Setup Guide — DB Training 2026

Option A · Automated Script (recommended)

Download and run the setup script — it handles all four steps automatically.

bash

bash setup-hdf5.sh

An optional install prefix can be passed as the first argument (default: $HOME/tools/hdf5-1.8.23).

Or follow Option B below to run each step manually.

Option B · Manual Steps

This guide walks through installing dependencies, building HDF5 from source, and compiling the loadmatrix_geno program step by step.

ⓘ Designed for Linux systems, particularly Ubuntu. Windows users: use WSL2 or a Linux virtual machine before proceeding.

0 Install Required Software

Update package lists and install bcftools and the C++ build tools:

bash

sudo apt update
sudo apt install -y bcftools build-essential

1 Obtain HDF5

Download the HDF5 1.8.23 source package from the HDF Group:

https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.23/src/hdf5-1.8.23.tar.gz

Or download directly from the terminal:

bash

wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.23/src/hdf5-1.8.23.tar.gz

2 Extract and Navigate

Extract the archive and change into the source directory:

bash

tar -xzvf hdf5-1.8.23.tar.gz
cd hdf5-1.8.23

3 Configure and Build HDF5

Run the standard build sequence. This may take several minutes:

bash

./configure
make
make install

The library will be installed under hdf5-1.8.23/hdf5/ by default. Note the path to the lib/ and include/ subdirectories — you will need them in the next step.

4 Compile Roven's Program

Download the source file

Download loadmatrix_SNP-annot.cpp and place it in your working directory:

📄 loadmatrix_SNP-annot.cpp

Create the build script

Create a file named build.sh with the following content. Change the lib variable to match the directory where you installed the HDF5 library on your system (e.g., /home/yourname/Tools/hdf5-1.8.23/hdf5/lib):

build.sh

#!/bin/bash

main=/home/riza/Tools/hdf5-1.8.23
lib=$main/hdf5/lib
include=$main/hdf5/include
header=$include

export PATH=$main/hdf5/bin:$PATH
export LD_RUN_PATH=$lib
export LDFLAGS="-L$lib"
export CPPFLAGS="-I$include"

g++ -Wno-narrowing -o loadmatrix_geno -I $header loadmatrix_SNP-annot.cpp -lhdf5 -L$lib

ⓘ Change the path assigned to the lib variable to match the directory where you installed the HDF5 library on your system.

Make executable and run

bash

chmod u+x build.sh
./build.sh

Verify the build

Run the compiled program to confirm it built successfully. It should display usage parameters and an error indicating it requires arguments — this is expected:

bash

./loadmatrix_geno