technical:recipes:vasp-6-darwin

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technical:recipes:vasp-6-darwin [2021-02-15 11:45] – freytechnical:recipes:vasp-6-darwin [2021-02-16 10:00] (current) – [Runtime environment] anita
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 ====== Building VASP 6 on Caviness/DARWIN ====== ====== Building VASP 6 on Caviness/DARWIN ======
  
-Over the years the VASP build system has changed significantly.  In version 6 the use of the ''makefile.include'' to encapsulate machine-specific options has improved the portability and reproducibility of the build procedures.+Over the years the VASP build system has changed significantly.  In version 6, the use of the ''makefile.include'' to encapsulate machine-specific options has improved the portability and reproducibility of the build procedures.
  
 The build procedure outlined herein uses Open MPI on top of the Intel compiler suite in conjunction with CUDA 11 with the target executable destined for use on Volta- and Turing-generation NVIDIA devices. The build procedure outlined herein uses Open MPI on top of the Intel compiler suite in conjunction with CUDA 11 with the target executable destined for use on Volta- and Turing-generation NVIDIA devices.
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 To begin, choose a directory in which the VASP version(s) will be built and installed.  To build in your home directory, for example: To begin, choose a directory in which the VASP version(s) will be built and installed.  To build in your home directory, for example:
 <code bash> <code bash>
-[user@login00.darwin ~]$ export VASP_BASEDIR=~/sw/vasp+[user@login00.darwin ~]$ VASP_BASEDIR=~/sw/vasp
 [user@login00.darwin ~]$ VASP_BASEDIR_PRIVS=0700 [user@login00.darwin ~]$ VASP_BASEDIR_PRIVS=0700
 </code> </code>
 If you are managing VASP software for your entire workgroup, you could instead use If you are managing VASP software for your entire workgroup, you could instead use
 <code bash> <code bash>
-[user@login00.darwin ~]$ export VASP_BASEDIR="${WORKDIR}/sw/vasp"+[user@login00.darwin ~]$ VASP_BASEDIR="${WORKDIR}/sw/vasp"
 [user@login00.darwin ~]$ VASP_BASEDIR_PRIVS=2770 [user@login00.darwin ~]$ VASP_BASEDIR_PRIVS=2770
 </code> </code>
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 ==== Build Environment ==== ==== Build Environment ====
  
-The ''makefile.include'' above includes comments that reference the VALET commands used to configure the build (and runtime) environment for the copy of VASP being built.  Two package must be added; in case you have already added packages to your login shell environment, first rollback to a clean environment:+The ''makefile.include'' above includes comments that reference the VALET commands used to configure the build (and runtime) environment for the copy of VASP being built.  Two packages must be added; in case you have already added packages to your login shell environment, first rollback to a clean environment:
 <code bash> <code bash>
 [user@login00.darwin src]$ vpkg_rollback all [user@login00.darwin src]$ vpkg_rollback all
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 </code> </code>
  
-The ''--backup=numbered'' ensures that if executables already exist in the install location, they will be renamed with a numbered file extension rather than being simply replaced by the new copy.  If, for some reason, the old executable needs to be restored, the backup can be renamed to effect that change.+The ''%%--%%backup=numbered'' option ensures that if executables already exist in the install location, they will be renamed with a numbered file extension rather than being simply replaced by the new copy.  If, for some reason, the old executable needs to be restored, the backup can be renamed to effect that change.
  
 The ''-C'' option checks if the source and destination files differ, and only performs the copy operation if they do. The ''-C'' option checks if the source and destination files differ, and only performs the copy operation if they do.
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 With this version of VASP 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 ''vasp'' is very straightforward.  First, note your installation path: With this version of VASP 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 ''vasp'' is very straightforward.  First, note your installation path:
 <code bash> <code bash>
 +[user@login00.darwin src]$ vpkg_rollback all
 [user@login00.darwin src]$ cd [user@login00.darwin src]$ cd
 [user@login00.darwin ~]$ echo $VASP_BASEDIR [user@login00.darwin ~]$ echo $VASP_BASEDIR
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 [user@login00.darwin ~]$ VALET_PKG_DIR=~/.valet ; VALET_PKG_DIR_MODE=0700 [user@login00.darwin ~]$ VALET_PKG_DIR=~/.valet ; VALET_PKG_DIR_MODE=0700
 </code> </code>
-versus an installation made for an entire workgroup, which would store package definition files in ''$WORKDIR/sw/valet''+versus an installation made for an entire workgroup, which would store the VALET package definition files in ''$WORKDIR/sw/valet''
 <code bash> <code bash>
 [user@login00.darwin ~]$ VALET_PKG_DIR="$WORKDIR/sw/valet" ; VALET_PKG_DIR_MODE=2770 [user@login00.darwin ~]$ VALET_PKG_DIR="$WORKDIR/sw/valet" ; VALET_PKG_DIR_MODE=2770
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 VALET allows package definitions in a variety of formats (XML, JSON, YAML) but YAML tends to be the simplest format so we will use it here. VALET allows package definitions in a variety of formats (XML, JSON, YAML) but YAML tends to be the simplest format so we will use it here.
 +
 +==== Package section ====
 +
 +The //package section// of the definition file includes items that apply to all versions/variants of the software:
 +<code yaml>
 +vasp:
 +    prefix: /home/user/sw/vasp
 +    description: Vienna Ab-initio Simulation Package
 +    url: "http://cms.mpi.univie.ac.at/vasp/"
 +</code>
 +The //package identifier// is the top-level key in the document — ''vasp'' — and the value of ''$VASP_BASEDIR'' is the value of the ''prefix'' key in this section.  The URL and description are information taken from the official VASP web site.
 +
 +==== Versions ====
 +
 +The ''versions'' key is used to provide a list of the versions/variants of the software:
 +<code yaml>
 +vasp:
 +    prefix: /home/user/sw/vasp
 +    description: Vienna Ab-initio Simulation Package
 +    url: "http://cms.mpi.univie.ac.at/vasp/"
 +    
 +    versions:
 +        "6.1.0":
 +            description: compiled with Open MPI, Intel compilers, MKL, ScaLAPACK, CUDA
 +            dependencies:
 +                - openmpi/4.1.0:intel-2020
 +                - cuda/11.1.1
 +</code>
 +
 +<WRAP center round tip 80%>
 +The version identifier ''6.1.0'' is inferred to be the path prefix to the version in question here.  The package's prefix (''/home/user/sw/vasp'') with the version identifier appended (''/home/user/sw/vasp/6.1.0'') 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 vasp.vpkg_yaml>
 +vasp:
 +    prefix: /home/user/sw/vasp
 +    description: Vienna Ab-initio Simulation Package
 +    url: "http://cms.mpi.univie.ac.at/vasp/"
 +    
 +    default-version: "6.1.0"
 +    
 +    versions:
 +        "6.1.0":
 +            description: compiled with Open MPI, Intel compilers, MKL, ScaLAPACK, CUDA
 +            dependencies:
 +                - openmpi/4.1.0:intel-2020
 +                - cuda/11.1.1
 +</file>
 +
 +saved at ''$VALET_PKG_DIR/vasp.vpkg_yaml''.
 +
 +==== Checking the definition file ====
 +
 +The package definition file can be checked for proper syntax using the VALET command ''vpkg_check'':
 +<code bash>
 +[user@login00.darwin ~]$ vpkg_check "$VALET_PKG_DIR/vasp.vpkg_yaml"
 +/home/user/.valet/vasp.vpkg_yaml is OK
 +
 +[vasp] {
 +  contexts: all
 +  actions: {
 +    VASP_PREFIX=${VALET_PATH_PREFIX} (contexts: development)
 +  }
 +  http://cms.mpi.univie.ac.at/vasp/
 +  Vienna Ab-initio Simulation Package
 +  prefix: /home/user/sw/vasp
 +  source file: /home/user/.valet/vasp.vpkg_yaml
 +  default version: vasp/6.1.0
 +  versions: {
 +    [vasp/6.1.0] {
 +      contexts: all
 +      dependencies: {
 +        openmpi/4.1.0:intel-2020
 +        cuda/11.1.1
 +      }
 +      compiled with Open MPI, Intel compilers, MKL, ScaLAPACK, CUDA
 +      prefix: /home/user/sw/vasp/6.1.0
 +      standard paths: {
 +        bin: /home/user/sw/vasp/6.1.0/bin
 +      }
 +    }
 +  }
 +}
 +</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 **vasp** 6.1.0 into the runtime environment, the ''vpkg_require'' command is used:
 +<code bash>
 +[user@login00.darwin ~]$ vpkg_require vasp/6.1.0
 +Adding dependency `intel/2020u4` to your environment
 +Adding dependency `openmpi/4.1.0:intel-2020` to your environment
 +Adding dependency `cuda/11.1.1-455.32.00` to your environment
 +Adding package `vasp/6.1.0` to your environment
 +[user@login00.darwin ~]$ which vasp_std
 +~/sw/vasp/6.1.0/bin/vasp_std
 +</code>
 +The ''vasp_std'' command is used //without a leading path// which implies that the shell will check directories in the ''$PATH'' environment variable for an executable with that name.  If a different version/variant of **vasp** is chosen, the command would still be ''vasp_std'' but the shell would find it at a different location.  This abstraction (no full paths to executables) makes it easier to alter complex job scripts by simply changing the variant of **vasp** added using ''vpkg_require''.
 +
 +
  • technical/recipes/vasp-6-darwin.1613407525.txt.gz
  • Last modified: 2021-02-15 11:45
  • by frey