Update headers, add authors and cavity3D tutorial

README.md

+## Coherent I/O format for OpenFOAM
+The new "coherent" OpenFOAM file format is designed for input/output (I/O) on high performance parallel file systems. The developments were conducted in a reduced version of foam-extend 4.1 comprising the core `foam` and `finiteVolume` libraries.
+
+### Installation
+For the reduced version the same steps apply as for foam-extend-4.1, see
+https://openfoamwiki.net/index.php/Installation/Linux/foam-extend-4.1.
+
+In particular, use `Allwmake.firstInstall` to download and install the dependency to ADIOS2 in the ThirdParty folder.
+
+```
+source etc/bashrc [WM_MPLIB=XXX MPI_ROOT=/path/to/mpi]
+Allwmake.firstInstall
+```
+
+Sourcing the bashrc for a second time enables usage of ADIOS2 tools like `bpls`.
+
+### Usage
+Check out the `lid-driven-cavity-3D` case in the `tutorials` folder. The following workflow works straightforward:
+
+```
+blockMesh
+[decomposePar]
+mpirun -n X icoFoam -parallel
+```
+
+Note that `decomposePar` actually is optional because a *naive* decomposition can be used during start-up phase of `icoFoam`. Also, if the number of processors in `decomposeParDict` does not match the number of ranks in `mpirun -n X`, the *naive* decomposition is used. Hence, `decomposePar` becomes optional and restarts on arbitrary number of MPI ranks is possible.
+
+After the first run the time folder contain a ADIOS2 bp-file. The data can be observed using the bpls command line tool.
+
+```
+bpls 0.001/data.bp/
+  double   U/internalField                     {3000000}
+  double   p/internalField                     {1000000}
+  double   phi/boundaryField/movingWall/value  {10000}
+  double   phi/internalField                   {2970000}
+```
+
+Please also refer to https://adios2.readthedocs.io/en/v2.9.1/ about viewing and extracting data from ADIOS2 files, for instance using the tool `bpls`
+
+If the `system/controlDict` sets `writeBulkData yes;` the the data of all time steps is stored in a case-global ADIOS2 bp-file. The time steps share one common `data.bp` file in the case folder. In that case, asynchronous out can be activate in the `system/config.xml`:
+
+```
+<parameter key="AsyncOpen" value="true"/>
+<parameter key="AsyncWrite" value="true"/>
+```
+
+The activated asynchronous output into the case-global data file can hide the overheads of the I/O latencies.
+
+#### Contributors
+The work has been carried out in Task 3.4 — Parallel I/O — of the exaFOAM project.
+Participating partners (partner in **bold** is the task lead): **HLRS**, Wikki GmbH
+
+HLRS: Gregor Weiss, Flavio Galeazzo, and Andreas Ruopp
+
+Wikki GmbH: Sergey Lesnik and Henrik Rusche
+
+#### Acknowledgment
+This application has been developed as part of the exaFOAM Project
+https://www.exafoam.eu, which has received funding from the European
+High-Performance Computing Joint Undertaking (JU) under grant agreement No
+956416. The JU receives support from the European Union's Horizon 2020 research
+and innovation programme and France, Germany, Italy, Croatia, Spain, Greece,
+and Portugal.

applications/utilities/parallelProcessing/decomposePar/controlDict

 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  v2006                                 |
-|   \\  /    A nd           | Website:  www.openfoam.com                      |
-|    \\/     M anipulation  |                                                 |
+| \\      /  F ield         | foam-extend: Open Source CFD                    |
+|  \\    /   O peration     | Version:     4.1                                |
+|   \\  /    A nd           | Web:         http://www.foam-extend.org         |
+|    \\/     M anipulation  | For copyright notice see file Copyright         |
 \*---------------------------------------------------------------------------*/
 FoamFile
 {
@@ -15,7 +15,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-application     icoFoamTar;
+application     icoFoam;
 
 startFrom       startTime;
 
@@ -33,7 +33,7 @@ writeInterval   1;
 
 purgeWrite      1;
 
-writeFormat     ascii;
+writeFormat     coherent;
 
 writePrecision  6;
 

applications/utilities/parallelProcessing/decomposePar/decomposeParDict

@@ -3,7 +3,7 @@
 | \\      /  F ield         | foam-extend: Open Source CFD                    |
 |  \\    /   O peration     | Version:     4.1                                |
 |   \\  /    A nd           | Web:         http://www.foam-extend.org         |
-|    \\/     M anipulation  |                                                 |
+|    \\/     M anipulation  | For copyright notice see file Copyright         |
 \*---------------------------------------------------------------------------*/
 FoamFile
 {
@@ -87,5 +87,4 @@ manualCoeffs
 //    "/tmp"
 //);
 
-
 // ************************************************************************* //

src/foam/Make/files

@@ -177,7 +177,6 @@ $(SliceStreams)/create/InputFeatures.C
 $(SliceStreams)/create/SliceWriting.C
 $(SliceStreams)/create/SliceReading.C
 $(SliceStreams)/buffer/SliceBuffer.C
-$(SliceStreams)/buffer/variableBuffer.C
 $(SliceStreams)/fieldDataEntry.C
 $(SliceStreams)/formattingEntry.C
 $(SliceStreams)/fieldTag.C

src/foam/db/IOstreams/SliceStreams/FileSliceStream.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | foam-extend: Open Source CFD
+   \\    /   O peration     | Version:     4.1
+    \\  /    A nd           | Web:         http://www.foam-extend.org
+     \\/     M anipulation  | For copyright notice see file Copyright
+-------------------------------------------------------------------------------
+License
+    This file is part of foam-extend.
+
+    foam-extend is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by the
+    Free Software Foundation, either version 3 of the License, or (at your
+    option) any later version.
+
+    foam-extend is distributed in the hope that it will be useful, but
+    WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+    General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
+
+Author
+    Gregor Weiss, HLRS University of Stuttgart, 2023
+    Sergey Lesnik, Wikki GmbH, 2023
+    Henrik Rusche, Wikki GmbH, 2023
+
+\*---------------------------------------------------------------------------*/
 
 #include "FileSliceStream.H"
 #include "StreamFeatures.H"

src/foam/db/IOstreams/SliceStreams/FileSliceStream.H

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | foam-extend: Open Source CFD
+   \\    /   O peration     | Version:     4.1
+    \\  /    A nd           | Web:         http://www.foam-extend.org
+     \\/     M anipulation  | For copyright notice see file Copyright
+-------------------------------------------------------------------------------
+License
+    This file is part of foam-extend.
+
+    foam-extend is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by the
+    Free Software Foundation, either version 3 of the License, or (at your
+    option) any later version.
+
+    foam-extend is distributed in the hope that it will be useful, but
+    WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+    General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
+
+Class
+    Foam::FileSliceStream
+
+Description
+    Child class from SliceStream implementing the parallel I/O streaming
+    into a file
+
+Author
+    Gregor Weiss, HLRS University of Stuttgart, 2023
+    Sergey Lesnik, Wikki GmbH, 2023
+    Henrik Rusche, Wikki GmbH, 2023
+
+SourceFiles
+    FileSliceStream.C
+
+\*---------------------------------------------------------------------------*/
+
 #ifndef FileSliceStream_H
 #define FileSliceStream_H
 

src/foam/db/IOstreams/SliceStreams/IFCstream.C

@@ -21,6 +21,11 @@ License
     You should have received a copy of the GNU General Public License
     along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
 
+Author
+    Sergey Lesnik, Wikki GmbH, 2023
+    Gregor Weiss, HLRS University of Stuttgart, 2023
+    Henrik Rusche, Wikki GmbH, 2023
+
 \*---------------------------------------------------------------------------*/
 
 #include "IFCstream.H"

src/foam/db/IOstreams/SliceStreams/IFCstream.H

@@ -31,7 +31,13 @@ Description
     in the coherent format. GeometricField constructor obtains the ready-to-use
     dictionary.
 
+Author
+    Sergey Lesnik, Wikki GmbH, 2023
+    Gregor Weiss, HLRS University of Stuttgart, 2023
+    Henrik Rusche, Wikki GmbH, 2023
+
 SourceFiles
+    IFCstreamI.H
     IFCstream.C
 
 \*---------------------------------------------------------------------------*/

src/foam/db/IOstreams/SliceStreams/IFCstreamI.H

@@ -21,6 +21,11 @@ License
     You should have received a copy of the GNU General Public License
     along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
 
+Author
+    Sergey Lesnik, Wikki GmbH, 2023
+    Gregor Weiss, HLRS University of Stuttgart, 2023
+    Henrik Rusche, Wikki GmbH, 2023
+
 \*---------------------------------------------------------------------------*/
 
 // * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //

src/foam/db/IOstreams/SliceStreams/OFCstream.C

@@ -21,6 +21,11 @@ License
     You should have received a copy of the GNU General Public License
     along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
 
+Author
+    Sergey Lesnik, Wikki GmbH, 2023
+    Gregor Weiss, HLRS University of Stuttgart, 2023
+    Henrik Rusche, Wikki GmbH, 2023
+
 \*---------------------------------------------------------------------------*/
 
 #include "OFCstream.H"

src/foam/db/IOstreams/SliceStreams/OFCstream.H

@@ -27,6 +27,11 @@ Class
 Description
     Output to file stream for coherent mesh and fields.
 
+Author
+    Sergey Lesnik, Wikki GmbH, 2023
+    Gregor Weiss, HLRS University of Stuttgart, 2023
+    Henrik Rusche, Wikki GmbH, 2023
+
 SourceFiles
     OFCstream.C
 

src/foam/db/IOstreams/SliceStreams/SliceStream.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | foam-extend: Open Source CFD
+   \\    /   O peration     | Version:     4.1
+    \\  /    A nd           | Web:         http://www.foam-extend.org
+     \\/     M anipulation  | For copyright notice see file Copyright
+-------------------------------------------------------------------------------
+License
+    This file is part of foam-extend.
+
+    foam-extend is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by the
+    Free Software Foundation, either version 3 of the License, or (at your
+    option) any later version.
+
+    foam-extend is distributed in the hope that it will be useful, but
+    WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+    General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
+
+Author
+    Gregor Weiss, HLRS University of Stuttgart, 2023
+    Sergey Lesnik, Wikki GmbH, 2023
+    Henrik Rusche, Wikki GmbH, 2023
+
+\*---------------------------------------------------------------------------*/
 
 #include "SliceStream.H"
 

src/foam/db/IOstreams/SliceStreams/SliceStream.H

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | foam-extend: Open Source CFD
+   \\    /   O peration     | Version:     4.1
+    \\  /    A nd           | Web:         http://www.foam-extend.org
+     \\/     M anipulation  | For copyright notice see file Copyright
+-------------------------------------------------------------------------------
+License
+    This file is part of foam-extend.
+
+    foam-extend is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by the
+    Free Software Foundation, either version 3 of the License, or (at your
+    option) any later version.
+
+    foam-extend is distributed in the hope that it will be useful, but
+    WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+    General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
+
+Class
+    Foam::SliceStream
+
+Description
+    A parallel I/O streaming class for contiguous data access patterns
+
+Author
+    Gregor Weiss, HLRS University of Stuttgart, 2023
+    Sergey Lesnik, Wikki GmbH, 2023
+    Henrik Rusche, Wikki GmbH, 2023
+
+SourceFiles
+    SliceStream.C
+    SliceStreamImpl.H (include in SliceStream.C)
+
+\*---------------------------------------------------------------------------*/
+
 #ifndef SliceStream_H
 #define SliceStream_H
 

src/foam/db/IOstreams/SliceStreams/SliceStreamImpl.H

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | foam-extend: Open Source CFD
+   \\    /   O peration     | Version:     4.1
+    \\  /    A nd           | Web:         http://www.foam-extend.org
+     \\/     M anipulation  | For copyright notice see file Copyright
+-------------------------------------------------------------------------------
+License
+    This file is part of foam-extend.
+
+    foam-extend is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by the
+    Free Software Foundation, either version 3 of the License, or (at your
+    option) any later version.
+
+    foam-extend is distributed in the hope that it will be useful, but
+    WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+    General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
+
+Author
+    Gregor Weiss, HLRS University of Stuttgart, 2023
+    Sergey Lesnik, Wikki GmbH, 2023
+    Henrik Rusche, Wikki GmbH, 2023
+
+\*---------------------------------------------------------------------------*/
 
 #include "adios2.h"
 

src/foam/db/IOstreams/SliceStreams/SliceStreamPaths.C

 
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | foam-extend: Open Source CFD
+   \\    /   O peration     | Version:     4.1
+    \\  /    A nd           | Web:         http://www.foam-extend.org
+     \\/     M anipulation  | For copyright notice see file Copyright
+-------------------------------------------------------------------------------
+License
+    This file is part of foam-extend.
+
+    foam-extend is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by the
+    Free Software Foundation, either version 3 of the License, or (at your
+    option) any later version.
+
+    foam-extend is distributed in the hope that it will be useful, but
+    WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+    General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
+
+Author
+    Gregor Weiss, HLRS University of Stuttgart, 2023
+    Sergey Lesnik, Wikki GmbH, 2023
+    Henrik Rusche, Wikki GmbH, 2023
+
+\*---------------------------------------------------------------------------*/
+
+// ToDoIO Formatting
+
 #include "SliceStreamPaths.H"
 
 #include "OSspecific.H" // isDir

src/foam/db/IOstreams/SliceStreams/SliceStreamPaths.H

@@ -27,6 +27,11 @@ Class
 Description
     Class to manage and fix file naming for ADIOS2 files
 
+Author
+    Gregor Weiss, HLRS University of Stuttgart, 2023
+    Sergey Lesnik, Wikki GmbH, 2023
+    Henrik Rusche, Wikki GmbH, 2023
+
 SourceFiles
     SliceStreamPaths.C
 

src/foam/db/IOstreams/SliceStreams/SliceStreamRepo.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | foam-extend: Open Source CFD
+   \\    /   O peration     | Version:     4.1
+    \\  /    A nd           | Web:         http://www.foam-extend.org
+     \\/     M anipulation  | For copyright notice see file Copyright
+-------------------------------------------------------------------------------
+License
+    This file is part of foam-extend.
+
+    foam-extend is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by the
+    Free Software Foundation, either version 3 of the License, or (at your
+    option) any later version.
+
+    foam-extend is distributed in the hope that it will be useful, but
+    WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+    General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
+
+Author
+    Gregor Weiss, HLRS University of Stuttgart, 2023
+    Sergey Lesnik, Wikki GmbH, 2023
+    Henrik Rusche, Wikki GmbH, 2023
+
+\*---------------------------------------------------------------------------*/
 
 #include "SliceStreamRepo.H"
 

src/foam/db/IOstreams/SliceStreams/SliceStreamRepo.H

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | foam-extend: Open Source CFD
+   \\    /   O peration     | Version:     4.1
+    \\  /    A nd           | Web:         http://www.foam-extend.org
+     \\/     M anipulation  | For copyright notice see file Copyright
+-------------------------------------------------------------------------------
+License
+    This file is part of foam-extend.
+
+    foam-extend is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by the
+    Free Software Foundation, either version 3 of the License, or (at your
+    option) any later version.
+
+    foam-extend is distributed in the hope that it will be useful, but
+    WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+    General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
+
+Class
+    Foam::SliceStreamRepo
+
+Description
+    A repository for streaming resources for parallel I/O.
+
+Author
+    Gregor Weiss, HLRS University of Stuttgart, 2023
+    Sergey Lesnik, Wikki GmbH, 2023
+    Henrik Rusche, Wikki GmbH, 2023
+
+SourceFiles
+    SliceStreamRepoI.H
+    SliceStreamRepo.C
+
+\*---------------------------------------------------------------------------*/
+
 #ifndef SliceStreamRepo_H
 #define SliceStreamRepo_H
 

src/foam/db/IOstreams/SliceStreams/SliceStreamRepoI.H

@@ -21,6 +21,11 @@ License
     You should have received a copy of the GNU General Public License
     along with foam-extend.  If not, see <http://www.gnu.org/licenses/>.
 
+Author
+    Gregor Weiss, HLRS University of Stuttgart, 2023
+    Sergey Lesnik, Wikki GmbH, 2023
+    Henrik Rusche, Wikki GmbH, 2023
+
 \*---------------------------------------------------------------------------*/
 
 #include "label.H"