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Setup LINCX cluster with LING aligner workers

Below is the steps required to setup hosts with aligner workers. Assuming that aligner master already launched on host 172.16.1.254. (Master IP can be assigned via '-worker_bwt_app master_ip {A,B,C,D}' option in extra section of domain_config).

Dom0 network setup

Each worker seats on separate bridge, so we need to create bridges:

$ brctl addbr brX
$ ip link set brX address 00:16:EF:01:00:0X

(replace X with bridge number)

Create bridge for LINCX configurator:

$ brctl addbr xenbr0
$ ip ad ad 192.168.1.1/24 dev xenbr0

Create bridge for cross-host worker traffic:

$ brctl addbr xenbr1
$ ip ad ad 172.16.X.252/24 dev xenbr1

(replace X with host number)

Enable forwarding for cross-host traffic:

$ echo 1 > /proc/sys/net/ipv4/ip_forward
$ echo 1 > /proc/sys/net/ipv4/conf/all/proxy_arp

LINCX setup

Get and compile sources:

$ git clone https://github.com/FlowForwarding/lincx.git
$ cd lincx
$ ./rebar get-deps compile

Create lincx.yml (assuming you will have 8 workers per host):

ipconf:
  ipaddr: 192.168.1.2
  netmask: 255.255.255.0
  gateway: 192.168.1.1

ports:
  - {id: 1, bridge: br1}
  - {id: 2, bridge: br2}
  - {id: 3, bridge: br3}
  - {id: 4, bridge: br4}
  - {id: 5, bridge: br5}
  - {id: 6, bridge: br6}
  - {id: 7, bridge: br7}
  - {id: 8, bridge: br8}
  - {id: 9, bridge: xenbr1}

controllers:
  - 192.168.1.1:6653

listen: 0.0.0.0:6653

memory: 512

Build image:

$ ./railing image

Launch LINCX:

$ xl create domain_config

Setup LINCX flow tables:

$ ./scripts/hetzner.erl X

(replace X with host number)

Networking part is done!

Setup BWT

Build image:

$ git clone -b bwtling https://github.com/cloudozer/BWT.git
$ cd BWT
$ ./rebar get-deps compile
$ ./railing image -i bwt_files -lsasl

Create domain config bwtX.dom for each worker:

name = "bwtX"
kernel = "BWT.img"
extra = "-ipaddr 172.16.Y.X -netmask 255.255.0.0 -worker_bwt_app master_ip {172,16,1,254} -home /BWT -pz /BWT/apps/master/ebin /BWT/apps/worker_bwt_app/ebin /BWT/bwt_files /BWT/deps/goldrush/ebin /BWT/deps/lager/ebin /BWT/ebin -eval 'application:start(sasl),application:start(bwt),application:start(worker_bwt_app)'"
memory = 1024
vif = ['bridge=brX']

(replace X with worker number and Y with host number)

Launch workers:

$ xl create bwtX.dom

Workers setup is done! Now you can attach to master, ensure that workers are succesfully connected and issue some work to them:

$ gen_server:call(master , {run, "bwt_files/SRR770176_1.fastq", "GL000193.1", Z}).

(replace Z with total number of your workers)