sander_classic, erratic on IBM

From: Giovanni Fossati <>
Date: Thu 30 May 2002 01:17:07 -0500 (CDT)

                                              Wednesday May 29, 2002

Good morning,
I have been trying to compile (and run) sander_classic (from Amber6
distribution) on a IBM, serial (the machine is a 16proc 1.3GHz Regatta).
It compiled, apparently smoothly, and it seemed to run ok on the first test
protein (85 residues).
Then I tried another one, with 125 residues and sander_classic still seems to
run, and to the MD, but ...
First of all it decides, autonomously, to open also the mdvel file (NB:
ntwv=0), and moreover it never writes anything in mdcrd and mden!
I tried a handful more of test with proteins of different lengths, and the
same binary runs just fine on shorter proteins, and behaves it that weird way
with the longer proteins.
I am very puzzled because I really don't see how a/the code can decide to
change by itself its behavior, without crashing, without any other sign of

I have a second question, this time about another weird behavior on a Linux
box. I am using the Intel compiler on this one, which comes with optimized
lapack libraries too.
I succesfully compiled on other very similar boxes, but on this one I am
unexpected having problems.
First of all when compiling the whole package I was either getting an error
for 'multiple definitions' of 'second' (it is defined in sys.f, and in the
Intel lapack library), or -when I was using a tweaked sys.f- and 'undefined
symbol' error....
I am not very familiar with the subtleties of Makefiles and stuff like that,
just enough to make minor changes and checks.
So I might be missing something, although the changes that I had to make here
and there to compile with ifc and Intel lapack worked in other cases.
Anyway, sander_classic does not link lapacks, and then I could compile it with
the plain sys.f, i.e. the one including 'second'.
Now, I try to run sander_classic and I get "Illegal instruction", immediately.
After some struggle with the ddd debugger (I am not big in debugging) it seems
that the problem has to do with -probably- "second" again.
In fact, the debugger diagnosis is:

program received signal SIGILL, Illegal instruction.
timit (index=Cannot access memory at address 0x7fffffff
) at _misc_.f:98
98 in _misc_.f

And "timit" calls "second".
I don't get it...on at least 4 other similar Linux boxes, in all cases with
Intel compiler, I did not have a problem.

I really hope that somebody out there could help me out.
Thank you very much.
Have a great day,


 Dr. Giovanni Fossati +---------------------------+
 Dept. of Physics and Astronomy, MS 108 | Ph : (713)-348-3425 |
 Rice University | Fax : (713)-348-5143 |
 6100 Main street, Houston, TX 77005, USA | e-mail: |
Received on Wed May 29 2002 - 23:17:07 PDT
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