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How to replace Sgminer-Troky with the latest code from the main sgminer branch on Github?
and subsequently become able to mine vertcoin without having to deal with vertminer 0.5.3
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ssh into your bamt box. (use putty on windows, ssh root@your.ip  on a mac, default password is live, change this using passwd once inside)

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$ mine stop
$ cd /opt/miners
$ mv sgminer-4.1.0-troky sgminer-4.1.0-troky-orig
$ git clone https://github.com/veox/sgminer.git sgminer-4.1.0-troky
$ cd sgminer-4.1.0-troky
$ cp -r ../sgminer-4.1.0-troky-orig/ADL_SDK .
$ ./autogen.sh
$ CFLAGS="-O2 -Wall -march=native" ./configure
$ make

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Once done with this, make sure you enable sgminer-troky in /etc/bamt/bamt.conf

$ nano /etc/bamt/bamt.conf
to save and exit hit Ctrl-X, then Y, then enter

find the following part and set it up like this:
  # CONFIG OPTIONS :
  #cgminer_opts: --api-listen --config /etc/bamt/vertminer.conf
  cgminer_opts: --api-listen --config /etc/bamt/sgminer-troky.conf
  #cgminer_opts: --api-listen --config /etc/bamt/sgminer-sph.conf
  #cgminer_opts: --api-listen --config /etc/bamt/cgminer.conf

  # Set miner over-ride if you want something other than cgminer.

  # MINER OPTIONS :
  # Vertminer 0.5.2 "the kev"
  # Sgminer 4.1.0 "troky"
  # Sgminer 4.1.0 "sph - aka - DarkCoin/QubitCoin/Quark"
  # Cgminer 3.7.2 "kalroth"

  # !! Set all to 0 for cgminer. !!

  miner-vertminer-thekev: 0
  miner-sgminer-troky: 1
  miner-sgminer-sph: 0

Indentation is important.
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Now, set up your sgminer config
$ nano /etc/bamt/sgminer-troky.conf

The following lines need to be added/present.

"algorithm" : "nscrypt",

Kernel needs to be one of the included kernels, not scrypt or nscrypt. ie:
"kernel": "zuikkis",

Once happy, save and start the mine.