Let me suggest you to make a 'wiki' of how to install AmberTools/Amber on
Mac Snow Leopard. This is precious information.

Cheers,
Alan

On Tue, Dec 15, 2009 at 12:54, David Watson <dewatson_at_olemiss.edu> wrote:

> On Dec 15, 2009, at 4:26 AM, Alan wrote:
>
> > Hi David W! I always follow anything you wright about Amber on Mac and
> best
> > Xmas gift would Ambertools 1.3. And thanks for your offlist emails with
> > tips.
> >
> > I didn't check today, but did Intel finally release its compilers to work
> > with Snow Leopard? There were serious issues about it.
> >
> > Your recipe AFAIR is for 32 bits only right?
> >
>
> SurferRosa:ddi dewatson$ file /usr/local/amber10/bin/sander*
> /usr/local/amber10/bin/sander: Mach-O 64-bit executable x86_64
> /usr/local/amber10/bin/sander.LES: Mach-O 64-bit executable x86_64
> /usr/local/amber10/bin/sander.LES.MPI: Mach-O 64-bit executable x86_64
> /usr/local/amber10/bin/sander.MPI: Mach-O 64-bit executable x86_64
> SurferRosa:ddi dewatson$ file /usr/local/amber10/bin/pmemd
> /usr/local/amber10/bin/pmemd: Mach-O 64-bit executable x86_64
>
> Looks all 64 bit to me :)
>
> > And do you still see this with intel MKL (excerpt from another email):
> >
> > "I got the absolute values identical to
> 1rrb_vac_distcovarmat_evecs.dat.save
> > except for the sign where with MKL they were inverted (like a matrix
> > multiplied by -1), e.g.:
> >
> > 537c537
> > < 0.00237 -0.00485 0.00133 0.00259 -0.00563 0.00178
> > 0.00236 (save)
> >> -0.00237 0.00485 -0.00133 -0.00259 0.00563 -0.00178
> > -0.00236 (mine)"
> >
>
> Lets see, do we still have those pesky vectors?
>
> SurferRosa:ddi dewatson$ grep -i -A 1 -B 2 "FAIL"
> /usr/local/amber10/test/make_at.txt
> ==============================================================
> diffing 1rrb_vac_mwcovarmat_evecs.dat.save with
> 1rrb_vac_mwcovarmat_evecs.dat
> possible FAILURE: check 1rrb_vac_mwcovarmat_evecs.dat.dif
> ==============================================================
> --
> cd antechamber/tp && ./Run.tp
> diffing tp.mol2.save with tp.mol2
> possible FAILURE: check tp.mol2.dif
> ==============================================================
> --
> cd antechamber/guanine_amber && ./Run.guanine_amber
> diffing DGN.mol2.save with DGN.mol2
> possible FAILURE: check DGN.mol2.dif
> ==============================================================
> --
>
> Unfortunately, yes.
> Maybe (crosses fingers) fixed in AT1.3?
> I'm fairly certain that it's MKL related, though.
>
> This is with Intel 11.1 (067).
> I haven't tried to recompile with 11.1 (076) yet.
>
>
> _______________________________________________
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> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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