Re: Seg fault after 2 days of simulation

[Jan Kreft]

Tried to send this off yesterday, but didn't get through somehow. Second
try now. Apologies if you got this already.

Dear Marcus,

On 13 Oct 1999, Marcus G. Daniels wrote:

> >>>>> "JK" == Jan Kreft <address@hidden> writes:
> 
> JK> BTW, would be better as an array of BOOL instead of char, does
> JK> anyone know if that's possible?
> 
> You'd have to use bit shift operations and masking to do that, e.g.
> "value |= (1 << offset)", "value &= ~(1 << offset)".  It's usually not
> worth it unless the sequences are really big.  If the sequences have
> *known* top-end size, you can allocate an ivar of sequence-size / 8 or
> use the ": size" bitfield syntax. 
> 
> Btw, I really want to get away from use of raw memory in Swarm.  These
> nasty consequences to unexpected allocation requirements are way too
> nasty.  Even with a lot of experience and good tools, debugging memory
> corruption problems can be a big time sink that ends up teaching you
> nothing (except the benefits of obsessive behavior).  This bug
> wouldn't have occurred if you were using the Java layer, because you'd
> have used automatically sized and garbage collected Strings.

I would love such automatically sized strings. But, and this is a long
but, my sims already run for about 2 days, and I plan to go to 3D next
year, probably slowing them down to a standstill. Or possibly include
hydrodynamics. In other words, soon I'll have to use some sort of
supercomputer to run my models, and that will mean going to pure C rather
than Java from Objective C.  Preemptively, I have made this years
additions to BacSim as close to C as I could within the limits imposed by
the existing code. Not that I'm proud of it, but I see no other way. I
looked around for something like Java for Cray, but all I found was very
experimental support for SMP in Java, and certainly no Java for Cray. HP
Fortran would be even better, I suppose, but I've never used Fortran, so
that's above my league. Given the current focus of Swarm development, I
doubt Swarm on Cray will be ready when I would need it.

Cheers, Jan.





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