Apptainer build Process: Added def file, README, required debian packages

.gitignore

@@ -2,3 +2,4 @@
 /.vscode
 *.cache
 *.code-workspace
+miscs/apptainer/vortex_fpga.sif

docs/fpga_setup.md

@@ -63,6 +63,12 @@ $ source /opt/xilinx/xrt/setup.sh
 $ source /tools/reconfig/xilinx/Vitis/2023.1/settings64.sh
 ```
 
+If you are using an apptainer,
+```
+$ export LD_LIBRARY_PATH=/opt/boost-1.66/lib/:/opt/openssl-1.1/lib/:$LD_LIBRARY_PATH
+```
+
+
 ### Check Installed FPGA Platforms
 `platforminfo -l` which tells us the correct name of the platform installed on the current fpga node. It should be used for the `PLATFORM` variable below. Otherwise, if there is an error then there was an issue with the previous two commands.
 

miscs/apptainer/README.md

@@ -0,0 +1,39 @@
+# Apptainer Build Process
+
+Use the Slurm scheduler to request an interactive job on Flubber9
+```
+salloc -p rg-fpga --nodes=1 --ntasks-per-node=64 --mem=16G --nodelist flubber9 --time=01:00:00
+```
+
+Go to `apptainer` directory
+
+```
+$ pwd
+vortex/miscs/apptainer
+
+$  apptainer build --no-https vortex_fpga.sif vortex_fpga.def 
+
+```
+To start the apptainer,
+```
+$ apptainer shell --fakeroot  --cleanenv --writable-tmpfs --bind /opt/xilinx/:/opt/xilinx/ --bind /netscratch/rn84/devnull:/dev/null --bind /dev/bus/usb,/sys/bus/pci --bind /projects:/projects --bind /tools:/tools  --bind /netscratch:/netscratch vortex_fpga.sif
+```
+
+Inside the Apptainer,
+```
+Apptainer> lsusb
+
+should show devices connected to machine on which you are running this command
+```
+
+
+```
+Apptainer> source /opt/xilinx/xrt/setup.sh
+Apptainer> source /tools/reconfig/xilinx/Vitis/2023.1/settings64.sh
+
+Apptainer> platforminfo -l
+```
+
+
+
+

miscs/apptainer/install_boost_openssl.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+
+set -e  # Exit on error
+echo "Installing Boost and OpenSSL from .deb packages"
+
+# Extract and install Boost
+echo "Extracting Boost..."
+ar -x boost-package.deb
+ls
+mkdir -p /tmp/boost-extract
+tar --zstd --no-same-owner -xvf data.tar.zst -C /tmp/boost-extract
+ls -l /tmp/boost-extract/
+cp -r /tmp/boost-extract/opt/boost-1.66/ /opt/
+ls -l /opt/boost-1.66/
+rm -rf data.tar
+
+# Extract and install OpenSSL
+echo "Extracting OpenSSL..."
+ar -x openssl-package.deb
+mkdir -p /tmp/openssl-extract
+tar --zstd --no-same-owner -xvf data.tar.zst -C /tmp/openssl-extract
+ls -l /tmp/openssl-extract/
+cp -r /tmp/openssl-extract/opt/openssl-1.1/ /opt/
+ls -l /opt/openssl-1.1/
+rm -rf data.tar
+
+
+
+echo "Boost and OpenSSL installation complete!"

miscs/apptainer/vortex_fpga.def

@@ -0,0 +1,97 @@
+Bootstrap: docker
+From: ubuntu:22.04
+
+
+%files
+    install_boost_openssl.sh .
+    openssl-package.deb .
+    boost-package.deb .
+
+%post
+    echo "Setting up the environment..."
+
+
+    touch /var/log/apt/term.log
+    if [ -f /var/log/apt/term.log ]; then
+        chown root:adm /var/log/apt/term.log || true
+    fi
+
+
+    # Set environment variable to avoid interactive prompts during installation
+    export DEBIAN_FRONTEND=noninteractive
+    echo 'APT::Sandbox::User "root";' > /etc/apt/apt.conf.d/no-sandbox
+    mkdir -p /netscratch
+
+    # Update and install base dependencies
+    apt-get update
+    apt-get install -y libc6 fakeroot
+
+    # Fix dependency issues
+    apt-get install -f -y || true
+    dpkg --configure -a || true
+
+    # Reinstall problematic packages
+    apt-get remove --purge -y dbus fontconfig-config || true
+    apt-get install -y dbus fontconfig-config || true
+
+    rm -f /var/lib/dpkg/lock-frontend
+    rm -f /var/lib/dpkg/lock
+    rm -f /var/cache/apt/archives/lock
+
+    # mount -o remount,rw /usr
+    # mount -o remount,rw /var
+    chown -R root:root /usr/lib/dbus-1.0/dbus-daemon-launch-helper || true
+
+
+    # Install necessary packages
+    apt-get install -y fontconfig libfontconfig1 libpangoft2-1.0-0 libbluray2 \
+                       libpangocairo-1.0-0 libavformat58 libpango-1.0-0 \
+                       openjdk-11-jre-headless libcairo2 librsvg2-2 librsvg2-common \
+                       openjdk-11-jre-zero libtheora0 libavcodec58 libcairo-gobject2 \
+                       ca-certificates-java libchromaprint1 software-properties-common perl-modules bzip2 \
+                       unzip zlib1g-dev libtinfo5 g++ usbutils gawk bison gcc make wget tar python3.9 locales zstd uuid-dev git || true
+
+    ln -s /usr/bin/python3 /usr/bin/python
+
+    locale-gen en_US.UTF-8
+    update-locale LANG=en_US.UTF-8 LANGUAGE=en_US.UTF-8 LC_ALL=en_US.UTF-8
+
+    # Run dpkg to ensure everything is properly configured
+    dpkg --configure -a || true
+
+    # Clean up apt cache
+    apt-get clean
+    rm -rf /var/lib/apt/lists/*
+
+    echo "Setting up the environment..."
+
+    # Copy the installation script into the container
+    cp install_boost_openssl.sh /tmp/
+
+    # Execute the script
+    chmod +x /tmp/install_boost_openssl.sh
+    /tmp/install_boost_openssl.sh
+
+    # Clean up
+    rm -f /tmp/install_boost_openssl.sh
+
+%environment
+    export LANG=en_US.UTF-8
+    export LANGUAGE=en_US.UTF-8
+    export LC_ALL=en_US.UTF-8
+    export HOME=/home/developer
+
+
+
+%runscript
+    exec /bin/bash
+
+%labels
+    Author Rahul
+    Version 1.0
+
+%test
+    echo "Container test successful!"
+    locale
+    lsusb || echo "lsusb not available"
+    ls -l /dev/null