Unable to build

[THoltgrefe]

I tried to build an apptainer/singularity container with vina-gpu2.1, but it fails because certain files from boost can't be found. I tried this on my local computer (which is the .def file I provided) and on a HPC with boost and cuda modules, but neither work.

gcc -o AutoDock-Vina-GPU-2-1 -I/root/boost_1_84_0 -I/root/boost_1_84_0/boost -I/opt/autodock-vina/AutoDock-Vina-GPU-2.1/lib -I/opt/autodock-vina/AutoDock-Vina-GPU-2.1/OpenCL/inc -I/usr/local/cuda/include ./main/main.cpp -O3 ./lib/*.cpp ./OpenCL/src/wrapcl.cpp /root/boost_1_84_0/libs/thread/src/pthread/thread.cpp /root/boost_1_84_0/libs/thread/src/pthread/once.cpp -lboost_program_options -lboost_system -lboost_filesystem -lOpenCL -lstdc++ -lstdc++fs -lm -lpthread -L/root/boost_1_84_0/stage/lib -L/usr/local/cuda/lib64 -DOPENCL_3_0 -DNVIDIA_PLATFORM -DSMALL_BOX -DBOOST_TIMER_ENABLE_DEPRECATED -DNDEBUG -DBUILD_KERNEL_FROM_SOURCE
./main/main.cpp:28:10: fatal error: boost/program_options.hpp: No such file or directory
28 | #include <boost/program_options.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
./lib/cache.cpp:32:18: fatal error: boost/archive/text_oarchive.hpp: No such file or directory
32 | #include <boost/archive/text_oarchive.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/coords.h:26,
from ./lib/coords.cpp:23:
./lib/conf.h:26:10: fatal error: boost/ptr_container/ptr_vector.hpp: No such file or directory
26 | #include <boost/ptr_container/ptr_vector.hpp> // typedef output_container
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/current_weights.h:26,
from ./lib/current_weights.cpp:23:
./lib/terms.h:26:10: fatal error: boost/ptr_container/ptr_vector.hpp: No such file or directory
26 | #include <boost/ptr_container/ptr_vector.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/everything.h:26,
from ./lib/everything.cpp:23:
./lib/terms.h:26:10: fatal error: boost/ptr_container/ptr_vector.hpp: No such file or directory
26 | #include <boost/ptr_container/ptr_vector.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/array3d.h:27,
from ./lib/grid.h:26,
from ./lib/grid.cpp:23:
./lib/common.h:39:10: fatal error: boost/serialization/vector.hpp: No such file or directory
39 | #include <boost/serialization/vector.hpp> // can't come before the above two - wart fixed in upcoming Boost versions
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/igrid.h:26,
from ./lib/cache.h:27,
from ./lib/main_procedure_cl.cpp:1:
./lib/common.h:39:10: fatal error: boost/serialization/vector.hpp: No such file or directory
39 | #include <boost/serialization/vector.hpp> // can't come before the above two - wart fixed in upcoming Boost versions
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/ssd.h:35,
from ./lib/manifold.h:28,
from ./lib/manifold.cpp:23:
./lib/model.h:26:10: fatal error: boost/optional.hpp: No such file or directory
26 | #include <boost/optional.hpp> // for context
| ^~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/model.cpp:23:
./lib/model.h:26:10: fatal error: boost/optional.hpp: No such file or directory
26 | #include <boost/optional.hpp> // for context
| ^~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/ssd.h:35,
from ./lib/monte_carlo.h:26,
from ./lib/monte_carlo.cpp:23:
./lib/model.h:26:10: fatal error: boost/optional.hpp: No such file or directory
26 | #include <boost/optional.hpp> // for context
| ^~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/mutate.h:26,
from ./lib/mutate.cpp:23:
./lib/model.h:26:10: fatal error: boost/optional.hpp: No such file or directory
26 | #include <boost/optional.hpp> // for context
| ^~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/igrid.h:26,
from ./lib/naive_non_cache.h:26,
from ./lib/naive_non_cache.cpp:23:
./lib/common.h:39:10: fatal error: boost/serialization/vector.hpp: No such file or directory
39 | #include <boost/serialization/vector.hpp> // can't come before the above two - wart fixed in upcoming Boost versions
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/igrid.h:26,
from ./lib/non_cache.h:26,
from ./lib/non_cache.cpp:23:
./lib/common.h:39:10: fatal error: boost/serialization/vector.hpp: No such file or directory
39 | #include <boost/serialization/vector.hpp> // can't come before the above two - wart fixed in upcoming Boost versions
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/parallel.h:28,
from ./lib/parallel_mc.cpp:23:
./lib/common.h:39:10: fatal error: boost/serialization/vector.hpp: No such file or directory
39 | #include <boost/serialization/vector.hpp> // can't come before the above two - wart fixed in upcoming Boost versions
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/parallel_progress.cpp:25:
./lib/parallel_progress.h:26:10: fatal error: boost/progress.hpp: No such file or directory
26 | #include <boost/progress.hpp>
| ^~~~~~~~~~~~~~~~~~~~
compilation terminated.
./lib/parse_pdbqt.cpp:26:10: fatal error: boost/utility.hpp: No such file or directory
26 | #include <boost/utility.hpp> // for noncopyable
| ^~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/pdb.h:26,
from ./lib/pdb.cpp:23:
./lib/common.h:39:10: fatal error: boost/serialization/vector.hpp: No such file or directory
39 | #include <boost/serialization/vector.hpp> // can't come before the above two - wart fixed in upcoming Boost versions
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/quasi_newton.h:26,
from ./lib/quasi_newton.cpp:23:
./lib/model.h:26:10: fatal error: boost/optional.hpp: No such file or directory
26 | #include <boost/optional.hpp> // for context
| ^~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/quaternion.cpp:23:
./lib/quaternion.h:26:10: fatal error: boost/math/quaternion.hpp: No such file or directory
26 | #include <boost/math/quaternion.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/random.cpp:25:
./lib/random.h:26:10: fatal error: boost/random.hpp: No such file or directory
26 | #include <boost/random.hpp>
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/ssd.h:35,
from ./lib/ssd.cpp:23:
./lib/model.h:26:10: fatal error: boost/optional.hpp: No such file or directory
26 | #include <boost/optional.hpp> // for context
| ^~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/szv_grid.h:26,
from ./lib/szv_grid.cpp:23:
./lib/model.h:26:10: fatal error: boost/optional.hpp: No such file or directory
26 | #include <boost/optional.hpp> // for context
| ^~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/terms.cpp:23:
./lib/terms.h:26:10: fatal error: boost/ptr_container/ptr_vector.hpp: No such file or directory
26 | #include <boost/ptr_container/ptr_vector.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/weighted_terms.h:26,
from ./lib/weighted_terms.cpp:23:
./lib/terms.h:26:10: fatal error: boost/ptr_container/ptr_vector.hpp: No such file or directory
26 | #include <boost/ptr_container/ptr_vector.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from /opt/autodock-vina/AutoDock-Vina-GPU-2.1/OpenCL/inc/wrapcl.h:2,
from ./OpenCL/src/wrapcl.cpp:1:
/opt/autodock-vina/AutoDock-Vina-GPU-2.1/OpenCL/inc/commonMacros.h:13:18: fatal error: CL/opencl.h: No such file or directory
13 | #include "CL/opencl.h"
| ^~~~~~~~~~~~~
compilation terminated.
cc1plus: fatal error: /root/boost_1_84_0/libs/thread/src/pthread/thread.cpp: No such file or directory
compilation terminated.
cc1plus: fatal error: /root/boost_1_84_0/libs/thread/src/pthread/once.cpp: No such file or directory
compilation terminated.
make: *** [Makefile:23: source] Error 1

This is my .def file:

Bootstrap: docker
From: python:3.9-slim

%environment
    export CUDA_PATH=/usr/local/cuda
    export PATH=/usr/local/cuda/bin:$PATH
    export CPATH=/usr/local/cuda/include:$CPATH
    export LIBRARY_PATH=/usr/local/cuda/lib64:$LIBRARY_PATH
    export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
    export CUDA_INCLUDE_PATH=$CUDA_PATH/include
    export CUDA_LIB_PATH=$CUDA_PATH/lib64
    export OPENCL_LIB_PATH=$CUDA_PATH/lib64
    export LD_LIBRARY_PATH=$BOOST_LIB_PATH:$OPENCL_LIB_PATH:$LD_LIBRARY_PATH
    export PATH=/opt/autodock-vina/quickvina2-gpu:$PATH
    export PYTHONPATH=/usr/local/lib/python3.9/site-packages:$PYTHONPATH

%post
    # Set working directory
    mkdir -p /app
    export DEBIAN_FRONTEND=noninteractive
    
    # Update and install packages
    apt-get update && apt-get install -y \
        wget \
        curl \
        unzip \
        cmake \
        ca-certificates \
        git \
        build-essential \
	vim \
	#libboost-all-dev \
        lsb-release && \
    rm -rf /var/lib/apt/lists/*

    # Clone the AutoDock Vina GPU repository
    git clone https://github.com/DeltaGroupNJUPT/Vina-GPU-2.1.git /opt/autodock-vina
    echo "Cloned AutoDock Vina. Current directory: $PWD"

    # Go into the AutoDock-Vina-GPU-2.1 directory
    cd /opt/autodock-vina/AutoDock-Vina-GPU-2.1
    echo "Changed directory to /opt/autodock-vina/AutoDock-Vina-GPU-2.1. Current directory: $PWD"
    chmod +x /opt/autodock-vina/AutoDock-Vina-GPU-2.1

    wget https://boostorg.jfrog.io/artifactory/main/release/1.84.0/source/boost_1_84_0.tar.gz
    tar -xvzf boost_1_84_0.tar.gz
    cd boost_1_84_0

    ./bootstrap.sh --prefix=$HOME/boost_1_84_0
    ./b2 install


    # Set Boost environment variables
    export BOOST_ROOT=$HOME/boost_1_84_0

    # Set Boost environment variables
    #export BOOST_ROOT=/usr/lib/x86_64-linux-gnu
    #export BOOST_ROOT=/apps/arch/2024r1/software/linux-rhel8-cascadelake/gcc-11.3.0/boost-1.83.0-zopo3kmij4kawnp4yx2gh4pqheedk426
    export BOOST_LIB_PATH=$BOOST_ROOT/lib
    export BOOST_INCLUDE_PATH=$BOOST_ROOT/include

    # Set CUDA environment variables
    export CUDA_PATH=/usr/local/cuda
    export CPATH=/usr/local/cuda/include:$CPATH
    export LIBRARY_PATH=/usr/local/cuda/lib64:$LIBRARY_PATH
    export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH

    # Additional environment variables for CUDA
    export CUDA_INCLUDE_PATH=$CUDA_PATH/include
    export CUDA_LIB_PATH=$CUDA_PATH/lib64
    #export OPENCL_LIB_PATH=$CUDA_PATH/lib64
    export OPENCL_LIB_PATH=$CUDA_PATH

    # Set LD_LIBRARY_PATH to include Boost and CUDA libraries
    export LD_LIBRARY_PATH=$BOOST_LIB_PATH:$OPENCL_LIB_PATH:$LD_LIBRARY_PATH
    echo "Environment variables set. Current directory: $PWD"

    # Check if the directory exists and print its contents
    echo "Checking if directory /opt/autodock-vina/AutoDock-Vina-GPU-2.1 exists..."
    if [ -d "/opt/autodock-vina/AutoDock-Vina-GPU-2.1" ]; then
        echo "Directory exists."
        ls -l /opt/autodock-vina/AutoDock-Vina-GPU-2.1
    else
        echo "Error: Directory does not exist!"
        exit 1
    fi

    # Try to change into the directory again
    cd /opt/autodock-vina/AutoDock-Vina-GPU-2.1
    echo "Changed directory again. Current directory: $PWD"

    # Modify the Makefile to use the correct paths for Boost and OpenCL
    sed -i "s|BOOST_LIB_PATH=.*|BOOST_LIB_PATH=${BOOST_ROOT}|" Makefile
    #sed -i "s|BOOST_INCLUDE_PATH=.*|BOOST_INCLUDE_PATH=${BOOST_INCLUDE_PATH}|" Makefile
    sed -i "s|OPENCL_LIB_PATH=.*|OPENCL_LIB_PATH=${OPENCL_LIB_PATH}|" Makefile
    sed -i "s|GPU_PLATFORM=.*|GPU_PLATFORM=-DNVIDIA_PLATFORM|" Makefile
    sed -i "s|OPENCL_VERSION=.*|OPENCL_VERSION=-DOPENCL_3_0|" Makefile
    sed -i "s|WORK_DIR=.*|WORK_DIR=${PWD}|" Makefile
    cat Makefile

    # Build AutoDock Vina GPU
    make clean
    make source

%runscript
    # The default command to run when the container is executed
    exec "$@"

%labels
    Author "Tim Holtgrefe"
    Version "1.0"
    Description "Apptainer container with PIPSA, APBS and pdb2pqr"