technical:recipes:quantum-espresso

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technical:recipes:quantum-espresso [2024-05-10 10:40] – [Compilation and Installation] bkangtechnical:recipes:quantum-espresso [2024-05-12 11:05] (current) – [Runtime environment] bkang
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 In this example version 7.3 of quantum-espresso will be built. Our standard recipes for quantum-espresso will entail use of the Intel compilers, the MKL for BLAS/LAPACK/FFTW/ScaLAPACK/BLACS, and Open MPI for parallelism. In this example version 7.3 of quantum-espresso will be built. Our standard recipes for quantum-espresso will entail use of the Intel compilers, the MKL for BLAS/LAPACK/FFTW/ScaLAPACK/BLACS, and Open MPI for parallelism.
  
-We will create a directory to hold our base build of quantum-espresso 7.3, naming it with the version identifier:  ''qe-7.3''.  The source is then unpacked therein:+Unpack "qe-7.3-ReleasePack.tar.gz" will create a directory to hold our base build of quantum-espresso 7.3, naming it with the version identifier:  ''qe-7.3''.  The source is then unpacked therein:
 <code bash> <code bash>
-[user@login00.darwin ~]$ QE_SRC_PREFIX="${QE_BASEDIR}/qe-7.3" +[user@login00.darwin ~]$ tar -xvzf "${QE_BASEDIR}/qe-7.3-ReleasePack.tar.gz"
-[user@login00.darwin ~]$ mkdir -m $QE_BASEDIR_PRIVS "$QE_SRC_PREFIX" +
-[user@login00.darwin ~]$ cd "$QE_SRC_PREFIX" +
-[user@login00.darwin qe-7.3]$ tar -xf "${QE_BASEDIR}/qe-7.3-ReleasePack.tar.gz"+
 </code> </code>
  
Line 39: Line 36:
 <code bash> <code bash>
 [user@login00.darwin ~]$ QE_INSTALL_PREFIX="${QE_BASEDIR}/v7.3" [user@login00.darwin ~]$ QE_INSTALL_PREFIX="${QE_BASEDIR}/v7.3"
 +[user@login00.darwin ~]$ export QE_INSTALL_PREFIX
 +[user@login00.darwin ~]$ QE_SRC_PREFIX="${QE_BASEDIR}/qe-7.3"
 [user@login00.darwin ~]$ mkdir -m $QE_BASEDIR_PRIVS "$QE_INSTALL_PREFIX" [user@login00.darwin ~]$ mkdir -m $QE_BASEDIR_PRIVS "$QE_INSTALL_PREFIX"
 [user@login00.darwin ~]$ QE_BUILDDIR="${QE_SRC_PREFIX}/build" [user@login00.darwin ~]$ QE_BUILDDIR="${QE_SRC_PREFIX}/build"
Line 47: Line 46:
 Here, we create ''build.sh'' : Here, we create ''build.sh'' :
 <file make build.sh.darwin> <file make build.sh.darwin>
 +#!/bin/bash -l
 +
 +vpkg_require cmake/3.28.3 openmpi/4.1.5:intel-oneapi-2023 git
 +
 +PREFIX="${QE_INSTALL_PREFIX}"
 +
 +cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx \
 +-DCMAKE_Fortran_COMPILER=mpifort \
 +-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
 +-DCMAKE_C_FLAGS="-msse3 -axsse3,sse4.2,AVX,core-AVX2,CORE-AVX512" \
 +-DCMAKE_Fortran_FLAGS="-msse3 -axsse3,sse4.2,AVX,core-AVX2,CORE-AVX512" \
 +-DQE_ENABLE_OPENMP=ON -DCMAKE_BUILD_TYPE:STRING=RELWITHDEBINFO ../
 +
 +make -j 20
 +make install
 +</file>
 +
 +<file make build.sh.caviness>
 #!/bin/bash -l #!/bin/bash -l
  
Line 63: Line 80:
 make install make install
 </file> </file>
 +
 Executing the script compile and install quantum-expresso 7.3. Executing the script compile and install quantum-expresso 7.3.
 <code bash> <code bash>
 [user@login00.darwin build]$ ./build.sh [user@login00.darwin build]$ ./build.sh
 </code>  </code> 
 +
 +===== 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:
 +<code bash>
 +[user@login00.darwin build]$ vpkg_rollback all
 +[user@login00.darwin build]$ cd
 +[user@login00.darwin ~]$ echo $QE_BASEDIR
 +/home/user/sw/quantum-espresso
 +</code>
 +Since this build was done in the user's home directory, they were personal copies of the software and should use a //VALET package definition file// stored in ''~/.valet''
 +<code bash>
 +[user@login00.darwin ~]$ VALET_PKG_DIR=~/.valet ; VALET_PKG_DIR_MODE=0700
 +</code>
 +versus an installation made for an entire workgroup, which would store the VALET package definition files in ''$WORKDIR/sw/valet''
 +<code bash>
 +[user@login00.darwin ~]$ VALET_PKG_DIR="$WORKDIR/sw/valet" ; VALET_PKG_DIR_MODE=2770
 +</code>
 +Whichever scheme is in-use, ensure the directory exists:
 +<code bash>
 +[user@login00.darwin ~]$ mkdir -p --mode=$VALET_PKG_DIR_MODE "$VALET_PKG_DIR"
 +</code>
 +
 +VALET allows package definitions in a variety of formats (XML, JSON, YAML) but YAML tends to be the simplest format so we will use it here.
 +
 +==== Package section ====
 +
 +The //package section// of the definition file includes items that apply to all versions/variants of the software:
 +<code yaml>
 +quantum-espresso:
 +    prefix: /home/user/sw/quantum-espresso
 +    description: quantum-espresso
 +    url: "https://www.quantum-espresso.org/"
 +</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.
 +
 +==== Versions ====
 +
 +The ''versions'' key is used to provide a list of the versions/variants of the software:
 +<code yaml>
 +quantum-espresso:
 +    prefix: /home/user/sw/quantum-espresso
 +    description: quantum-espresso
 +    url: "https://www.quantum-espresso.org/"
 +    
 +    versions:
 +        "v7.3":
 +            description: compiled with Open MPI, Intel compilers, MKL, ScaLAPACK
 +            dependencies:
 +                - openmpi/4.1.5:intel-oneapi-2023
 +               
 +</code>
 +
 +<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 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.
 +</WRAP>
 +
 +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>
 +quantum-espresso:
 +    prefix: /home/user/sw/quantum-espresso
 +    description: quantum-espresso
 +    url: "https://www.quantum-espresso.org/"
 +    
 +    default-version: "v7.3"
 +    
 +    versions:
 +        "v7.3":
 +            description: compiled with Open MPI, Intel compilers, MKL, ScaLAPACK
 +            dependencies:
 +                - openmpi/4.1.5:intel-oneapi-2023
 +</file>
 +
 +<file yaml quantum-espresso.vpkg_yaml.caviness>
 +quantum-espresso:
 +    prefix: /home/user/sw/quantum-espresso
 +    description: quantum-espresso
 +    url: "https://www.quantum-espresso.org/"
 +    
 +    default-version: "v7.3"
 +    
 +    versions:
 +        "v7.3":
 +            description: compiled with Open MPI, Intel compilers, MKL, ScaLAPACK
 +            dependencies:
 +                - openmpi/4.1.4:intel-oneapi-2023
 +</file>
 +
 +saved at ''$VALET_PKG_DIR/quantum-espresso.vpkg_yaml''.
 +
 +==== Checking the definition file ====
 +
 +The package definition file can be checked for proper syntax using the VALET command ''vpkg_check'':
 +<code bash>
 +[user@login00.darwin ~]$ vpkg_check "$VALET_PKG_DIR/quantum-espresso.vpkg_yaml"
 +/home/user/.valet/quantum-espresso.vpkg_yaml is OK
 +[quantum-espresso] {
 +  contexts: all
 +  actions: {
 +    QUANTUM_DASH_ESPRESSO_PREFIX=${VALET_PATH_PREFIX} (contexts: development)
 +  }
 +  https://www.quantum-espresso.org/
 +  quantum-espresso
 +  prefix: /work/user/sw/quantum-espresso
 +  source file: /home/user/.valet/quantum-espresso.vpkg_yaml
 +  default version: quantum-espresso/v7.3
 +  versions: {
 +    [quantum-espresso/v7.3] {
 +      contexts: all
 +      dependencies: {
 +        openmpi/4.1.5:intel-oneapi-2023
 +      }
 +      compiled with Open MPI, Intel compilers, MKL, ScaLAPACK
 +      prefix: /work/user/sw/quantum-espresso/v7.3
 +    }
 +  }
 +}
 +
 +</code>
 +The file had no errors in its YAML syntax.  Notice also that the standard path (''bin'') is found and noted by VALET!
 +
 +==== Runtime environment ====
 +
 +To load **quantum-espresso** 7.3 into the runtime environment, the ''vpkg_require'' command is used:
 +<code bash>
 +[user@login00.darwin ~]$ vpkg_require quantum-espresso/v7.3
 +Adding dependency `binutils/2.35.1` to your environment
 +Adding dependency `gcc/12.2.0` to your environment
 +Adding dependency `intel-oneapi/2023.0.0.25537` 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 package `quantum-espresso/v7.3` to your environment
 +[user@login00.darwin ~]$ which pw.x
 +~/sw/quantum-espresso/v7.3/bin/pw.x
 +</code>
 +
 +===== 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.
 +
 +{{:technical:recipes:scale.jpg?400|}}
 +
  • technical/recipes/quantum-espresso.1715352048.txt.gz
  • Last modified: 2024-05-10 10:40
  • by bkang