AMBER Archive (2009)

Subject: Re: [AMBER] Installation on MacOSX

From: David Watson (dewatson_at_olemiss.edu)
Date: Tue Dec 15 2009 - 06:54:06 CST

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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