technical:recipes:gromacs-plumed

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technical:recipes:gromacs-plumed [2024-05-12 13:41] – [Compilation and Installation: Plumed-patched Gromacs] bkangtechnical:recipes:gromacs-plumed [2024-05-12 15:03] (current) – [Scaling] bkang
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 [user@login00.darwin Gromacs]$ G_SRC_PREFIX="${G_BASEDIR}/gromacs-2022.5" [user@login00.darwin Gromacs]$ G_SRC_PREFIX="${G_BASEDIR}/gromacs-2022.5"
 [user@login00.darwin Gromacs]$ mkdir -m $GP_BASEDIR_PRIVS "$G_INSTALL_PREFIX" [user@login00.darwin Gromacs]$ mkdir -m $GP_BASEDIR_PRIVS "$G_INSTALL_PREFIX"
 +[user@login00.darwin Gromacs]$ G_BUILDDIR="${G_SRC_PREFIX}/build"
 +[user@login00.darwin Gromacs]$ mkdir -m $GP_BASEDIR_PRIVS "$G_BUILDDIR"
 [user@login00.darwin Gromacs]$ cd "$G_SRC_PREFIX" [user@login00.darwin Gromacs]$ cd "$G_SRC_PREFIX"
 +</code>
 +Hear, we patch Plumed on Gromacs. 
 +<code bash>
 +[user@login00.darwin gromacs-2022.5]$ plumed patch -p --static
 +</code>
  
-[user@login00.darwin plumed-2.8.3]$ vpkg_devrequire openmpi/4.1.5:intel-oneapi-2023 +Select 4: 
-[user@login00.darwin plumed-2.8.3]$ ./configure --prefix=$P_INSTALL_PREFIX  CC=mpicc CXX=mpicxx FC=mpifort  LDFLAGS=-qmkl=sequential  +<code bash> 
-[user@login00.darwin plumed-2.8.3]$ make +1) gromacs-2019.6     5) gromacs-4.5.7    9) qespresso-5.0.2 
-[user@login00.darwin plumed-2.8.3]$ make install+2) gromacs-2020.7     6) namd-2.12   10) qespresso-6.2 
 +3) gromacs-2021.7     7) namd-2.13 
 +4) gromacs-2022.5     8) namd-2.14
 </code> </code>
-Our current working directory is now the source directory. 
-Here, we create ''sourceme.sh'' : 
-<file make sourceme.sh> 
-TPATH="${P_INSTALL_PREFIX}" 
-export PATH="$TPATH/bin/:$PATH" 
-export LIBRARY_PATH="$TPATH/lib/:$LIBRARY_PATH" 
-export LD_LIBRARY_PATH="$TPATH/lib/:$LD_LIBRARY_PATH" 
-export PLUMED_KERNEL="$TPATH/lib/libplumedKernel.so" 
-export PLUMED_VIMPATH="$TPATH/lib/plumed/vim/" 
-export PYTHONPATH="$TPATH/lib/python/:$PYTHONPATH" 
  
-export CPATH="$TPATH/include/:$CPATH” +<code bash> 
-export INCLUDE="$TPATH/include/:$INCLUDE”+[user@login00.darwin gromacs-2022.5]$ cd "$G_BUILDDIR" 
 +</code>  
 +Our current working directory is now the //build root//. 
 +Here, we create ''SWMGR-build.sh'' : 
 +<file make SWMGR-build.sh.darwin> 
 +#!/bin/bash -l 
 + 
 +vpkg_require cmake/default openmpi/4.1.5:intel-oneapi-2023 
 + 
 +PREFIX="${G_INSTALL_PREFIX}" 
 + 
 +CPU_GMX_SIMD=AVX2_256 
 + 
 +BASE_BUILD_FLAGS=" 
 +    -DCMAKE_BUILD_TYPE=Release 
 +    -DGMX_SIMD=${CPU_GMX_SIMD} 
 +    -DGMX_FFT_LIBRARY=mkl 
 +    -DMKL_MPI=openmpi 
 +    -DBUILD_SHARED_LIBS=OFF 
 +    -DGMX_PREFER_STATIC_LIBS=ON 
 +" 
 +# BASE_BUILD_FLAGS="$BASE_BUILD_FLAGS -DGMX_GPU=SYCL" 
 +#    -DMKL_INCLUDE_DIR=$MKLROOT/include 
 +#    -DMKL_LIBRARIES=-mkl=sequential 
 +#" 
 + 
 +build_variant() 
 +{ 
 +    local DBL=$1 MPI=$2 
 +    local build_dir="" 
 +    local build_flags="" 
 + 
 +    if [ $DBL -ne 0 ]; then 
 +        build_dir="double" 
 + build_flags="${build_flags} -DGMX_DOUBLE=on" 
 +    else 
 +        build_dir="single" 
 +        build_flags="${build_flags} -DGMX_DOUBLE=off" 
 +    fi 
 +    if [ $MPI -eq 0 ]; then 
 +        build_dir="${build_dir}-thread" 
 +        build_flags="${build_flags} -DGMX_MPI=off -DGMX_THREAD_MPI=on -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on" 
 +        CC=icx CXX=icpx FC=ifx 
 +    else 
 +        build_dir="${build_dir}-mpi" 
 +        build_flags="${build_flags} -DGMX_MPI=on -DGMX_THREAD_MPI=off" 
 + CC=mpicc CXX=mpicxx FC=mpifort 
 +    fi 
 +    [ -d "build-${build_dir}" ] && rm -rf "build-${build_dir}" 
 +    mkdir "build-${build_dir}" ; pushd "build-${build_dir}" 
 +    CC=$CC CXX=$CXX FC=$FC \ 
 +        cmake \ 
 +     -DCMAKE_INSTALL_PREFIX="${PREFIX}/${build_dir}" \ 
 +            $BASE_BUILD_FLAGS $build_flags \ 
 + ../.. 
 +    if [ $? -eq 0 ]; then 
 +        make -j 20 
 +        if [ $? -eq 0 ]; then 
 +            make install 
 +        fi 
 +    fi 
 +    popd 
 +} 
 + 
 +## 
 +## SYCL only supports single precision. 
 +## 
 +#             DOUBLE?    MPI? 
 +#build_variant 0          0 
 +#build_variant 1          0 
 +#build_variant 0          1 
 +build_variant 1          1 
 </file> </file>
  
 +<file make SWMGR-build.sh.caviness>
 +#!/bin/bash -l
 +
 +vpkg_require cmake/default openmpi/4.1.4:intel-oneapi-2023
 +
 +PREFIX="${G_INSTALL_PREFIX}"
 +
 +CPU_GMX_SIMD=AVX2_256
 +
 +BASE_BUILD_FLAGS="
 +    -DCMAKE_BUILD_TYPE=Release
 +    -DGMX_SIMD=${CPU_GMX_SIMD}
 +    -DGMX_FFT_LIBRARY=mkl
 +    -DMKL_MPI=openmpi
 +    -DBUILD_SHARED_LIBS=OFF
 +    -DGMX_PREFER_STATIC_LIBS=ON
 +"
 +# BASE_BUILD_FLAGS="$BASE_BUILD_FLAGS -DGMX_GPU=SYCL"
 +#    -DMKL_INCLUDE_DIR=$MKLROOT/include
 +#    -DMKL_LIBRARIES=-mkl=sequential
 +#"
 +
 +build_variant()
 +{
 +    local DBL=$1 MPI=$2
 +    local build_dir=""
 +    local build_flags=""
 +
 +    if [ $DBL -ne 0 ]; then
 +        build_dir="double"
 + build_flags="${build_flags} -DGMX_DOUBLE=on"
 +    else
 +        build_dir="single"
 +        build_flags="${build_flags} -DGMX_DOUBLE=off"
 +    fi
 +    if [ $MPI -eq 0 ]; then
 +        build_dir="${build_dir}-thread"
 +        build_flags="${build_flags} -DGMX_MPI=off -DGMX_THREAD_MPI=on -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on"
 +        CC=icx CXX=icpx FC=ifx
 +    else
 +        build_dir="${build_dir}-mpi"
 +        build_flags="${build_flags} -DGMX_MPI=on -DGMX_THREAD_MPI=off"
 + CC=mpicc CXX=mpicxx FC=mpifort
 +    fi
 +    [ -d "build-${build_dir}" ] && rm -rf "build-${build_dir}"
 +    mkdir "build-${build_dir}" ; pushd "build-${build_dir}"
 +    CC=$CC CXX=$CXX FC=$FC \
 +        cmake \
 +     -DCMAKE_INSTALL_PREFIX="${PREFIX}/${build_dir}" \
 +            $BASE_BUILD_FLAGS $build_flags \
 + ../..
 +    if [ $? -eq 0 ]; then
 +        make -j 20
 +        if [ $? -eq 0 ]; then
 +            make install
 +        fi
 +    fi
 +    popd
 +}
 +
 +##
 +## SYCL only supports single precision.
 +##
 +#             DOUBLE?    MPI?
 +#build_variant 0          0
 +#build_variant 1          0
 +#build_variant 0          1
 +build_variant 1          1
 +
 +</file>
  
-Executing the script.+Executing the script compile and install plumed-patched gromacs.
 <code bash> <code bash>
-[user@login00.darwin plumed-2.8.3]$ source sourceme.sh+[user@login00.darwin build]$ ./SWMGR-build.sh
 </code>  </code> 
  
 ===== VALET Package Definition ===== ===== VALET Package Definition =====
  
-With this version of quantum espresso built, the remaining step is to leverage VALET for setup of the runtime environment when you use the software.  VALET automatically recognizes the standard directory layout, so configuring versions/variants of ''quantum espresso'' is very straightforward.  First, note your installation path:+With this version of Gromacs_Plumed built, the remaining step is to leverage VALET for setup of the runtime environment when you use the software.  VALET automatically recognizes the standard directory layout, so configuring versions/variants of ''Gromacs_Plumed'' is very straightforward.  First, note your installation path:
 <code bash> <code bash>
 [user@login00.darwin build]$ vpkg_rollback all [user@login00.darwin build]$ vpkg_rollback all
 [user@login00.darwin build]$ cd [user@login00.darwin build]$ cd
-[user@login00.darwin ~]$ echo $QE_BASEDIR +[user@login00.darwin ~]$ echo $GP_BASEDIR 
-/home/user/sw/quantum-espresso+/home/user/sw/Gromacs_Plumed
 </code> </code>
 Since this build was done in the user's home directory, they were personal copies of the software and should use a //VALET package definition file// stored in ''~/.valet'' Since this build was done in the user's home directory, they were personal copies of the software and should use a //VALET package definition file// stored in ''~/.valet''
Line 149: Line 290:
 The //package section// of the definition file includes items that apply to all versions/variants of the software: The //package section// of the definition file includes items that apply to all versions/variants of the software:
 <code yaml> <code yaml>
-quantum-espresso: +Gromacs_Plumed: 
-    prefix: /home/user/sw/quantum-espresso +    prefix: /home/user/sw/Gromacs_Plumed/Gromacs 
-    description: quantum-espresso +    description: Gromacs_Plumed 
-    url: "https://www.quantum-espresso.org/"+    url: "https://www.gromacs.org/"
 </code> </code>
-The //package identifier// is the top-level key in the document — ''quantum-espresso'' — and the value of ''$QE_BASEDIR'' is the value of the ''prefix'' key in this section.  The URL and description are information taken from the official quantum-espresso web site.+The //package identifier// is the top-level key in the document — ''Gromacs_Plumed'' — and the value of ''$GP_BASEDIR'' is the value of the ''prefix'' key in this section.  The URL and description are information taken from the official Gromacs web site.
  
 ==== Versions ==== ==== Versions ====
Line 160: Line 301:
 The ''versions'' key is used to provide a list of the versions/variants of the software: The ''versions'' key is used to provide a list of the versions/variants of the software:
 <code yaml> <code yaml>
-quantum-espresso: +gromacs-plumed: 
-    prefix: /home/user/sw/quantum-espresso +    prefix: /home/user/sw/Gromacs_Plumed/Gromacs 
-    description: quantum-espresso +    description: Gromacs_Plumed 
-    url: "https://www.quantum-espresso.org/"+    url: "https://www.gromacs.org/" 
 +     
 +    default-version: "v2022.5"
          
     versions:     versions:
-        "v7.3": +        "v2022.5": 
-            description: compiled with Open MPI, Intel compilers, MKL, ScaLAPACK+            prefix: "v2022.5/double-mpi" 
 +            description:  Gromacs patched with Plumed v2.8.3
             dependencies:             dependencies:
-                - openmpi/4.1.5:intel-oneapi-2023+                 - openmpi/4.1.5:intel-oneapi-2023
                                
 </code> </code>
  
 <WRAP center round tip 80%> <WRAP center round tip 80%>
-The version identifier ''v7.3'' is inferred to be the path prefix to the version in question here.  The package's prefix (''/home/user/sw/quantum-espresso'') with the version identifier appended (''/home/user/sw/quantum-espresso/v7.3'') is implicit.+The version identifier ''v7.3'' is inferred to be the path prefix to the version in question here.  The package's prefix (''/home/user/sw/Gromacs_Plumed'') with the version identifier appended (''/home/user/sw/Gromacs_Plumed/Gromacs/v2022.5'') is implicit.
  
 The implicit behavior is overridden by providing a ''prefix'' key in the version definition:  a relative path is appended to the package's prefix, an absolute path is used as-is. The implicit behavior is overridden by providing a ''prefix'' key in the version definition:  a relative path is appended to the package's prefix, an absolute path is used as-is.
Line 181: Line 325:
 It is a good idea to specify which version definition should act as the default.  This yields the following package definition file It is a good idea to specify which version definition should act as the default.  This yields the following package definition file
  
-<file yaml quantum-espresso.vpkg_yaml.darwin> +<file yaml gromacs-plumed.vpkg_yaml.darwin> 
-quantum-espresso: +gromacs-plumed: 
-    prefix: /home/user/sw/quantum-espresso +    prefix: /home/user/sw/Gromacs_Plumed/Gromacs 
-    description: quantum-espresso +    description: Gromacs_Plumed 
-    url: "https://www.quantum-espresso.org/"+    url: "https://www.gromacs.org/"
          
-    default-version: "v7.3"+    default-version: "v2022.5"
          
     versions:     versions:
-        "v7.3": +        "v2022.5": 
-            description: compiled with Open MPI, Intel compilers, MKL, ScaLAPACK+            prefix: "v2022.5/double-mpi" 
 +            description:  Gromacs patched with Plumed v2.8.3
             dependencies:             dependencies:
-                - openmpi/4.1.5:intel-oneapi-2023+                 - openmpi/4.1.5:intel-oneapi-2023
 </file> </file>
  
-<file yaml quantum-espresso.vpkg_yaml.caviness> +<file yaml gromacs-plumed.vpkg_yaml.caviness> 
-quantum-espresso: +gromacs-plumed: 
-    prefix: /home/user/sw/quantum-espresso +    prefix: /home/user/sw/Gromacs_Plumed/Gromacs 
-    description: quantum-espresso +    description: Gromacs_Plumed 
-    url: "https://www.quantum-espresso.org/" +    url: "https://www.gromacs.org/"
-     +
-    default-version: "v7.3"+
          
 +    default-version: "v2022.5"
 +        
     versions:     versions:
-        "v7.3": +        "v2022.5": 
-            description: compiled with Open MPI, Intel compilers, MKL, ScaLAPACK+            prefix: "v2022.5/double-mpi" 
 +            description:  Gromacs patched with Plumed v2.8.3
             dependencies:             dependencies:
-                - openmpi/4.1.4:intel-oneapi-2023+                 - openmpi/4.1.4:intel-oneapi-2023
 </file> </file>
  
-saved at ''$VALET_PKG_DIR/quantum-espresso.vpkg_yaml''.+saved at ''$VALET_PKG_DIR/gromacs-plumed.vpkg_yaml''.
  
 ==== Checking the definition file ==== ==== Checking the definition file ====
Line 217: Line 363:
 The package definition file can be checked for proper syntax using the VALET command ''vpkg_check'': The package definition file can be checked for proper syntax using the VALET command ''vpkg_check'':
 <code bash> <code bash>
-[user@login00.darwin ~]$ vpkg_check "$VALET_PKG_DIR/quantum-espresso.vpkg_yaml" +[user@login00.darwin ~]$ vpkg_check "$VALET_PKG_DIR/gromacs-plumed.vpkg_yaml" 
-/home/user/.valet/quantum-espresso.vpkg_yaml is OK +/home/user/.valet/gromacs-plumed.vpkg_yaml is OK 
-[quantum-espresso] {+[gromacs-plumed] {
   contexts: all   contexts: all
   actions: {   actions: {
-    QUANTUM_DASH_ESPRESSO_PREFIX=${VALET_PATH_PREFIX} (contexts: development)+    GROMACS_PLUMED_PREFIX=${VALET_PATH_PREFIX} (contexts: development)
   }   }
-  https://www.quantum-espresso.org/ +  https://www.gromacs.org/ 
-  quantum-espresso +  Gromacs_Plumed 
-  prefix: /work/user/sw/quantum-espresso +  prefix: /home/user/sw/Gromacs_Plumed/Gromacs 
-  source file: /home/user/.valet/quantum-espresso.vpkg_yaml +  source file: /home/user/.valet/gromacs-plumed.vpkg_yaml 
-  default version: quantum-espresso/v7.3+  default version: gromacs-plumed/v2022.5
   versions: {   versions: {
-    [quantum-espresso/v7.3] {+    [gromacs-plumed/v2022.5] {
       contexts: all       contexts: all
       dependencies: {       dependencies: {
         openmpi/4.1.5:intel-oneapi-2023         openmpi/4.1.5:intel-oneapi-2023
       }       }
-      compiled with Open MPI, Intel compilers, MKL, ScaLAPACK +      Gromacs patched with Plumed v2.8.3 
-      prefix: /work/user/sw/quantum-espresso/v7.3+      prefix: /home/user/sw/Gromacs_Plumed/Gromacs/v2022.5/double-mpi 
 +      standard paths: { 
 +        bin: /home/user/sw/Gromacs_Plumed/Gromacs/v2022.5/double-mpi/bin 
 +        lib: /home/user/sw/Gromacs_Plumed/Gromacs/v2022.5/double-mpi/lib64 
 +        man: /home/user/sw/Gromacs_Plumed/Gromacs/v2022.5/double-mpi/share/man 
 +        include: /home/user/sw/Gromacs_Plumed/Gromacs/v2022.5/double-mpi/include 
 +      }
     }     }
   }   }
Line 246: Line 398:
 ==== Runtime environment ==== ==== Runtime environment ====
  
-To load **quantum-espresso** 7.3 into the runtime environment, the ''vpkg_require'' command is used:+To load **Gromacs_Plumed** v2022.5 into the runtime environment, the ''vpkg_require'' command is used:
 <code bash> <code bash>
-[user@login00.darwin ~]$ vpkg_require quantum-espresso/v7.3+[user@login00.darwin ~]$ vpkg_require gromacs-plumed/v2022.5
 Adding dependency `binutils/2.35.1` to your environment Adding dependency `binutils/2.35.1` to your environment
 Adding dependency `gcc/12.2.0` to your environment Adding dependency `gcc/12.2.0` to your environment
Line 254: Line 406:
 Adding dependency `ucx/1.13.1` to your environment Adding dependency `ucx/1.13.1` to your environment
 Adding dependency `openmpi/4.1.5:intel-oneapi-2023` to your environment Adding dependency `openmpi/4.1.5:intel-oneapi-2023` to your environment
-Adding package `quantum-espresso/v7.3` to your environment +Adding package `gromacs-plumed/v2022.5` to your environment 
-[user@login00.darwin ~]$ which pw.x +[user@login00.darwin ~]$ which gmx_mpi_d 
-~/sw/quantum-espresso/v7.3/bin/pw.x+~/sw/Gromacs_Plumed/Gromacs/v2022.5/double-mpi/bin/gmx_mpi_d
 </code> </code>
  
 ===== Scaling ===== ===== Scaling =====
  
-This is the wall time for the structure relaxation of silicon with respect to the number of cores. The wall time decreases with an increased number of cores.+This is the wall time for MD run of 41057 atom, and nsteps=10000 with metadynamics by combining Gromacs and Plumed. The wall time decreases with an increased number of cores.
  
-{{:technical:recipes:scale.jpg?400|}}+{{:technical:recipes:scale_gromacs_plumed.jpg?400|}}
  • technical/recipes/gromacs-plumed.1715535714.txt.gz
  • Last modified: 2024-05-12 13:41
  • by bkang