milc_centos.conf

BootStrap: yum
OSVersion: 7
MirrorURL: http://linux-ftp.jf.intel.com/pub/mirrors/centos/7.4.1708/os/$basearch/

Include: yum

#Commands in the %setup section are executed on the host system outside of the container after the base OS has been installed
%setup
	echo "Looking in the directory '$SINGULARITY_ROOTFS'"
        echo "Copying the dist files into '$SINGULARITY_ROOTFS'"
        mkdir -p $SINGULARITY_ROOTFS/tempdir
        if [ ! -x "$SINGULARITY_ROOTFS/tempdir" ]; then
           echo "failed to create tempdir directory..."
           exit 1
        fi

        DIR="/localdisk/sdouyeb/milc/run/"
        cp -r $DIR. $SINGULARITY_ROOTFS/tempdir
        if [ "$(ls -A $SINGULARITY_ROOTFS/tempdir/)" ]; then
                   echo "Files are copies here $SINGULARITY_ROOTFS/tempdir"
                   ls $SINGULARITY_ROOTFS/tempdir/
        fi

        chmod -R 777 $SINGULARITY_ROOTFS/tempdir

        exit 0


#Commands in the %post section are executed within the container after the base OS has been installed at build time
%post
        echo "Hello from inside the post container"

		#set the proxy in the post script
        export http_proxy="http://proxy-us.intel.com:911"		
        export https_proxy="http://proxy-us.intel.com:912"

		#install compiler run time libraries 
        rpm --import https://yum.repos.intel.com/2018/setup/RPM-GPG-KEY-intel-psxe-runtime-2018 	
        rpm -Uhv https://yum.repos.intel.com/2018/setup/intel-psxe-runtime-2018-reposetup-1-0.noarch.rpm

        echo "installing runtime"
        yum install intel-psxe-runtime -y
        yum install gcc -y
		yum install bc -y

        
# Set environment variables to be sourced at runtime
%environment
        echo "set the env variable"
        OMP_NUM_THREADS=5
        KMP_AFFINITY='granularity=fine,scatter'

#The %runscript gets persisted within the container to a file which is the execution driver when the container image is run
%runscript
        echo "This is what happens when you run the container..."

        source /opt/intel/psxe_runtime_2018.1.161/linux/bin/compilervars.sh intel64
        echo "run milc for SKL"

        cd $SINGULARITY_ROOTFS/tempdir/
        echo "current dir"
        mpiexec.hydra -n 8 $SINGULARITY_ROOTFS/tempdir/su3_rhmd_hisq.skx < $SINGULARITY_ROOTFS/tempdir/params.24x24x24x24 |tee $SINGULARITY_ROOTFS/tempdir/milc.su3_rhmd_hisq.log

        echo "parse milc results to $SINGULARITY_ROOTFS/tempdir"
        $SINGULARITY_ROOTFS/tempdir/parse_milc.sh -l qphix -m flops -r $SINGULARITY_ROOTFS/milc.su3_rhmd_hisq.log