MES Tools to Train and Test Models

MES Tools to Train and Test Models

Overview

These are command-line executables for training, testing, and manipulating models, as well as other utilities developed by MES.

You can download a prebuilt release from the Release page. The release is built with glibc 2.17 and will work out of the box on systems with glibc ≥ 2.17 (e.g., Ubuntu >= 13.04, Centos>=7, eg.). If you need to build from source, follow the instructions below.

Installation Steps

1. Install Boost Libraries. Compilation is not required, you might install from pacakge manager.
2. Clone the required repositories:

   git clone git@github.com:Medial-EarlySign/MR_Tools.git
   git clone git@github.com:Medial-EarlySign/medpython.git
   

3. Change to the MR_Tools directory:

   cd MR_Tools
   

4. Edit All_Tools/CMakeLists.txt to set LIBS_PATH to the path of your MR_LIBS clone. If your directory structure is:

   Root Directory
   ├── MR_LIBS
   └── MR_Tools
   

   then no changes are needed. If you compiled Boost, also set BOOST_ROOT in the CMakeLists.txt file.
5. Edit All_Tools/CMakeLists.txt and add/edit line:

   set(BOOST_ROOT "$ENV{HOME}/boost-pic-install")
   

   Set this path to your Boost build directory (WORK_BUILD_FOLDER from step 2). Make sure the compiled libraries are in /libs and headers in /include. Alternatively you can just set your environment variable BOOST_ROOT to reference the Boost build directory.
6. Build the tools:

   AllTools/full_build.sh
   

A full docker image for compilation steps can be found under this link:

• 01.basic_boost A base docker image with Boost
• 02.build_tools A build with tools prepared for usage

Common Issues

1. Can't find Boost libray errors in compilation - Please delete the "./build" folder to recreate all Makefiles again. It holds some bad settings of Boost in cache.

2. Can't find boost_atomic.so in runtime. Please add atomic in CMakeLists.txt under BOOST_LIBS and recompile

3. Running an executable may fail with:

   $> Flow ...
   Flow: error while loading shared libraries: libboost_regex.so.1.85.0: cannot open shared object file: No such file or directory
   

   This indicates the Boost shared libraries are not found at runtime. Set LD_LIBRARY_PATH to point to your Boost lib directory. Add to your ~/.bashrc or run once per session:

   export LD_LIBRARY_PATH=/path/to/BOOST_ROOT/lib
   

   If Boost was installed via the system packages (Ubuntu 22.04 uses 1.74, 24.04 uses 1.83), install the appropriate dev packages instead of adjusting LD_LIBRARY_PATH:

   sudo apt install libboost-program-options1.83-dev -y
   

   Replace 1.83 with 1.74 on Ubuntu 22.04 when needed.