AMBER Archive (2007)

Subject: AMBER: SANDER bug

From: Ichinkhorloo Erdenebaatar (ichinkhorloo_erdenebaatar_at_hotmail.com)
Date: Tue Feb 13 2007 - 19:19:21 CST

Jagshemash! [means 'Hello Everybody!' in Mongolian]

I hope that everybody in the high-performance computing have
already heard about the "dynamic memory of AMBER" -- revolutionary
new concept routinely employed in recent releases of AMBER.
This radically new technology had already helped to dramatically
increase ... [5 more pages omitted -- I am on dial-up from
very center of the Ulaanbaatar, our glorious capital].

Careless usage of this ground-breaking, high-performance, technology
can sometimes lead to undesired results. As a matter of example,
let me draw your attention to the following "misfeature"
(I suspect this is a "bug"; on the other hand, it would be
too rude to use the word "bug" alone with "SANDER of AMBER" in
one e-mail; thus -- "misfeature"):

*************** subroutine sander()
*** 222,227 ****
--- 222,229 ----
        allocate( x(lastr), ix(lasti), ipairs(lastpr), ih(lasth), stat = ier
)
        REQUIRE( ier == 0 )

+ ix(1:lasti) = 0 ! hurts performance, @#$!@$#
+
        if(igb /= 0 .and. igb /= 10)call allocate_gb( natom, ncopy )

        if( idecomp > 0 ) then

Without this silly, performance (is 'performance' okay here? maybe
'intensity' would be better) hurting line 'ix(1:lasti) = 0' the SANDER
of AMBER does malfunctioning sometimes. In particular, a part of the
array determines whether apply SHAKE to some bond or not. If you are
lucky enough, the SANDER of AMBER will do SHAKE randomly without affecting
your results much; if you are not ... it will stop and suggest to
look for a 'deeper problem ...' (that what happened to me).

That is all for now. God bless FORTRAN !

Yours,
  Ichinkhorloo

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