1. 26 Jun, 2020 1 commit
  2. 11 Jun, 2020 1 commit
  3. 02 Jun, 2020 1 commit
    • Mark Olesen's avatar
      ENH: support predicate checks for argList (similar to dictionary methods) · 31b17221
      Mark Olesen authored
      - Favour use of argList methods that are more similar to dictionary
        method names with the aim of reducing the cognitive load.
      
        * Silently deprecate two-parameter get() method in favour of the
          more familiar getOrDefault.
        * Silently deprecate opt() method in favour of get()
      
        These may be verbosely deprecated in future versions.
      31b17221
  4. 26 Nov, 2019 1 commit
  5. 31 Oct, 2019 1 commit
  6. 06 Feb, 2019 1 commit
  7. 07 Jan, 2019 1 commit
  8. 11 Dec, 2018 1 commit
  9. 12 Dec, 2018 1 commit
  10. 11 Oct, 2018 1 commit
  11. 01 Oct, 2018 1 commit
  12. 02 Aug, 2018 1 commit
    • Mark Olesen's avatar
      ENH: IOobject::selectIO helper method · 88e5334a
      Mark Olesen authored
      - centralizes IOobject handling and treatment of alternative locations.
        If an alternative file location is specified, it will be used instead.
      
      - provide decompositionMethod::canonicalName instead of using
        "decomposeParDict" in various places.
      88e5334a
  13. 31 Jul, 2018 1 commit
  14. 30 Jul, 2018 1 commit
  15. 27 Jun, 2018 1 commit
    • Will Bainbridge's avatar
      fileHandler: Added flush method · 2ae4bf73
      Will Bainbridge authored
      This method waits until all the threads have completed IO operations and
      then clears any cached information about the files on disk. This
      replaces the deactivation of threading by means of zeroing the buffer
      size when writing and reading of a file happen in sequence. It also
      allows paraFoam to update the list of available times.
      
      Patch contributed by Mattijs Janssens
      Resolves bug report https://bugs.openfoam.org/view.php?id=2962
      2ae4bf73
  16. 29 May, 2018 1 commit
  17. 14 Mar, 2018 1 commit
  18. 08 Jan, 2018 1 commit
    • Mark Olesen's avatar
      ENH: simplify method names for reading argList options and arguments · 345a2a42
      Mark Olesen authored
      - use succincter method names that more closely resemble dictionary
        and HashTable method names. This improves method name consistency
        between classes and also requires less typing effort:
      
          args.found(optName)        vs.  args.optionFound(optName)
          args.readIfPresent(..)     vs.  args.optionReadIfPresent(..)
          ...
          args.opt<scalar>(optName)  vs.  args.optionRead<scalar>(optName)
          args.read<scalar>(index)   vs.  args.argRead<scalar>(index)
      
      - the older method names forms have been retained for code compatibility,
        but are now deprecated
      345a2a42
  19. 08 Dec, 2017 1 commit
  20. 08 Nov, 2017 1 commit
  21. 19 Jul, 2018 2 commits
  22. 09 Nov, 2017 1 commit
    • Mark Olesen's avatar
      ENH: region-wise decomposition specification for decomposeParDict · a9ffcab5
      Mark Olesen authored
        Within decomposeParDict, it is now possible to specify a different
        decomposition method, methods coefficients or number of subdomains
        for each region individually.
      
        The top-level numberOfSubdomains remains mandatory, since this
        specifies the number of domains for the entire simulation.
        The individual regions may use the same number or fewer domains.
      
        Any optional method coefficients can be specified in a general
        "coeffs" entry or a method-specific one, eg "metisCoeffs".
      
        For multiLevel, only the method-specific "multiLevelCoeffs" dictionary
        is used, and is also mandatory.
      
      ----
      
      ENH: shortcut specification for multiLevel.
      
        In addition to the longer dictionary form, it is also possible to
        use a shorter notation for multiLevel decomposition when the same
        decomposition method applies to each level.
      a9ffcab5
  23. 26 Sep, 2017 1 commit
  24. 15 Sep, 2017 1 commit
  25. 21 Mar, 2018 1 commit
    • Henry Weller's avatar
      ENH: Improvements to the fileHandler and collated IO · 8959b8e0
      Henry Weller authored
      Improvements to existing functionality
      --------------------------------------
        - MPI is initialised without thread support if it is not needed e.g. uncollated
        - Use native c++11 threading; avoids problem with static destruction order.
        - etc/cellModels now only read if needed.
        - etc/controlDict can now be read from the environment variable FOAM_CONTROLDICT
        - Uniform files (e.g. '0/uniform/time') are now read only once on the master only
          (with the masterUncollated or collated file handlers)
        - collated format writes to 'processorsNNN' instead of 'processors'.  The file
          format is unchanged.
        - Thread buffer and file buffer size are no longer limited to 2Gb.
      
      The global controlDict file contains parameters for file handling.  Under some
      circumstances, e.g. running in parallel on a system without NFS, the user may
      need to set some parameters, e.g. fileHandler, before the global controlDict
      file is read from file.  To support this, OpenFOAM now allows the global
      controlDict to be read as a string set to the FOAM_CONTROLDICT environment
      variable.
      
      The FOAM_CONTROLDICT environment variable can be set to the content the global
      controlDict file, e.g. from a sh/bash shell:
      
          export FOAM_CONTROLDICT=$(foamDictionary $FOAM_ETC/controlDict)
      
      FOAM_CONTROLDICT can then be passed to mpirun using the -x option, e.g.:
      
          mpirun -np 2 -x FOAM_CONTROLDICT simpleFoam -parallel
      
      Note that while this avoids the need for NFS to read the OpenFOAM configuration
      the executable still needs to load shared libraries which must either be copied
      locally or available via NFS or equivalent.
      
      New: Multiple IO ranks
      ----------------------
      The masterUncollated and collated fileHandlers can now use multiple ranks for
      writing e.g.:
      
          mpirun -np 6 simpleFoam -parallel -ioRanks '(0 3)'
      
      In this example ranks 0 ('processor0') and 3 ('processor3') now handle all the
      I/O.  Rank 0 handles 0,1,2 and rank 3 handles 3,4,5.  The set of IO ranks should always
      include 0 as first element and be sorted in increasing order.
      
      The collated fileHandler uses the directory naming processorsNNN_XXX-YYY where
      NNN is the total number of processors and XXX and YYY are first and last
      processor in the rank, e.g. in above example the directories would be
      
          processors6_0-2
          processors6_3-5
      
      and each of the collated files in these contains data of the local ranks
      only. The same naming also applies when e.g. running decomposePar:
      
      decomposePar -fileHandler collated -ioRanks '(0 3)'
      
      New: Distributed data
      ---------------------
      
      The individual root directories can be placed on different hosts with different
      paths if necessary.  In the current framework it is necessary to specify the
      root per slave process but this has been simplified with the option of specifying
      the root per host with the -hostRoots command line option:
      
          mpirun -np 6 simpleFoam -parallel -ioRanks '(0 3)' \
              -hostRoots '("machineA" "/tmp/" "machineB" "/tmp")'
      
      The hostRoots option is followed by a list of machine name + root directory, the
      machine name can contain regular expressions.
      
      New: hostCollated
      -----------------
      
      The new hostCollated fileHandler automatically sets the 'ioRanks' according to
      the host name with the lowest rank e.g. to run simpleFoam on 6 processors with
      ranks 0-2 on machineA and ranks 3-5 on machineB with the machines specified in
      the hostfile:
      
          mpirun -np 6 --hostfile hostfile simpleFoam -parallel -fileHandler hostCollated
      
      This is equivalent to
      
          mpirun -np 6 --hostfile hostfile simpleFoam -parallel -fileHandler collated -ioRanks '(0 3)'
      
      This example will write directories:
      
          processors6_0-2/
          processors6_3-5/
      
      A typical example would use distributed data e.g. no two nodes, machineA and
      machineB, each with three processes:
      
          decomposePar -fileHandler collated -case cavity
      
          # Copy case (constant/*, system/*, processors6/) to master:
          rsync -a cavity machineA:/tmp/
      
          # Create root on slave:
          ssh machineB mkdir -p /tmp/cavity
      
          # Run
          mpirun --hostfile hostfile icoFoam \
              -case /tmp/cavity -parallel -fileHandler hostCollated \
              -hostRoots '("machineA" "/tmp" "machineB" "/tmp")'
      
      Contributed by Mattijs Janssens
      8959b8e0
  26. 24 Oct, 2017 1 commit
  27. 13 Sep, 2017 1 commit
    • Andrew Heather's avatar
      ENH: Lagrangian - provided backwards compatibility for cases using the · 2defba00
      Andrew Heather authored
      old "positions" file form
      
      The change to barycentric-based tracking changed the contents of the
      cloud "positions" file to a new format comprising the barycentric
      co-ordinates and other cell position-based info.  This broke
      backwards compatibility, providing no option to restart old cases
      (v1706 and earlier), and caused difficulties for dependent code, e.g.
      for post-processing utilities that could only infer the contents only
      after reading.
      
      The barycentric position info is now written to a file called
      "coordinates" with provision to restart old cases for which only the
      "positions" file is available. Related utilities, e.g. for parallel
      running and data conversion have been updated to be able to support both
      file types.
      
      To write the "positions" file by default, use set the following option
      in the InfoSwitches section of the controlDict:
      
          writeLagrangianPositions 1;
      2defba00
  28. 10 Aug, 2017 1 commit
  29. 06 Sep, 2017 1 commit
  30. 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
  31. 28 Mar, 2017 1 commit
  32. 08 Mar, 2017 1 commit
    • Henry Weller's avatar
      decomposePar: Added 'copyZero' option · 1be5f699
      Henry Weller authored
      Using
      
      decomposePar -copyZero
      
      The mesh is decomposed as usual but the '0' directory is recursively copied to
      the 'processor.*' directories rather than decomposing the fields.  This is a
      convenient option to handle cases where the initial field files are generic and
      can be used for serial or parallel running.  See for example the
      incompressible/simpleFoam/motorBike tutorial case.
      1be5f699
  33. 24 Nov, 2016 1 commit
  34. 25 Oct, 2016 1 commit
    • Mark Olesen's avatar
      BUG: resolve some decomposeParDict problems (issues #60, #265). · 52d0289e
      Mark Olesen authored
      - Cleanup/centralize handling of -decomposeParDict by relocating
        common code into argList. Ensures that all processes receive
        identical information about the -decomposeParDict opton.
      
      - Only use alternative decomposeParDict for simpleFoam/motorBike
        tutorial so that this will be included in the test loop for snappy.
      
      - Added Mattijs' fix for surfaceRedistributePar.
      52d0289e
  35. 04 Oct, 2016 1 commit
  36. 23 Sep, 2016 1 commit
  37. 05 Aug, 2016 1 commit
  38. 02 Aug, 2016 2 commits