Monthly Archives: March 2019

Dual Networks Profiles Ubuntu 18.04

The setup

I have 2 network adapters, a 10G and a 1G network. In order to connect to both networks, you must have two profiles.

Two profiles: 10G and 1G profile, across 2 adapters.

If you have a single profile, then changing settings for one network adapter will also affect the other. In Ubuntu's Network UI, this is non-obvious.

Once setup correctly, you can verify by being able to ping both networks.

jsun@computer ~ [1]> ping 192.168.1.200
PING 192.168.1.200 (192.168.1.200) 56(84) bytes of data.
64 bytes from 192.168.1.200: icmp_seq=1 ttl=128 time=0.338 ms
64 bytes from 192.168.1.200: icmp_seq=2 ttl=128 time=0.172 ms
^C
--- 192.168.1.200 ping statistics ---
2 packets transmitted, 2 received, 0% packet loss, time 1028ms
rtt min/avg/max/mdev = 0.172/0.255/0.338/0.083 ms

jsun@computer ~> ping 10.10.50.1
PING 10.10.50.1 (10.10.50.1) 56(84) bytes of data.
64 bytes from 10.10.50.1: icmp_seq=1 ttl=64 time=0.585 ms
64 bytes from 10.10.50.1: icmp_seq=2 ttl=64 time=0.226 ms
^C
--- 10.10.50.1 ping statistics ---
2 packets transmitted, 2 received, 0% packet loss, time 1022ms
rtt min/avg/max/mdev = 0.226/0.405/0.585/0.180 ms

Space Filling Curves vs. Octree

Octree

An octree is a tree data structure in which each internal node has exactly eight children. Octrees are most often used to partition a three-dimensional space by recursively subdividing it into eight octants. Octrees are the three-dimensional analog of quadtrees.

We humans mostly deal with low dimensional data, so we give this type of structure some names:

  • 1-D data: binary tree
  • 2-D data: quadtree
  • 3-D data: octree
  • K-D data: k-d tree, or k-dimensional tree, is a data structure used in computer science for organizing some number of points in a space with k dimensions.

These are all tree-like data structures, which are very useful for range and nearest neighbor searches.

Octree example

Space Filling Curves

Space filling curves refers to a class of functions that k dimensional data to 1 dimension.

Meaning a class of functions that can map k-dimensional data into a single number n

f(n_1, n_2, ..., n_k) -> n

The caveat is there is a restriction on the number it maps, i.e. n_1, as space filling curves are a fractal functions, it cannot be extended to the reals, but rather to the binary fractions (a subset of the rationals). This lets you get arbitrarily close to any number you want (and cover all the IEEE floating points).

Class of functions means that there are many functions that can be considered a space filling curve. Common to use Hibert and Z-order.

Visualization of a 3D space filling curve may look like with a Hilbert curve function.

Compare and contrast

There are certain optimal use cases for each of these.

  • Trees have the benefit being able to limit the depth of your queries, which makes it especially useful in computer graphics so you can stop querying for points that you don't need.
  • Space filling curves have the benefit of modify data faster, because the location to store that data can be calculated. Because trees have the cost of potentially rebalancing subtrees and creating/updating/deleting.

Other structures?

There are some variants on structures for storing multi-dimensional data.

R-Tree

It's yet another type of tree.

Visualization of an R*-tree for 3D points using ELKI.Hilbert R-Tree is a variant on the R-Tree to achieve better performance.

Data Stores

I won't go in too much detail because this is out of scope, but in programming there are databases and data stores which can handle large amount of high dimensional data.

First, a distinction. A database can handle complex queries. A data store can be dumber, simple storage format and won't handle things like transaction for you.

An analogy could be like "database is like an accountant, who you can ask for certain data and operations, such as 'give me all last year's data for people with last names in T'", whereas "data store is like a library and you have to go find and collect that data yourself, but it's stored in an organized fashion".

Mount locked partition with same volume group name

Background/Setup

  • I have two physical 1TB disks with identical setup.
  • Both are encrypted.
  • I unlocked and booted off one of them.
  • The other disk is still locked at this point.
  • I am using fish shell.

1. Identify which disk you want to unlock

root@computer ~# lsblk -f
sda                                                                                                    
├─sda1                                        vfat              7F3B-9703                              /boot/efi
├─sda2                                        ext2              b6220db2-916c-4322-b64b-c86769f6b18b   /boot
└─sda3                                        crypto_LUKS       3a07b8a9-3e75-41a9-88d4-3be937181613   
  └─luks-3a07b8a9-3e75-41a9-88d4-3be937181613 LVM2_member       uCvHaW-RlQc-PT2d-cBg2-SWyY-WS0A-ZCEvA6 
    ├─ubuntu--vg-root                         ext4              a78662e2-d582-4faa-88b6-b6db5e23aed2   /
    └─ubuntu--vg-swap_1                       swap              5c4ba6cc-4735-4417-9e87-74a76a7fc415   [SWAP]
sdb                                                                                                    
├─sdb1                                        vfat              1EC8-1F58                              
├─sdb2                                        ext2              7108fe1d-dc37-4213-a3bc-8070a8f84f31   /media/jsun/7108fe1d-dc37-4213-a3bc-8070a8f84f31
└─sdb3                                        crypto_LUKS       fc560468-588c-4455-af2c-295998c41c88   

We see that sdb3 is the unmounted target.

2. Unlock the partition

root@computer ~# udisksctl unlock -b /dev/sdb3 
Passphrase:
Unlocked /dev/sdb3 as /dev/dm-3.

See which one is the new unlocked

root@computer ~# ls -la /dev/mapper/ | grep dm-3 
lrwxrwxrwx 1 root root 7 Mar 22 17:32 luks-fc560468-588c-4455-af2c-295998c41c88 -> ../dm-3

luks-fc560468-588c-4455-af2c-295998c41c88 is our target. Let's remember that with a variable.

set target luks-fc560468-588c-4455-af2c-295998c41c88

3.

The VG Name of both drives is the same; this is problematic and will prevent you from being able to mount the drives both at the same time.

root@computer ~# pvdisplay
--- Physical volume ---
PV Name /dev/mapper/luks-3a07b8a9-3e75-41a9-88d4-3be937181613
VG Name ubuntu-vg PV Size 930.53 GiB / not usable 2.00 MiB
Allocatable yes (but full)
PE Size 4.00 MiB
Total PE 238216
Free PE 0
Allocated PE 238216
PV UUID uCvHaW-RlQc-PT2d-cBg2-SWyY-WS0A-ZCEvA6
--- Physical volume ---
PV Name /dev/mapper/luks-fc560468-588c-4455-af2c-295998c41c88
VG Name ubuntu-vg
PV Size 930.53 GiB / not usable 2.00 MiB
Allocatable yes (but full)
PE Size 4.00 MiB
Total PE 238216
Free PE 0
Allocated PE 238216
PV UUID lbvecI-E6w6-fpuj-P61G-5NCb-obOK-ooivpe

Get the uuid of the volume

root@computer ~# uuidgen
1ec80451-b05b-4d59-94c1-f1ad70b24255
root@computer ~# vgrename $uuid 1ec80451-b05b-4d59-94c1-f1ad70b24255
Processing VG ubuntu-vg because of matching UUID TJgeFw-xDcf-TaJ2-07dL-RlUQ-yCsb-zGGp4v
Volume group "TJgeFw-xDcf-TaJ2-07dL-RlUQ-yCsb-zGGp4v" successfully renamed to "1ec80451-b05b-4d59-94c1-f1ad70b24255"
root@computer ~# pvs -o +vg_uuid
PV VG Fmt Attr PSize PFree VG UUID
/dev/mapper/luks-3a07b8a9-3e75-41a9-88d4-3be937181613 ubuntu-vg lvm2 a-- 930.53g 0 TAva2M-zNnV-Wh5h-3YcY-Vc5U-W4se-TI27Du
/dev/mapper/luks-fc560468-588c-4455-af2c-295998c41c88 1ec80451-b05b-4d59-94c1-f1ad70b24255 lvm2 a-- 930.53g 0 TJgeFw-xDcf-TaJ2-07dL-RlUQ-yCsb-zGGp4v

The device UUID is TJgeFw-xDcf-TaJ2-07dL-RlUQ-yCsb-zGGp4v. Let's remember that with a variable.

set uuid TJgeFw-xDcf-TaJ2-07dL-RlUQ-yCsb-zGGp4v

Change the volume group

I'm going to generate a UUID, but you can name whatever you want.

root@computer ~# uuidgen
1ec80451-b05b-4d59-94c1-f1ad70b24255
root@computer ~# vgrename $uuid 1ec80451-b05b-4d59-94c1-f1ad70b24255
Processing VG ubuntu-vg because of matching UUID TJgeFw-xDcf-TaJ2-07dL-RlUQ-yCsb-zGGp4v
Volume group "TJgeFw-xDcf-TaJ2-07dL-RlUQ-yCsb-zGGp4v" successfully renamed to "1ec80451-b05b-4d59-94c1-f1ad70b24255"
root@computer ~# pvs -o +vg_uuid
PV VG Fmt Attr PSize PFree VG UUID
/dev/mapper/luks-3a07b8a9-3e75-41a9-88d4-3be937181613 ubuntu-vg lvm2 a-- 930.53g 0 TAva2M-zNnV-Wh5h-3YcY-Vc5U-W4se-TI27Du
/dev/mapper/luks-fc560468-588c-4455-af2c-295998c41c88 1ec80451-b05b-4d59-94c1-f1ad70b24255 lvm2 a-- 930.53g 0 TJgeFw-xDcf-TaJ2-07dL-RlUQ-yCsb-zGGp4v

Check/notice the new volume group name 1ec80451-b05b-4d59-94c1-f1ad70b24255.

Confirm the change

root@computer ~# vgchange -a y
2 logical volume(s) in volume group "ubuntu-vg" now active
2 logical volume(s) in volume group "1ec80451-b05b-4d59-94c1-f1ad70b24255" now active

Remember to rename your volume group back to ubuntu-vg if you want the volume to still be bootable.

Mount

root@computer ~# mkdir /media/badboy
root@computer ~# mount /dev/1ec80451-b05b-4d59-94c1-f1ad70b24255/root /media/badboy
root@computer ~# cd /media/badboy/
root@computer /m/badboy# ls
bin/ cdrom/ etc/ initrd.img@ lib/ lib64/ media/ opt/ root/ sbin/ srv/ tmp/ var/
boot/ dev/ home/ initrd.img.old@ lib32/ lost+found/ mnt/ proc/ run/ snap/ sys/ usr/ vmlinuz@

You can now access your data.

Merge EPT Entwine Point Tile Maps

EPT format is a storage method for point clouds, base on an octree structure. The encoding of the point cloud is up to the user, whether las/laz, binary, or whatever custom format. So let's say you store it in laz. What EPT does is to generate the octree to manage how those laz files are stored.

Merging EPT

Given two geographically separated point clouds, it is possible to merge them into the same EPT structure, given they use the same frame of reference. Because Potree doesn't handle latitude and longitude rendering (as they are angles and not euclidean), you have to use euclidean systems, such as UTM coordinates.

Merging two point clouds together

You must first specify a large bounds for the initial build, and add more files later like this:

entwine build -i ~/data/xyz -o ~/entwine/xyz -b "[100, 100, 0, 400, 400, 200]"
entwine build -i ~/data/abc -o ~/entwine/xyz

See Entwine issue 109

Caveats

A caveat is that when you're generating the first frame, you need to custom input the bounding cube bounds, because by EPT design the octree cannot be rebalanced (without recomputing for all points).

Another caveat is that UTM zone is not encoded in the laz file, using UTM cannot be extended over geographical regions. Thus we may have to store xyz points in lat/lng/alt format.

Yet another caveat is the source ID for these points are going to collide. E.g. in file1.laz you have frames ID 0-100 and file2.laz you have frames ID 0-10, then the 0-10 IDs would collide. A workaround would be to assign global unique IDs.

WD 8TB Hard Drive Shucking For NAS

The Western Digital (WD) Easystore 8TB is an external hard drive sold exclusively by Best Buy. It's highly sought after because it contains a WD Red or unlabelled WD White 8TB drive, which can be "shucked" and used in a home server.

Typically you can get 8TB for $140+tax when on sale, whereas a regular WD 8TB NAS drive costs around $260+tax.

There are more details in this reddit post about the drives and how to shuck them.

Start by inserting plastic cards into these places and pry them out.

Wiggle out the drive.

Two screws hold the PCB board on the drive.

Slide out the connector

Done, now to mount into the Synology drive mount.

Insert and then configure in Synology.
Disk 3 shows up in Synology Storage Manager.
Add the disk, and it'll take some time to wipe and initialize.

After a few hours the volume is expanded.

Install g++-8 compiler

The new C++17 language requires g++ >= 8.0. To install it in Ubuntu 18.04:

$ sudo apt install g++-8
...
$ which g++
/usr/bin/g++
$ which g++-8
/usr/bin/g++-8
$ sudo unlink g++
$ sudo link -s /usr/bin/g++-8 /usr/bin/g++
$ g++ --version
g++ (Ubuntu 8.2.0-1ubuntu2~18.04) 8.2.0
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Re-link After Make Install

The magical command sudo /sbin/ldconfig -v reconfigures/indexes the files you installed into the lib.

For example, if you see errors such as:

~/w/h/build (master) [127]> curse
curse: error while loading shared libraries: libhexer.so.1.1.0: cannot open shared object file: No such file or directory

Or similiarly

~/w/e/build (master)> entwine
entwine: error while loading shared libraries: libentwine.so.2: cannot open shared object file: No such file or directory

Then go and run the magical command.

Typically this is needed when you do sudo make install after compiling some C++ code. I suppose you don't need the -v verbose flag, because ldconfig - configure dynamic linker run-time bindings.