Patch / Compile

Amber + QMhub + Torchmd-net

Create Conda Environment

1. Create a torchmd-net conda environment, and load modules.

conda create -f torchmd-net.yml
conda activate torchmd-net

module load intel/2021.2.0
module load impi/2021.2.0
export MKLROOT=/opt/intel/oneapi/mkl/2021.2.0
export LD_PRELOAD=$MKLROOT/lib/intel64/libmkl_core.so:$MKLROOT/lib/intel64/libmkl_sequential.so

2. Clone repository to Programs/ and change branch to torchnet-ext

git clone https://github.com/panxl/torchmd-net.git
cd torchmd-net
pip install .

3. Clone and to Programs/. We’ll compile qmhub first.

git clone https://github.com/panxl/qmhub.git
cd qmhub
pip install .
cd ..

git clone https://github.com/andysim/helpme.git
cd helpme 
mkdir -p build && cd build

CXX=icpc PKG_CONFIG_PATH=~/miniforge3/lib/pkgconfig \
    cmake .. \
    -DFFTW_INCLUDES=$MKLROOT/include/fftw \
    -DFFTW_LIBRARIES=$MKLROOT/lib/intel64

make helpmelib

4. Copy the python/helpme*** file to minforge3/envs/torchmd-net/lib/python3.10/site-packages/qmhub/

5. Then compile Amber