Support building HOOMD-blue in RET

requirements/hoomdblue.yml

@@ -0,0 +1,25 @@
+# This file contains only dependencies required by HOOMD-Blue
+---
+- name: hipsparse
+  version: latest
+- name: rocfft
+  version: latest
+- name: hipcub
+  version: latest
+- name: rocrand
+  version: latest
+- name: rocthrust
+  version: latest
+- name: roctracer-dev
+  version: latest
+
+# Define here Ubuntu Packages
+- Ubuntu:
+  - name: python3-dev
+    version: latest
+
+# Define here CentOS Packages
+- CentOS:
+  - name: python36-devel
+    version: latest
+...

requirements/req.yml

@@ -164,6 +164,9 @@ dependencies:
   - namd:
     - req_file: namd.yml
 
+  - hoomdblue:
+    - req_file: hoomdblue.yml
+
 # Project description
 description: ROCm Machine Learning one-script installer xxxxxxxxxxxx xxxxxxxxxxxxxxxxxx xx xxxxxxxxxxxxxxxx 
 ...

src/cmd

@@ -29,6 +29,7 @@ function printUsage {
     echo -e "    [pytorch]                          ${FG_LIGHT_BLUE}: Pytorch Framework${END}"
     echo -e ""
     echo -e "${BOLD}HPC Package:${END}"
+    echo -e "    [hoomdblue]                        ${FG_LIGHT_BLUE}: HOOMD-Blue is a general-purpose particle simulation toolkit. http://glotzerlab.engin.umich.edu/hoomd-blue/ ${END}"
     echo -e "    [namd]                             ${FG_LIGHT_BLUE}: NAMD HPC Application${END}"
     echo -e ""
     echo -e "${BOLD}Container:${END}"
@@ -137,7 +138,7 @@ function parseArgs {
             ;;
 
             # Set Packages ########################################################################
-            "rocm" | "tensorflow" | "pytorch" | "namd")
+            "rocm" | "tensorflow" | "pytorch" | "namd" | "hoomdblue" )
                 # Permitted commands: install, remove and update
                 if [[ ! "$__cmd_parseArgs" =~ ^("install"|"update"|"remove"|"benchmark")$ ]]; then logPrint "ERR" "Wrong command! Did you mean: $0 install $__arg_parseArgs"; exit; fi
                 if [[ "$__arg_parseArgs" =~ ^("tensorflow"|"pytorch")$ ]]; then 
@@ -146,6 +147,7 @@ function parseArgs {
                 fi
 
                 [[ "$__arg_parseArgs" = "namd" ]] && { __arg_parseArgs="$__arg_parseArgs:src"; __isROCmRequired_parseArgs=0; }
+                [[ "$__arg_parseArgs" = "hoomdblue" ]] && { __arg_parseArgs="$__arg_parseArgs:src"; __isROCmRequired_parseArgs=0; }
                 __pkgs_parseArgs+=("$__arg_parseArgs");
               shift
             ;;
@@ -252,6 +254,9 @@ function installCmd {
             namd*)
                 __cmd_array_installCmd=("source /etc/profile.d/namd.sh"); runCmd __cmd_array_installCmd "ERR" 0
             ;;
+            hoomdblue*)
+                __cmd_array_installCmd=("source /etc/profile.d/hoomdblue.sh"); runCmd __cmd_array_installCmd "ERR" 0
+            ;;
 	    esac
         # Install Package
         runInstall "$pkg"
@@ -296,6 +301,9 @@ function runInstall {
                 namd)
                     installNAMD;
                 ;;
+                hoomdblue)
+                    installHOOMDBlue;
+                ;;
             esac
 
             # Run post installation
@@ -376,7 +384,7 @@ function runPreInstallation {
             local __docker_pkg_runPreInstallation=("docker-*"); removePkg __docker_pkg_runPreInstallation
         ;;
 
-        py2 | py3 | singularity | namd)
+        py2 | py3 | singularity | namd | hoomdblue )
             PRE="DONOTHING"
         ;;
     esac
@@ -426,6 +434,9 @@ function runPostInstallation {
             addPATH "namd" "$PWD/../RET_NAMD"
             stopLoadBar
         ;;
+        hoomdblue)
+            POST="DONOTHING"
+        ;;
     esac
 }
 
@@ -475,6 +486,17 @@ function runVerification {
             namdVerification
             return "$?";
         ;;
+        hoomdblue)
+            HOOMD_HEADER="${HOME}/miniconda3/lib/python3.8/site-packages/hoomd/include/HOOMDVersion.h"
+            if [ ! -f "${HOOMD_HEADER}" ]; then
+                return 7;
+            fi
+            #__py_vers_runVerification=$(su -p $SUDO_USER -c "source /etc/profile.d/hoomdblue.sh source /etc/profile.d/mpi.sh && ${HOME}/miniconda3/bin/python3 -c 'import hoomd; print(hoomd.__version__)' 2>&1 | tail -1")
+	    __py_vers_runVerification=$(grep "HOOMD_VERSION " ${HOOMD_HEADER} | sed 's/.*HOOMD_VERSION "\(.*\)"/\1/')
+            logPrint "NOTE" "The current HOOMD-Blue version is: $__py_vers_runVerification"
+            hoomdblueVerification
+            return "$?";
+        ;;
     esac
 }
 
@@ -577,5 +599,10 @@ function runBenchmark {
             namdBenchmark
             return "$?";
         ;;
+        hoomdblue)
+            hoomdblueBenchmark
+            return "$?";
+        ;;
     esac
-}
+}
+

src/cmd_utils

@@ -58,7 +58,7 @@ function addDockerRepo {
     stopLoadBar
 }
 
-# Verify if ROCm installation was successful 
+# Verify if ROCm installation was successful
 function rocmVerification {
     local __cmd_ret_rocmVerification
     local __cmd_rocmVerification="/opt/rocm/bin/rocminfo"
@@ -130,6 +130,17 @@ function namdVerification {
     fi
 }
 
+# Verify if HOOMD-Blue installation was successful
+function hoomdblueVerification {
+    if (confirmYn "Run HOOMD-Blue benchmark? [Y/n] "); then
+        startLoadBar "Run HOOMD-Blue Verification"; printf '\n'
+        runBenchmark "hoomdblue" EMPTY_ARRAY
+        stopLoadBar
+        return "$?"
+    fi
+    return 0;
+}
+
 # Run TensorFlow benchmark
 function tfBenchmark {
     local -n __models_tfBenchmark=$1
@@ -180,6 +191,33 @@ function namdBenchmark {
     return $__ret_value_namdBenchmark;    
 }
 
+# Run HOOMD-Blue benchmark
+function hoomdblueBenchmark {
+    local __url_hoomdblueBenchmark="https://jglaser@github.com/glotzerlab/hoomd-benchmarks.git"
+    local __cmd_array_hoomdblueBenchmark=()
+    local __cmd_python_hoomdblueBenchmark="${HOME}/miniconda3/bin/python3"
+    local __ret_value_hoomdblueBenchmark=0
+
+    if [ ! -d "$WORK_DIRECTRORY/hoomd-benchmarks" ]; then
+        __cmd_array_hoomdblueBenchmark=("su -p $SUDO_USER -c 'git clone $__url_hoomdblueBenchmark $WORK_DIRECTRORY/hoomd-benchmarks && cd $WORK_DIRECTRORY/hoomd-benchmarks && git checkout next'"); runCmd __cmd_array_hoomdblueBenchmark "ERR"
+    fi
+
+    # Run the benchmark
+    startLoadBar "Run LJ Liquid 1M particles - Single Precision"; printf '\n'
+
+    SOURCE_FILES=""
+    if [ -f /etc/profile.d/hooomdblue.sh ]; then
+        SOURCE_FILES+="source /etc/profile.d/hoomdblue.sh && "
+    fi
+    if [ -f /etc/profile.d/mpi.sh ]; then
+        SOURCE_FILES+="source /etc/profile.d/mpi.sh && "
+    fi
+    __cmd_array_hoomdblueBenchmark=("su -p $SUDO_USER -c '$SOURCE_FILES cd $WORK_DIRECTRORY/hoomd-benchmarks && $__cmd_python_hoomdblueBenchmark ./project.py run lj_liquid-benchmark-gpu_np1'"); runCmd __cmd_array_hoomdblueBenchmark "ERR"
+    runCmd __cmd_array_hoomdblueBenchmark "ERR" 0 && stopLoadBar "LJ Liquid 1M particles benchmark Done" || { stopLoadBar "LJ Liquid 1M particules benchmark Failed" "ERR"; __ret_value_hoomdblueBenchmark=1; }
+
+    return $__ret_value_hoomdblueBenchmark;
+}
+
 # Build Package Array by key and check if packages already installed
 # Input  $1: Key
 # Output $2: Package array and updated array
@@ -426,6 +464,111 @@ function installNAMD {
                                        || stopLoadBar "Install Completed Successfully."
 }
 
+# Install HOOMD-Blue from Source
+# This should be removed once HOOMD-Blue support DEP & RPM package installation
+function installHOOMDBlue {
+    local __cmd_ret_installHOOMDBlue
+    local __retPath_installHOOMDBlue="${HOME}/miniconda3/lib/python3.8/site-packages/hoomd"
+    local __cmd_array_installHOOMDBlue=()
+    local __url_HOOMDBlue_installHOOMDBlue="https://github.com/glotzerlab/hoomd-blue.git"
+    local __url_Miniconda_installHOOMDBlue="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"
+
+    local __nProc_installHOOMDBlue=`grep -c ^processor /proc/cpuinfo`
+    local __inst_root_installHOOMDBlue="$TEMP_DIRECTRORY/hoomdblue"
+    local __inst_root_installMiniconda="$TEMP_DIRECTRORY/miniconda"
+
+    # Confirmation message
+    logPrint "STEP" "Build HOOMD-Blue"
+
+    # Set the ROCm binaries in PATH
+    __cmd_array_installHOOMDBlue=("source /etc/profile.d/rocm.sh"); runCmd __cmd_array_installHOOMDBlue "ERR"
+
+    # Install MPI ############*######################################################################################
+    #installMPI
+
+    # Build Miniconda3 ##############################################################################################
+    startLoadBar "Miniconda3 install"
+
+    CONDA="${HOME}/miniconda3/bin/conda"
+    CONDA_PREFIX="${HOME}/miniconda3"
+    if [ -d "${CONDA_PREFIX}" ]; then
+        if (confirmYn "Remove previous Miniconda3 install at ${HOME}/miniconda3? [Y/n] "); then
+            startLoadBar "Removing Miniconda3 at ${HOME}/miniconda3"; printf '\n'
+            __cmd_array_installHOOMDBlue=("su -p $SUDO_USER -c 'rm -fr ${HOME}/miniconda3'")
+            runCmd __cmd_array_installHOOMDBlue "ERR"
+            stopLoadBar
+        fi
+    fi
+
+    logPrint "STEP" "Miniconda3 download"
+
+    __cmd_array_installHOOMDBlue=("su -p $SUDO_USER -c 'mkdir -p $__inst_root_installMiniconda; cp $HOME/Miniconda3-latest-Linux-x86_64.sh $__inst_root_installMiniconda/Miniconda3-latest-Linux-x86_64.sh'")
+    runCmd __cmd_array_installHOOMDBlue "ERR"
+    #__cmd_array_installHOOMDBlue=("wget --progress=dot -P $__inst_root_installMiniconda $__url_Miniconda_installHOOMDBlue")
+    #runCmd __cmd_array_installHOOMDBlue "ERR" "1" "Download Miniconda3" "0"
+
+    export PATH="${HOME}/miniconda3/bin:${HOME}/miniconda3/bin:${PATH}"
+    __cmd_array_installHOOMDBlue=("su -p $SUDO_USER -c 'sh $__inst_root_installMiniconda/Miniconda3-latest-Linux-x86_64.sh -b -u && $CONDA init'")
+    runCmd __cmd_array_installHOOMDBlue "ERR"
+
+    __cmd_array_installHOOMDBlue=("su -l -p $SUDO_USER -c '$CONDA install -y -c anaconda python=3.8'")
+    runCmd __cmd_array_installHOOMDBlue "ERR"
+    __cmd_array_installHOOMDBlue=("su -l -p $SUDO_USER -c '$CONDA update -y --all'")
+    runCmd __cmd_array_installHOOMDBlue "ERR"
+
+    logPrint "STEP" "Miniconda3 installing cmake, numpy, pybind11, eigen, cereal, signac-flow"
+    __cmd_array_installHOOMDBlue=("su -p $SUDO_USER -c '$CONDA install -y cmake numpy pybind11 eigen && $CONDA install -y -c conda-forge cereal signac-flow'")
+    runCmd __cmd_array_installHOOMDBlue "ERR"
+
+    __cmd_array_installHOOMDBlue=("echo 'export CMAKE_PREFIX_PATH=$CONDA_PREFIX' >> ${HOME}/.bashrc")
+    runCmd __cmd_array_installHOOMDBlue "ERR"
+
+    stopLoadBar "Miniconda3 install completed successfully."
+
+    # Clone HOOMDBlue #######################################################################################################
+    startLoadBar "Clone HOOMD-Blue repository"
+
+    __cmd_array_installHOOMDBlue=("su -p $SUDO_USER -c \"git clone ${__url_HOOMDBlue_installHOOMDBlue} $__inst_root_installHOOMDBlue && cd $__inst_root_installHOOMDBlue && git checkout next && git submodule update --init"\")
+    runCmd __cmd_array_installHOOMDBlue "ERR"
+
+    stopLoadBar "Clone HOOMD-Blue completed successfully."
+
+    # Build the HOOMDBlue ###############################################################################################
+    startLoadBar "Build HOOMD-Blue"
+
+    if [ -d "$__inst_root_installHOOMDBlue/build" ]; then
+        __cmd_array_installHOOMDBlue=("su -p $SUDO_USER -c 'rm -fr $__inst_root_installHOOMDBlue/build'")
+        runCmd __cmd_array_installHOOMDBlue "ERR"
+    fi
+    __cmd_array_installHOOMDBlue=("su -p $SUDO_USER -c 'mkdir $__inst_root_installHOOMDBlue/build'")
+    runCmd __cmd_array_installHOOMDBlue "ERR"
+
+    CMAKE_CMD="cmake "
+    CMAKE_CMD+="-DPYTHON_EXECUTABLE=${HOME}/miniconda3/bin/python3 "
+    CMAKE_CMD+="-DENABLE_GPU=ON -DSINGLE_PRECISION=ON "
+    CMAKE_CMD+="-DENABLE_MPI=ON "
+    #CMAKE_CMD+="-D ENABLE_MPI_CUDA=ON " # Turn ON for ROCm-enabled MPI
+    CMAKE_CMD+="-DCMAKE_INSTALL_PREFIX=${HOME}/miniconda3 "
+    CMAKE_CMD+="-DPYTHON_SITE_INSTALL_DIR=${HOME}/miniconda3/lib/python3.8/site-packages/hoomd "
+    CMAKE_CMD+="-DCMAKE_PREFIX_PATH=${HOME}/miniconda3 "
+    CMAKE_CMD+="-B $__inst_root_installHOOMDBlue/build $__inst_root_installHOOMDBlue "
+
+    __cmd_array_installHOOMDBlue=("su -p $SUDO_USER -c 'source ~/.bashrc && cd $__inst_root_installHOOMDBlue/build && $CMAKE_CMD'")
+    runCmd __cmd_array_installHOOMDBlue "ERR"
+
+    __cmd_array_installHOOMDBlue=("su -p $SUDO_USER -c 'source ~/.bashrc && cd $__inst_root_installHOOMDBlue/build && make install -j$__nProc_installHOOMDBlue'")
+    runCmd __cmd_array_installHOOMDBlue "ERR"
+
+    stopLoadBar "Build HOOMD-Blue completed successfully."
+
+    ##################################################################################################################
+
+    # Back to the RET folder
+    cd "$__retPath_installHOOMDBlue"
+
+    [ $? -ne 0 ] && stopLoadBar "There was a problem building HOOMD-Blue!" "ERR" "make" \
+                                       || stopLoadBar "Install Completed Successfully."
+}
 
 # Build Package with cmake
 # Input $1: source code url
@@ -473,4 +616,4 @@ function buildFromSource {
         runCmd __cmd_array_buildFromSource "ERR" "1" "Build/Install $__dist_dir_name_buildFromSource" "0"
     done
     stopLoadBar
-}
+}