Aligners

Nov 20, 2022

• UPDATE: March 2024

1. Setup

A. JAMR

• java version: 1.8.0_392
  • installed with eclipse temurin (via sdkman)
• sbt version: 1.0.2
  • should be reflected in project/build.properties
  • installed with SDKMAN!
• scala version: 2.11.12
  • should be reflected in build.sbt and scripts/config.sh
  • installed with SDKMAN!
• see modified project/plugins.sbt
  • see references below
• make executables
  • chmod +x setup compile sbt scripts/config.sh
• run sbt first! (not ./sbt but just sbt)
  • setup, etc scripts
• see jamr_post_setup.sh which fixes outdated perl expression
• references:
  1. jflanigan/jamr#44
  2. https://github.com/DreamerDeo/JAMR

B. ISI

• requires python2
  • pip2 install virtualenv then python2 -m virtualenv python2-env
  • python2-env virtualenv within ISI dir by default; or set up new one separately
  • UPDATE: pyenv virtualenv 2.7.17 isi
• mgizapp requires Boost c++ libraries
  • sudo apt-get install libboost-all-dev
• read instructions in INSTALL inside mgizapp
• running scripts/jamr2isi.py on JAMR output prepares input data in required format

C. LEAMR

• requires python3 (3.7.3 or 3.7.6 on ubuntu 22.04)
  • UPDATE: 3.7.17 seems required, along with spacy==2.3.7
• pyenv virtualenv by default; or set up local venv separately and configure the script acordingly
• torch 1.13.1+cu117
• relies on Stanza and spaCy whose version may be different from what model uses
  • set up Stanza with STANZA_RESOURCES_DIR=./leamr/leamr_stanza_resources python -c "import stanza; stanza.download('en')"
• also need to set up neuralmonkey separately
  • pip install cython==0.29 --upgrade
• don't forget python -m spacy download en
• contains minor modifications
  • doesn't drop .txt in the outputs filename
  • uses pre-tokenized outputs

2. Run

May have to set pyenv global to Python2 + Python3, i.e.

pyenv global 2.7.15

• since Python3 are usually pre-installed, this exposes python2 and python3.

To run aligners in sequence (JAMR -> ISI -> LEAMR)

./scripts/run_aligners.sh [input_file]