Re: Total vs per-cpu memory
Hi Len:
I agree. However, these are no standardized codes. Actually, it is a code in
development that is faced with extreme situations that could not have been in
the mind of the developer. Docking a large molecule onto a protein without bias
is a challenging task, that the program accomplices nicely up to a certain size
of the ligand. I am pushing the program beyond the limits for which it was
devised. That "pushing" in order to tell where the program needs to be revised.
The developer is not putting together known routines, he is inventing the way
to come out.
That said, you are certainly able to answer my question about how RAM is used
by a single cpu in my Tyan (all 8 sets of memory occupied) when the other cpus
are dormant. If not, the only way I can invent is to look at top -i when the
ligand is large but not so large to induce segmentation fault.
Thanks
francesco
--- Lennart Sorensen <lsorense@csclub.uwaterloo.ca> wrote:
> On Thu, Jan 31, 2008 at 07:39:43AM -0800, Francesco Pietra wrote:
> > This question is related to problems in running a docking computation. With
> big
> > cases, RAM proves insufficient, resulting in immediate "segmentation
> fault", so
> > that "top" cannot inform. Though, from the code it is clear that memory is
> > insufficient to rotate the object in a non-parallelized part of the
> program.
> > Smaller objects do not give problems.
>
> Insufficient ram does not EVER cause a segmentation fault. Only buggy
> code causes segmentation faults.
>
> If a bad programmer simply calls malloc and doesn't check that it
> succeeded before using it, then you get a segmentation fault, but only
> because the programmer didn't write proper code.
>
> --
> Len Sorensen
>
>
> --
> To UNSUBSCRIBE, email to debian-amd64-REQUEST@lists.debian.org
> with a subject of "unsubscribe". Trouble? Contact listmaster@lists.debian.org
>
>
____________________________________________________________________________________
Looking for last minute shopping deals?
Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping
Reply to: