rocmsys · vickytsang · Nov 27, 2019 · Nov 28, 2019 · Dec 3, 2019
diff --git a/requirements/gromacs.yml b/requirements/gromacs.yml
@@ -0,0 +1,13 @@
+  - GDRCopy:
+    - name: autoconf
+      version: latest      
+    - name: automake
+      version: latest
+    - name: libtool
+      version: latest 
+    - name: libnuma-dev 
+      version: latest
+    - name: numactl
+      version: latest
+    - name: flex
+      version: latest
diff --git a/requirements/req.yml b/requirements/req.yml
@@ -164,6 +164,8 @@ dependencies:
   - namd:
     - req_file: namd.yml
 
+  - gromacs:
+    - req_file: gromacs.yml
 # Project description
 description: ROCm Machine Learning one-script installer xxxxxxxxxxxx xxxxxxxxxxxxxxxxxx xx xxxxxxxxxxxxxxxx 
 ...

diff --git a/src/cmd b/src/cmd
@@ -137,7 +137,7 @@ function parseArgs {
             ;;
 
             # Set Packages ########################################################################
-            "rocm" | "tensorflow" | "pytorch" | "namd")
+            "rocm" | "tensorflow" | "pytorch" | "namd" | "gromacs")
                 # 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 +146,7 @@ function parseArgs {
                 fi
 
                 [[ "$__arg_parseArgs" = "namd" ]] && { __arg_parseArgs="$__arg_parseArgs:src"; __isROCmRequired_parseArgs=0; }
+		[[ "$__arg_parseArgs" = "gromacs" ]] && { __arg_parseArgs="$__arg_parseArgs:src"; __isROCmRequired_parseArgs=0; }
                 __pkgs_parseArgs+=("$__arg_parseArgs");
               shift
             ;;
@@ -296,6 +297,9 @@ function runInstall {
                 namd)
                     installNAMD;
                 ;;
+		gromacs)
+                    installGROMACS;
+                ;;
             esac
 
             # Run post installation
@@ -578,4 +582,4 @@ function runBenchmark {
             return "$?";
         ;;
     esac
-}
+}
diff --git a/src/cmd_utils b/src/cmd_utils
@@ -473,4 +473,84 @@ function buildFromSource {
         runCmd __cmd_array_buildFromSource "ERR" "1" "Build/Install $__dist_dir_name_buildFromSource" "0"
     done
     stopLoadBar
-}
+}
+
+
+# Install GROMACS from Source
+# This should be removed once GROMACS support DEP & RPM package installation
+function installGROMACS {
+    local __cmd_ret_installGROMACS
+    local __retPath_installGROMACS=$(pwd)
+    local __cmd_array_installGROMACS=()
+    local __url_GROMACS_installGROMACS="http://gitlab1.amd.com/dc-hpc/gromacs-hip.git"
+    local __url_OpenMPI_installGROMACS="https://github.com/open-mpi/ompi.git -b v4.0.1"
+    local __url_GDRCOPY_installGROMACS="https://github.com/NVIDIA/gdrcopy.git -b v1.3"
+    local __url_UCX_installGROMACS="https://github.com/openucx/ucx.git -b v1.6.0"
+
+    #local __inst_root_installMPI="$TEMP_DIRECTRORY/mpi_install"
+    local __inst_root_installMPI="/home/amd/work/vicky/GROMACS/RET/mpi_install"
+
+    local __inst_root_installGROMACS="$__inst_root_installMPI/gromacs"
+    local __inst_root_installOpenMPI="$__inst_root_installMPI/ompi"
+    local __inst_root_installGDRCOPY="$__inst_root_installMPI/gdr"
+    local __inst_root_installGDRCOPY_SRC="$__inst_root_installMPI/gdrcopy"
+    local __inst_root_installGDRCOPY_LIB="$__inst_root_installGDRCOPY/lib64"
+    local __inst_root_installGDRCOPY_INCLUDE="$__inst_root_installGDRCOPY/include"
+    local __inst_root_installUCX="$__inst_root_installMPI/ucx"
+
+    # Confirmation message
+    logPrint "STEP" "Build GROMACS"
+
+    # Set the ROCm binaries in PATH
+    __cmd_array_installGROMACS=("source /etc/profile.d/rocm.sh"); runCmd __cmd_array_installGROMACS "ERR"
+
+    # Clone GDRCPY #######################################################################################################
+    startLoadBar "Clone GDRCOPY Repository"
+
+    __cmd_array_installGROMACS=("su -p $SUDO_USER -c 'git clone ${__url_GDRCOPY_installGROMACS} $__inst_root_installGDRCOPY_SRC'")
+    runCmd __cmd_array_installGROMACS "ERR"
+
+    stopLoadBar "Clone GDRCOPY Completed Successfully."    
+
+    # Build GDRCPY ##############################################################################################
+    startLoadBar "Build GDRCOPY"
+
+    __cmd_array_installGROMACS=("cd $__inst_root_installGDRCOPY_SRC && mkdir -p $__inst_root_installGDRCOPY_LIB $__inst_root_installGDRCOPY_INCLUDE")
+    runCmd __cmd_array_installGROMACS "ERR"
+
+    __cmd_array_installGROMACS=("make PREFIX=$__inst_root_installGDRCOPY lib install && cd $__inst_root_installMPI")
+    runCmd __cmd_array_installGROMACS "ERR"
+
+    stopLoadBar "Build GDRCOPY Completed Successfully."
+
+    # Build UCX ##############################################################################################
+    __cmd_array_installGROMACS=("cd $__inst_root_installUCX && ./autogen.sh" "mkdir build && cd build && ../contrib/configure-release --prefix=$__inst_root_installUCX --with-rocm=/opt/rocm --with-gdrcopy=$__inst_root_installGDRCOPY" "sudo make -j$(nproc) && sudo make -j$(nproc) install" "cd $__inst_root_installGROMACS")
+    buildFromSource "$__url_UCX_installGROMACS" "$__inst_root_installUCX" __cmd_array_installGROMACS "ucx" "ucx" "0"
+
+    # Build OMPI ##############################################################################################
+    __cmd_array_installGROMACS=("cd $__inst_root_installOpenMPI && ./autogen.pl && mkdir build && cd build && ../configure --prefix=$__inst_root_installOpenMPI/ompi --with-ucx=$__inst_root_install_UCX && sudo make -j\$(nproc) && sudo make -j\$(nproc) install && cd $__inst_root_installGROMACS")
+    #buildFromSource "$__url_OpenMPI_installGROMACS" "$__inst_root_installOpenMPI" __cmd_array_installGROMACS "ompi" "ompi" "0"
+
+    __cmd_array_installGROMACS=("echo 'export PATH=$ROCM_PATH/hcc/bin:$ROCM_PATH/hip/bin:$ROCM_PATH/bin:$ROCM_PATH/hcc/bin:\${PATH:+:\${PATH}}' | tee -a /etc/profile.d/gromacs.sh && echo 'export LD_LIBRARY_PATH=$ROCM_PATH/lib:/usr/local/lib:\${LD_LIBRARY_PATH:+:\${LD_LIBRARY_PATH}}' | tee -a /etc/profile.d/gromacs.sh && echo 'export PATH=$__inst_root_installOpenMPI/bin:$ROCM_PATH/bin:\${PATH:+:\${PATH}}' | tee -a /etc/profile.d/gromacs.sh && echo 'export CPLUS_INCLUDE_PATH=$__inst_root_installOpenMPI/include:\${CPLUS_INCLUDE_PATH:+:\${CPLUS_INCLUDE_PATH}}' | tee -a /etc/profile.d/gromacs.sh")
+
+    __cmd_array_installGROMACS=("source /etc/profile.d/gromacs.sh")
+    runCmd __cmd_array_installGROMACS "ERR"
+
+    # Build GROMACS ##############################################################################################
+    #__cmd_array_installGROMACS=("cd $__inst_root_installGROMACS" "git checkout master" "mkdir build && cd build && cmake -DBUILD_SHARED_LIBS=ON -DGMX_BUILD_FOR_COVERAGE=on -DCMAKE_BUILD_TYPE=Release  -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++ -DGMX_MPI=on -DGMX_GPU=on -DGMX_OPENMP=on -DGMX_GPU_USE_AMD=on -DGMX_GPU_DETECTION_DONE=on   -DGMX_SIMD=AVX2_128   -DREGRESSIONTEST_DOWNLOAD=OFF -DCMAKE_PREFIX_PATH=/opt/rocm -DCMAKE_INSTALL_PREFIX=RET_GROMACS/no_mpi .." "sudo make -j$(nproc) && sudo make -j$(nproc) install" "cd $__inst_root_installGROMACS")
+    #buildFromSource "$__url_GROMACS_installGROMACS" "$__inst_root_installGROMACS" __cmd_array_installGROMACS "gromacs" "gromacs" "0"
+    __cmd_array_installGROMACS=("cd $__inst_root_installGROMACS")
+    runCmd __cmd_array_installGROMACS "ERR"
+
+    __cmd_arry_installGRAMACS=("mkdir build && cd build && cmake -DBUILD_SHARED_LIBS=ON -DGMX_BUILD_FOR_COVERAGE=on -DCMAKE_BUILD_TYPE=Release  -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++ -DGMX_MPI=on -DGMX_GPU=on -DGMX_OPENMP=on -DGMX_GPU_USE_AMD=on -DGMX_GPU_DETECTION_DONE=on   -DGMX_SIMD=AVX2_128   -DREGRESSIONTEST_DOWNLOAD=OFF -DCMAKE_PREFIX_PATH=/opt/rocm -DCMAKE_INSTALL_PREFIX=RET_GROMACS/no_mpi .. && sudo make -j$(nproc) && sudo make -j$(nproc) install")
+    runCmd __cmd_array_installGROMACS "ERR"
+
+
+    ##################################################################################################################
+
+    # Back to the RET folder
+    cd "$__retPath_installGROMACS"
+
+    [ $? -ne 0 ] && stopLoadBar "There was a problem building GROMACS!" "ERR" "make" \
+                                       || stopLoadBar "Install Completed Successfully."
+}