Re: AMBER: Implicit precision in sander vs architecture

From: Robert Duke <>
Date: Mon, 20 Oct 2003 09:01:47 -0400

Stephane -
In theory, at least from my perspective, the programming language, be it
fortran 77, fortran 95, C, or whatever, should basically be where the
precision is determined in calculations. This is certainly the intention in
the various fortrans, and fortran 90/95 tries to abstract itself even
further from the machine by the concept of "kind" (they are almost reluctant
to let you figure out how many bytes are in a datatype - very annoying for
system-oriented guys), as well as functions that explicitly let you
determine ranges of values. If you know anything about C programming, they
actually at one point tied the language data types more to the machine than
to the precision and range of values available. Thus an "int" was the "best
length" of integer to use on a given machine, which basically meant it was
what fit in the base register set of the chip, and gave the best
performance. Never mind that it might overflow because it was 16 bits and
you needed 32, it was fastest, and that was what matters. This mess was
ameliorated somewhat with the introduction of defined constants in limits..h,
but C, to my way of thinking remains annoying to work with on the issues of
range and precision on a variety of platforms. SO, my point in all of this
is that in theory the guy who wrote the code should have defined the
necessary precision for the software. Now, several things mess this up.
First of all, when you look at different machines, some cpu's implement more
precision than promised by the underlying data type. So for instance, the
intel chips have a widely used 80 bit internal precision floating point mode
(note, every time you store something in an array, you just rounded to 64
bits, though). Other chips may have more precision for various reasons.
For instance, the ibm power 3/4 architecture chips can combine at least two
operations (like addition and multiplication) with less loss of precision
than would be implied by the number of bits in the operand. Because of
these architecture-specific issues, there are a slew of options available in
the various compilers to control precision, especially floating point
precision, and they also of course affect performance. I tend to select
options that give compliance to IEEE standards while at the same time giving
good performance. In the amber group, I have heard the opinion expressed
that folks don't worry about being consistent on this stuff because it is
all below various other sources of noise; I agree but like to see close
agreement between two machines, at least for a few hundred steps. Then
there is the networking. Here the order of operations becomes
indeterminate, so you get different rounding errors from run to run. This
is even slighltly more pronounced on pmemd, because it does dynamic load
balancing. Thus, if in one calculation one cpu slows down for some external
reason, it will have less workload than say in the average run, and the
order of operations (basically adding forces) will be affected (note when I
say "order of operations" here, I am speaking about the order of doing
specific additions, multiplications, or whatever, and this ordering affects
the rounding errors that actually occur; in computer science, when one
refers to order of operations, one is more often referring to operation
ordering implicit in expressions by operator precedence (eg., multiplication
has higher precedence than addition, so 3 + 4 * 5 is 23, not 35)).
Now, the sad truth is that all the above is really mostly academic to just
about everybody but guys like me that are worrying about whether their
software is doing the right thing. 1) The actual errors from all the
various force field assumptions are huge in comparison. 2) The actual
errors from the choice of numerical methods are huge in comparison. 3) And
floating point implemented on computers is really a bigger inaccurate mess
than is widely appreciated. For 1), just run different MD implementations.
For 2), a book by Hamming is wonderful - R. W. Hamming, "Numerical Methods
for Scientists and Engineers", Dover. For 3) there is a great review - D.
Goldberg, "What Every Computer Scientist Should Know About Floating-Point
Arithmetic", ACM Computing Surveys, Vol 23, pp 5-48 (1991). I am basically
a systems guy at heart and love integers. ;-)
Regards - Bob

----- Original Message -----
From: "Teletchéa Stéphane" <>
To: <>
Sent: Monday, October 20, 2003 4:45 AM
Subject: Re: AMBER: Implicit precision in sander vs architecture

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Received on Mon Oct 20 2003 - 14:53:01 PDT
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