Installing from source

When to install from source

• The software is not available as a module ( check module avail and conda search first)
• You need a newer version than provided, or specific compile-time options
• You're developing or modifying the software yourself
• The software needs architecture-specific optimizations

Choosing a location

Home (--prefix=$HOME/software/myapp-1.0) is backed up but capped at 20 GB; project space is large and shared but not backed up. Never install in scratch — the 45-day purge will break the installation.

Match the architecture

Load compilers and dependencies

module avail gcc && module avail intel
module load gcc/11.2.0            # or: module load intel/oneAPI/2023.1 compiler
module load cmake/3.24.2
module load openmpi/4.1.4

# specify compilers explicitly when needed
export CC=gcc CXX=g++ FC=gfortran        # GNU
export CC=icx CXX=icpx FC=ifx            # Intel oneAPI

Basic process

1. Download and extract.

   wget https://example.com/software-1.0.tar.gz
   tar -xzf software-1.0.tar.gz && cd software-1.0

2. Configure. Autotools:

   ./configure --prefix=$HOME/software/myapp-1.0 \
               CFLAGS="-O3 -march=skylake-avx512" \
               CXXFLAGS="-O3 -march=skylake-avx512"

   or CMake:

   mkdir build && cd build
   cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/software/myapp-1.0 \
            -DCMAKE_BUILD_TYPE=Release \
            -DCMAKE_C_FLAGS="-O3 -march=skylake-avx512"

3. Compile.

   make -j $(nproc)

   Avoid more than a few cores on login nodes — request an interactive job for large builds (see login node etiquette).

4. Test.

   make check   # or: make test

5. Install.

   make install

After installation

export PATH=$HOME/software/myapp-1.0/bin:$PATH
export LD_LIBRARY_PATH=$HOME/software/myapp-1.0/lib:$LD_LIBRARY_PATH

Add these to ~/.bashrc for interactive use, and include them in every SBATCH script that uses the software — loading the same modules at runtime that you used at compile time.

Personal modulefiles (advanced)

mkdir -p $HOME/privatemodules/myapp
# create $HOME/privatemodules/myapp/1.0 following the system modulefile format
module use $HOME/privatemodules    # add to ~/.bashrc
module load myapp/1.0

Troubleshooting

• Compiler not found — load a compiler module first
• Missing dependencies — check module avail dependency-name
• Crashes immediately — library path issue; check with ldd and fix LD_LIBRARY_PATH
• Undefined references — load the same modules as at compile time
• Poor performance — recompile with -O3 and the right -march flag
• Won't run on another node type — architecture-specific build; use generic flags or separate builds