Image problem

[Maria C]

Hello, I have a data set of 343373 cells and 338 species running in a
1GB RAM machine. My problem is that I can`t see the image of the
solutions in the SOLN panel, and in the problem panel the more data
option do not respond. Any idea if the problem is due to computer
requirement or due to the size of the problem?? Thanks,
Maria.

[Michael Ciarleglio]

Hi Maria,

There could be several things wrong. If the program is actually
locking up, then you may be running out of memory. You will want to
check the black window in the background to see if there are any
program exceptions (such as an out of memory error).

The next place to look would be the input file. I'm assuming that you
are using a rectangular grid, because the other options will not
provide any visualizations. Double check the grid spacing that is
listed in the header line of your input file. A type-o here could
cause strange results. Also in the input file, check the two columns
that hold the "row" and "column" position for the cell. If you
assigned these values yourself, check to make sure that they make
sense. Otherwise, they should be zero (and ConsNet will attempt to
place them on the grid based on their X and Y positions). NOTE: if
your dataset crosses the 180/-180 meridian, you must assign the row
and column values in the input file.

Another place to look is the final page of the problem loading
wizard. After you enter in all of your information and set the
targets, a final screen appears when the grid is created. It contains
some diagnostic messages such as:

GRID: data set fits in [rows x cols] = [364, 634]
GRID: checking grid integrity
GRID: performing neighbor index...
GRID: neighbor indexing complete
GRID: processing permanently included and excluded cells
GRID: sets 0 permanently included cells
GRID: sets 0 permanently excluded cells
GRID: computing clusters for this grid

The first line shows how your data will be arranged on the rectangular
grid (the dimensions of the grid). This is how ConsNet will create
the raster images. If these numbers are extremely large, then ConsNet
may have made a mistake when placing your cells on the grid (which
would affect the graphics).

Finally, I think you may be short on memory for a problem of this
size. With a problem of this size, you should be able to see the
graphics when the program starts, but you will run out of memory
during the search. Once we resolve this issue and you can visually
inspect your dataset, I would recommend disabling the graphics using
the -nographics command in the .bat file (see the instruction
manual) before running the search. You will also need to implement
memory reduction techniques described in Section 4.6 of the manual.

The ideal outcome would be to find a computer with more memory.
However, to deal with the memory limitations (and this is a fairly
extreme case), your .bat file may look something like this:

java -Xms700m -Xmx700m -showversion -verbosegc -jar consnet.jar -
trigger 500 -maxcache 50 -nographics
@pause

I chose 700m (megabytes), but you should allocate the maximum amount
that Windows will allow. In order to do this, you will want to kill
all unnecessary programs.

I hope one of those suggestions works. If not, we can pursue other
debugging options.

Michael Ciarleglio