1. 07 Jul, 2017 1 commit
    • Andrew Heather's avatar
      INT: Integration of Mattijs' collocated parallel IO additions · d8d6030a
      Andrew Heather authored
      Original commit message:
      ------------------------
      
      Parallel IO: New collated file format
      
      When an OpenFOAM simulation runs in parallel, the data for decomposed fields and
      mesh(es) has historically been stored in multiple files within separate
      directories for each processor.  Processor directories are named 'processorN',
      where N is the processor number.
      
      This commit introduces an alternative "collated" file format where the data for
      each decomposed field (and mesh) is collated into a single file, which is
      written and read on the master processor.  The files are stored in a single
      directory named 'processors'.
      
      The new format produces significantly fewer files - one per field, instead of N
      per field.  For large parallel cases, this avoids the restriction on the number
      of open files imposed by the operating system limits.
      
      The file writing can be threaded allowing the simulation to continue running
      while the data is being written to file.  NFS (Network File System) is not
      needed when using the the collated format and additionally, there is an option
      to run without NFS with the original uncollated approach, known as
      "masterUncollated".
      
      The controls for the file handling are in the OptimisationSwitches of
      etc/controlDict:
      
      OptimisationSwitches
      {
          ...
      
          //- Parallel IO file handler
          //  uncollated (default), collated or masterUncollated
          fileHandler uncollated;
      
          //- collated: thread buffer size for queued file writes.
          //  If set to 0 or not sufficient for the file size threading is not used.
          //  Default: 2e9
          maxThreadFileBufferSize 2e9;
      
          //- masterUncollated: non-blocking buffer size.
          //  If the file exceeds this buffer size scheduled transfer is used.
          //  Default: 2e9
          maxMasterFileBufferSize 2e9;
      }
      
      When using the collated file handling, memory is allocated for the data in the
      thread.  maxThreadFileBufferSize sets the maximum size of memory in bytes that
      is allocated.  If the data exceeds this size, the write does not use threading.
      
      When using the masterUncollated file handling, non-blocking MPI communication
      requires a sufficiently large memory buffer on the master node.
      maxMasterFileBufferSize sets the maximum size in bytes of the buffer.  If the
      data exceeds this size, the system uses scheduled communication.
      
      The installation defaults for the fileHandler choice, maxThreadFileBufferSize
      and maxMasterFileBufferSize (set in etc/controlDict) can be over-ridden within
      the case controlDict file, like other parameters.  Additionally the fileHandler
      can be set by:
      - the "-fileHandler" command line argument;
      - a FOAM_FILEHANDLER environment variable.
      
      A foamFormatConvert utility allows users to convert files between the collated
      and uncollated formats, e.g.
          mpirun -np 2 foamFormatConvert -parallel -fileHandler uncollated
      
      An example case demonstrating the file handling methods is provided in:
      $FOAM_TUTORIALS/IO/fileHandling
      
      The work was undertaken by Mattijs Janssens, in collaboration with Henry Weller.
      d8d6030a
  2. 26 Jun, 2017 2 commits
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  8. 11 Jun, 2017 1 commit
    • Henry Weller's avatar
      listSwitches: moved from argList to debug · 5403e977
      Henry Weller authored
      Initially the listSwitches functions depended directly on argList functionality
      but this has now been factored out so that the listSwitches functions are more
      general and require only debug functionality.
      5403e977
  9. 10 Jun, 2017 1 commit
    • Henry Weller's avatar
      Replace foamList utility with -list.* options · 02e33f49
      Henry Weller authored
      Provides better context for the available boundary conditions, fvOptions,
      functionObjects etc. and thus returns only those available to and compatible
      with the particular application.
      
      e.g.
      
      pimpleFoam -help
      
      Usage: pimpleFoam [OPTIONS]
      options:
        -case <dir>       specify alternate case directory, default is the cwd
        -listFunctionObjects
                          List functionObjects
        -listFvOptions    List fvOptions
        -listRegisteredSwitches
                          List switches registered for run-time modification
        -listScalarBCs    List scalar field boundary conditions (fvPatchField<scalar>)
        -listSwitches     List switches declared in libraries but not set in
                          etc/controlDict
        -listTurbulenceModels
                          List turbulenceModels
        -listUnsetSwitches
                          List switches declared in libraries but not set in
                          etc/controlDict
        -listVectorBCs    List vector field boundary conditions (fvPatchField<vector>)
        -noFunctionObjects
                          do not execute functionObjects
        -parallel         run in parallel
        -postProcess      Execute functionObjects only
        -roots <(dir1 .. dirN)>
                          slave root directories for distributed running
        -srcDoc           display source code in browser
        -doc              display application documentation in browser
        -help             print the usage
      
      pimpleFoam listTurbulenceModels
      
      pimpleFoam -listTurbulenceModels
      /*---------------------------------------------------------------------------*\
      | =========                 |                                                 |
      | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
      |  \\    /   O peration     | Version:  dev                                   |
      |   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
      |    \\/     M anipulation  |                                                 |
      \*---------------------------------------------------------------------------*/
      Build  : dev-39c46019e44f
      Exec   : pimpleFoam -listTurbulenceModels
      Date   : Jun 10 2017
      Time   : 21:37:49
      Host   : "dm"
      PID    : 675
      Case   : /home/dm2/henry/OpenFOAM/OpenFOAM-dev
      nProcs : 1
      sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
      SetNaN : Initialising allocated memory to NaN (FOAM_SETNAN).
      fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
      allowSystemOperations : Allowing user-supplied system call operations
      
      // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
      Turbulence models
      3
      (
      LES
      RAS
      laminar
      )
      
      RAS models
      18
      (
      LRR
      LamBremhorstKE
      LaunderSharmaKE
      LienCubicKE
      LienLeschziner
      RNGkEpsilon
      SSG
      ShihQuadraticKE
      SpalartAllmaras
      kEpsilon
      kOmega
      kOmegaSST
      kOmegaSSTLM
      kOmegaSSTSAS
      kkLOmega
      qZeta
      realizableKE
      v2f
      )
      
      LES models
      10
      (
      DeardorffDiffStress
      Smagorinsky
      SpalartAllmarasDDES
      SpalartAllmarasDES
      SpalartAllmarasIDDES
      WALE
      dynamicKEqn
      dynamicLagrangian
      kEqn
      kOmegaSSTDES
      )
      
      Further work will be needed to support the -listTurbulenceModels option in
      multiphase solvers.
      02e33f49
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