Please try to make the stderr output more compact. From

#132 Tue Dec 24 02:05:01 2013
Graph created File: complete_gene_net read Standard deviations computed Correlations computed l: 0 1 2 3 4 5 6 7 8 9 # of arcs: 2223
Writing checkpoint's file

132|13-12-24 02:05:01|G F S|C(9:2223)
CHK

Please try to make the stderr output more compact. From

#132 Tue Dec 24 02:05:01 2013
Graph created File: complete_gene_net read Standard deviations computed Correlations computed l: 0 1 2 3 4 5 6 7 8 9 # of arcs: 2223
Writing checkpoint's file

to something like

132|13-12-24 02:05:01|G F S|C(9:2223)
CHK

I mean, all the needed info squeezed in few bytes.

Also, do you need to read the complete_gene_net at every iteration? Shouldn't be more efficient to just read it at start or returning from checkpoint and keep it (or a copy of it) in memory?

Please try to make the stderr output more compact. From

#132 Tue Dec 24 02:05:01 2013
Graph created File: complete_gene_net read Standard deviations computed Correlations computed l: 0 1 2 3 4 5 6 7 8 9 # of arcs: 2223
Writing checkpoint's file

to something like

132|13-12-24 02:05:01|G F S|C(9:2223)
CHK

I mean, all the needed info squeezed in few bytes.

I did not work on that, but I think that the new version we already sent has a more compact stderr.

Also, do you need to read the complete_gene_net at every iteration? Shouldn't be more efficient to just read it at start or returning from checkpoint and keep it (or a copy of it) in memory?

When we developed the first versions of the application, we had no bounds on the complete_gene size, so the best strategy was to read on-the-fly the lines needed.
I think that we should discuss this with professor Blanzieri, reading it once should be faster, but I suspect that working with different species could lead to far bigger input files, compared to the Arabidopsis. Splitting those files may be a solution, though..

I've computed some wus with the new application... There are still a thousand lines in the stderr with 500 tiles, but I think that the lines printed are necessary for future debug!