Re: amber-developers: latest tarballs for AmberTools and Amber10

From: Lachele Foley <lfoley.ccrc.uga.edu>
Date: Sat, 29 Mar 2008 16:10:01 -0400

> please report formatting changes...I thought we had found all of those.
> I suppose you could go ahead and post the TEST_FAILURES.diff file so we can
> see round-off problems as well.

When I first wrote, I'd only gotten AmberTools to install. I still don't have the main amber10 package installed on the i686 systems (a newer gcc/gfortran should work, and I'll get busy installing that...). But, I got it all installed on the ia64. I saved the test results from all the different tests into separate files (attached tar.bz2) so you can see for yourself what's up. The file names should explain. There are more "formatting" (?) issues on the ia64 than on the i686 system. I don't know how important some of them are. I'm sure, for example, that the "%s" in the middle of the jaguar file header is insignificant (this happens both systems). But, I don't know if this difference (ia64 only) is ok:

possible FAILURE: check 1b2t.mol2.dif
/usr/local/programs/amber10/test/antechamber/chemokine
26c26
< 20 N 26.668 2.825 1.285 N.am 1 GLN 0. 
---
>      20 N          26.668    2.825    1.285 N.am*     1 GLN      0.
... (skip a few similar lines)
49c49
<      43 ND1        31.505    5.900    2.809 N.pl3     2 HIS      0.
---
>      43 ND1        31.505    5.900    2.809 N.pl*     2 HIS      0.
If you want me to send any of the diff files referenced in the test results, just ask.
> I've fixed the INSTALL file.  The pdf files look ok, but please be specific
> where you see problems.
Sorry! I'll try to be more specific next time.
Speaking of...  The INSTALL file's parallel instructions (item 8) don't flow quite as well as the previous instructions.  They assume the person installing knows what "sander" and "pmemd" are -- and whether or not they want them.  It might be useful to add a sentence or two listing the programs that can be run in parallel before talking about them, referring the installer to the manual, etc.  
:-) Lachele
--
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
706-542-0263
lfoley.ccrc.uga.edu
----- Original Message -----
From: David A. Case
[mailto:case.scripps.edu]
To: amber-developers.scripps.edu
Sent: Fri, 28 Mar
2008 20:00:43 -0400
Subject: Re: amber-developers: latest tarballs for
AmberTools and Amber10
> On Thu, Mar 27, 2008, Lachele Foley wrote:
> 
> > Do you want to know about the "possible test failures" even if I don't
> > think the differences are very important, just so you know? Some look like
> > formatting changes that might make for easy fixes.  The rest are
> almost-same
> > numbers.  And, I got slightly different differences on the ia64 than on
> the
> > i686's, if that matters.
> 
> please report formatting changes...I thought we had found all of those.
> I suppose you could go ahead and post the TEST_FAILURES.diff file so we can
> see round-off problems as well.
> > 
> > ...and another minor note -- will amber be a tgz or a tar.bz2?  The
> > instructions are for tgz.  Most of us can work that out, but it might as
> > well match.
> 
> I've fixed the INSTALL file.  The pdf files look ok, but please be specific
> where you see problems.
> 
> ...thanks...dac
> 
>
Received on Fri Apr 18 2008 - 21:15:08 PDT
Custom Search