Re: [AMBER-Developers] more on pme_setup problem

From: Lachele Foley <>
Date: Wed, 10 Mar 2010 12:15:08 -0500

I'm having a hell of a time with something that is probably a "compiler error," but to get assistance, I need to convince them it isn't a bug with Amber because "it doesn't happen with Gromacs." It is a most despicable bug, too (bug report #126 -- characters missing from output files).

Our Intel: 11.0 083
icc (ICC) 11.0 20090318
ifort (IFORT) 11.0 20090318

...sorry to whine. Just frustrated.

:-) Lachele
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
----- Original Message -----
From: case
Wed, 10 Mar 2010 11:12:47 -0500
Subject: [AMBER-Developers] more on
pme_setup problem
> I am ordinarily reluctant to assign problems as "compiler errors" since it
> is not uncommon for there to be subtle errors in our code that are only
> exposed with certain compilers or options.
> In this case, however, I am somewhat more willing to blame Intel.  Here
> are a few additional points of information:
> 1. It doesn't seem to be related to any recent code change: ifort 11.1 (069)
> gives the same failure for amber10 as for the amber11 in CVS.
> 2. In addition to working for various flavors of ifort 10, the current CVS
> code also works for ifort 11.0 (081) and ifort 11.1 (046).  I am working to
> narrow down further when the problem appears [known to fail for ifort 11.1
> (069), but I've not tested intermediate versions.]
> This kind of explains why all this has only come up recently: it is only
> quite recent versions of ifort that exhibit this behavior.  It seems to be
> related to the fact that pmemd is using a common block to pack module
> variables in a certain storage order.  [I'm not saying the code is wrong,
> just
> that this somehow seems to a part of the symptom.]
> If someone wants to look at this, here's a good question to start with:
> why does the use of "natom" in the check_neutral() subroutine in
> pme_setup.fpp
> not trigger a problem, whereas the very similar use in vdw_correct_setup()
> does trigger the error?  [Note: I've played with removing compiler
> optimzations, with no success.]
> However, it is not really a "solution" (to use Dan's phrase) to just tell
> people to go get an older compiler from intel, since (as far as I can see
> from
> Intel's web site) that is not such an easy thing to do.  If someone knows
> how
> this can be done, please post, and we'll get it on the wiki or the web site.
> ....more later....dac
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Received on Wed Mar 10 2010 - 09:30:04 PST
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