Visualizing autonomous components in de Bruijn graphs

-
In Ray Cloud Browser (demo on Amazon EC2), I just found some interesting bits: autonomous components occurring in free form in a de Bruijn graph. You can see these yourself by going at the location displayed in the figures below.







I am working on these strange things in the graph because those useless parts consume a sizable amount of compute time. So instead of patching this problem downstream (i.e.: removing the dust), I decided to write Ray Cloud Browser to fix things in the right places (i.e.: removing the source of dust instead of the dust being produced).

Comments

Post a Comment

Popular posts from this blog

The Thorium actor engine is operational now, we can start to work on actor applications for metagenomics

-
I have been very busy during the last months. In particular, I completed my doctorate on April 10th, 2014 and we moved from Canada to the United States on April 15th, 2014. I started a new occupation on April 21st, 2014 at Argonne National Laboratory (a U.S. Department of Energy laboratory). But the biggest change, perhaps, was not one listed in the enumeration above. The biggest change was to stop working on Ray. Ray is built on top of RayPlatform, which in turn uses MPI for the parallelism and distribution. But this approach is not an easy way of devising applications because message passing alone is a very leaky, not self-contained, abstraction. Ray usually works fine, but it has some bugs . The problem with leaky abstractions is that they lack simplicity and are way too complex to scale out. For example, it is hard to add new code to an existing code base without breaking anything. This is the case because MPI only offers a fixed number of ranks. Sure, the MPI standard has s...
Read more

Learning to solve the example 1 of puzzle 3aa6fb7a in the ARC prize

-
Image
Hi dear reader, Puzzle rules The example 1 of the puzzle 3aa6fb7a of the ARC prize looks like this: A playout starts with an blank board of width 7 and of height 7. There are therefore 49 cells. Each cell can be blank or can contain one of the 10 possible colors. The colors are identified from 0 to 9.  I added a rule. This rule is that each cell has to be changed exactly once.  The game ends when all cells have been changed. The player wins if all the cell colors match the cell colors in the expected output. Some numbers: Each cell has 11 possible values: 10 colors + blank state There are 49! ( 6.0828186e+62) distinct possible orders of cell changes in a playout.  There are 49!*10 ( 6.0828186e+63) 49 * 10 = 490 possible actions for the first action.  There are 11^49 ( 1.0671896e+51) possible board states The number of possible pairs (s, a) is even larger and upper-bounded by 11^49 * 49 * 10 = 5.2292289e+53 . Given a board state s and a proposed action a, an actio...
Read more

Adding ZVOL VIRTIO disks to a guest running on a host with the FreeBSD BHYVE hypervisor

-
On atlantis.domain (my FreeBSD BHYVE hypervisor host), I use these commands: Install FreeBSD on a 10G disk. vm create -s 10G guestname   vm install FreeBSD-12.1-RELEASE-amd64-memstick.img vm console guestname Add 8 30GB zvol-based disks vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname You will need to do vm poweroff guestname vm start guestname because the guest does not seem to see the 8 30GB without power cycling. (rebooting won't work) *** If you want the boot disk (the one create by "vm create") to be a zvol, you must edit the template: root@atlantis:~ # zfs snapshot tank/vm-bhyve@2020-06-11-2145 root@atlantis:~ # mount -t zfs tank/vm-bhyve@2020-06-11-2145 /tank/vm-bhyve@2020-06-11-2145 r...
Read more