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documentation: remove libSplash
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psychocoderHPC committed Sep 1, 2021
1 parent 2962af2 commit 16622c7
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44 changes: 1 addition & 43 deletions INSTALL.rst
Original file line number Diff line number Diff line change
Expand Up @@ -207,26 +207,7 @@ pngwriter
- *environment:* (assumes install from source in ``$HOME/lib/pngwriter``)

- ``export CMAKE_PREFIX_PATH=$HOME/lib/pngwriter:$CMAKE_PREFIX_PATH``
- ``export LD_LIBRARY_PATH=$HOME/lib/pngwriter/lib:$LD_LIBRARY_PATH``

libSplash
"""""""""
- 1.7.0+ (requires *HDF5*, *boost program-options*)
- *Debian/Ubuntu dependencies:* ``sudo apt-get install libhdf5-openmpi-dev libboost-program-options-dev``
- *Arch Linux dependencies:* ``sudo pacman --sync hdf5-openmpi boost``
- *Spack:* ``spack install libsplash ^hdf5~fortran``
- *from source:*

- ``mkdir -p ~/src ~/build ~/lib``
- ``git clone https://github.com/ComputationalRadiationPhysics/libSplash.git ~/src/splash/``
- ``cd ~/build && rm -rf ../build/*``
- ``cmake -DCMAKE_INSTALL_PREFIX=$HOME/lib/splash -DSplash_USE_MPI=ON -DSplash_USE_PARALLEL=ON ~/src/splash``
- ``make install``

- *environment:* (assumes install from source in ``$HOME/lib/splash``)

- ``export CMAKE_PREFIX_PATH=$HOME/lib/splash:$CMAKE_PREFIX_PATH``
- ``export LD_LIBRARY_PATH=$HOME/lib/splash/lib:$LD_LIBRARY_PATH``
- ``export LD_LIBRARY_PATH=$HOME/lib/pngwriter/lib:$LD_LIBRARY_PATH`
HDF5
""""
Expand Down Expand Up @@ -254,29 +235,6 @@ HDF5
- ``export HDF5_ROOT=$HOME/lib/hdf5``
- ``export LD_LIBRARY_PATH=$HDF5_ROOT/lib:$LD_LIBRARY_PATH``

splash2txt
""""""""""
- requires *libSplash* and *boost* ``program_options``
- converts slices in dumped hdf5 files to plain txt matrices
- assume you [downloaded](#requirements) PIConGPU to `PICSRC=$HOME/src/picongpu`
- ``mkdir -p ~/build && cd ~/build``
- ``cmake -DCMAKE_INSTALL_PREFIX=$PICSRC/src/tools/bin $PICSRC/src/tools/splash2txt``
- ``make``
- ``make install``
- *environment:*

- ``export PATH=$PATH:$PICSRC/src/splash2txt/build``
- options:

- ``splash2txt --help``
- list all available datasets: ``splash2txt --list <FILE_PREFIX>``

png2gas
"""""""
- requires *libSplash*, *pngwriter* and *boost* ``program_options``)
- converts png files to hdf5 files that can be used as an input for species initial density profiles
- compile and install exactly as *splash2txt* above

c-blosc
"""""""
- general purpose compressor, used in ADIOS2 for in situ data reduction
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5 changes: 2 additions & 3 deletions LICENSE.md
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Expand Up @@ -27,19 +27,18 @@ The **main simulation** is licensed under the **GPLv3+**. See
- `include/picongpu`
- `lib/python/picongpu`
- `share/picongpu`
- `src/tools` (without `splash2txt`)
- `src/tools`
- `src/mpiInfo`
- `test`


### PMacc & splash2txt
### PMacc

All **libraries** are licensed under the **LGPLv3+**. See
[COPYING.LESSER](COPYING.LESSER).
If not stated otherwise explicitly, that affects:
- `include/pmacc`
- `share/pmacc`
- `src/tools/splash2txt`


### Documentation
Expand Down
3 changes: 1 addition & 2 deletions README.md
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Expand Up @@ -54,8 +54,7 @@ a wide range of tools and diagnostics, e.g.:
- online, far-field radiation diagnostics for coherent and incoherent radiation
emitted by charged particles
- full restart and output capabilities via [openPMD](http://openPMD.org),
including [parallel HDF5](http://hdfgroup.org/) (via
[libSplash](https://github.com/ComputationalRadiationPhysics/libSplash)) and
including [parallel HDF5](http://hdfgroup.org/)
- 2D and 3D live view and diagnostics tools
- a large selection of extensible
[online-plugins](http://picongpu.readthedocs.io/en/latest/usage/plugins.html)
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2 changes: 0 additions & 2 deletions docs/source/install/libraryDependencies.dot
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Expand Up @@ -26,8 +26,6 @@ digraph PIConGPU {
hdf5 [label="hdf5-parallel"];
mpi -> hdf5;
zlib -> hdf5;
hdf5 -> libSplash;
boost -> libSplash [style=dashed label="tools"];

adios [label="ADIOS"];
mpi -> adios;
Expand Down
18 changes: 8 additions & 10 deletions docs/source/install/profile.rst
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Expand Up @@ -69,8 +69,6 @@ Summit (ORNL)
**Production directory:** usually ``$PROJWORK/$proj/`` (`link <https://www.olcf.ornl.gov/for-users/system-user-guides/summit/summit-user-guide/#file-systems>`_).
Note that ``$HOME`` is mounted on compute nodes as read-only.

For this profile to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`libSplash and PNGwriter <install-dependencies>` manually.

V100 GPUs (recommended)
^^^^^^^^^^^^^^^^^^^^^^^

Expand All @@ -86,7 +84,7 @@ Piz Daint (CSCS)

**Production directory:** ``$SCRATCH`` (`link <https://user.cscs.ch/storage/file_systems/>`_).

For this profile to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`boost, zlib, libpng, c-blosc, PNGwriter, libSplash and ADIOS <install-dependencies>` manually.
For this profile to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`boost, zlib, libpng, c-blosc, PNGwriter and ADIOS <install-dependencies>` manually.

.. note::

Expand All @@ -109,7 +107,7 @@ Taurus (TU Dresden)

**Production directory:** ``/scratch/$USER/`` and ``/scratch/$proj/``

For these profiles to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`PNGwriter and libSplash <install-dependencies>` manually.
For these profiles to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`PNGwriter <install-dependencies>` manually.

Queue: gpu1 (Nvidia K20x GPUs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Expand Down Expand Up @@ -157,7 +155,7 @@ Lawrencium (LBNL)

**Production directory:** ``/global/scratch/$USER/``

For this profile to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`boost, PNGwriter and libSplash <install-dependencies>` manually.
For this profile to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`boost and PNGwriter <install-dependencies>` manually.
Additionally, you need to make the ``rsync`` command available as written below.

.. literalinclude:: profiles/lawrencium-lbnl/picongpu.profile.example
Expand All @@ -172,7 +170,7 @@ Cori (NERSC)

**Production directory:** ``$SCRATCH`` (`link <https://www.nersc.gov/users/storage-and-file-systems/>`_).

For these profiles to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`PNGwriter and libSplash <install-dependencies>` manually.
For these profiles to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`PNGwriter <install-dependencies>` manually.

Queue: regular (Intel Xeon Phi - Knights Landing)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Expand All @@ -195,7 +193,7 @@ Draco (MPCDF)

**Production directory:** ``/ptmp/$USER/``

For this profile to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`libpng, PNGwriter and libSplash <install-dependencies>` manually.
For this profile to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`libpng and PNGwriter <install-dependencies>` manually.

.. literalinclude:: profiles/draco-mpcdf/picongpu.profile.example
:language: bash
Expand Down Expand Up @@ -226,7 +224,7 @@ JURECA (JSC)

**Production directory:** ``$SCRATCH`` (`link <http://www.fz-juelich.de/SharedDocs/FAQs/IAS/JSC/EN/JUST/FAQ_00_File_systems.html?nn=1297148>`_)

For these profiles to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`PNGwriter, openPMD and libSplash <install-dependencies>`, for the gpus partition also :ref:`Boost and HDF5 <install-dependencies>`, manually.
For these profiles to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`PNGwriter and openPMD <install-dependencies>`, for the gpus partition also :ref:`Boost and HDF5 <install-dependencies>`, manually.

Queue: batch (2 x Intel Xeon E5-2680 v3 CPUs, 12 Cores + 12 Hyperthreads/CPU)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Expand Down Expand Up @@ -255,7 +253,7 @@ JUWELS (JSC)

**Production directory:** ``$SCRATCH`` (`link <http://www.fz-juelich.de/ias/jsc/EN/Expertise/Supercomputers/JUWELS/FAQ/juwels_FAQ_node.html#faq1495160>`_)

For these profiles to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`PNGwriter, openPMD and libSplash <install-dependencies>`, for the gpus partition also :ref:`Boost and HDF5 <install-dependencies>`, manually.
For these profiles to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`PNGwriter and openPMD <install-dependencies>`, for the gpus partition also :ref:`Boost and HDF5 <install-dependencies>`, manually.

Queue: batch (2 x Intel Xeon Platinum 8168 CPUs, 24 Cores + 24 Hyperthreads/CPU)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Expand Down Expand Up @@ -293,7 +291,7 @@ Ascent (ORNL)

**Production directory:** usually ``$PROJWORK/$proj/`` (as on summit `link <https://www.olcf.ornl.gov/for-users/system-user-guides/summit/summit-user-guide/#file-systems>`_).

For this profile to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`openPMD-api, libSplash and PNGwriter <install-dependencies>` manually or use pre-installed libraries in the shared project directory.
For this profile to work, you need to download the :ref:`PIConGPU source code <install-dependencies-picongpu>` and install :ref:`openPMD-api and PNGwriter <install-dependencies>` manually or use pre-installed libraries in the shared project directory.

V100 GPUs (recommended)
^^^^^^^^^^^^^^^^^^^^^^^
Expand Down
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