Merge pull request #3 from ComputationalRadiationPhysics/dev

Dev

.gitlab-ci.yml

@@ -56,7 +56,7 @@ pull-request-validation:
 #                    "examples/KelvinHelmholtz" compile all cases within one gitlab job
 generate-reduced-matrix:
   variables:
-    PIC_INPUTS: "examples tests"
+    PIC_INPUTS: "examples tests benchmarks"
     TEST_TUPLE_NUM_ELEM: 1
   extends: ".base_generate-reduced-matrix"
 

INSTALL.rst

@@ -328,7 +328,7 @@ ADIOS
 
 openPMD API
 """""""""""
-- 0.12.0+ (yet to be released, requires *MPI*)
+- 0.12.0+ (bare minimum) / 0.13.0+ (for streaming IO)
 - *Spack*: ``spack install openpmd-api``
 - *from source:*
 

USAGE.rst

@@ -2,7 +2,14 @@
 
 .. seealso::
 
-   You need to have an :ref:`environment loaded <install-profile>` (``source $HOME/picongpu.profile``) that provides all :ref:`PIConGPU dependencies <install-dependencies>` to complete this chapter.
+   You need to have an :ref:`environment loaded <install-profile>` (``source $HOME/picongpu.profile`` when installing from source or ``spack load picongpu`` when using spack) that provides all :ref:`PIConGPU dependencies <install-dependencies>` to complete this chapter.
+
+.. warning::
+
+   PIConGPU source code is portable and can be compiled on all major operating systems.
+   However, helper tools like ``pic-create`` and ``pic-build`` described in this section rely on Linux utilities and thus are not expected to work on other platforms out-of-the-box.
+   Note that building and using PIConGPU on other operating systems is still possible but has to be done manually or with custom tools.
+   This case is not covered in the documentation, but we can assist users with it when needed.
 
 Basics
 ======

bin/cuda_memtest.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2013-2020 Rene Widera
+# Copyright 2013-2021 Rene Widera
 #
 # This file is part of PIConGPU.
 #

bin/egetopt

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2014-2020 Rene Widera
+# Copyright 2014-2021 Rene Widera
 #
 # This file is part of PIConGPU.
 #

bin/pic-build

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2017-2020 Axel Huebl
+# Copyright 2017-2021 Axel Huebl
 #
 # This file is part of PIConGPU.
 #

bin/pic-compile

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2013-2020 Axel Huebl, Rene Widera
+# Copyright 2013-2021 Axel Huebl, Rene Widera
 #
 # This file is part of PIConGPU.
 #

bin/pic-configure

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2013-2020 Axel Huebl, Rene Widera
+# Copyright 2013-2021 Axel Huebl, Rene Widera
 #
 # This file is part of PIConGPU.
 #
@@ -64,22 +64,22 @@ get_backend_flags()
             result+=" -DALPAKA_CUDA_ARCH=\"${backend_cfg[1]}\""
         fi
     elif [ "${backend_cfg[0]}" == "omp2b" ] ; then
-        result+=" -DALPAKA_ACC_CPU_B_OMP2_T_SEQ_ENABLE=ON"
+        result+=" -DALPAKA_ACC_CPU_B_OMP2_T_SEQ_ENABLE=ON -DCUPLA_STREAM_ASYNC_ENABLE=OFF"
         if [ $num_options -eq 2 ] ; then
             result+=" -DPMACC_CPU_ARCH=\"${backend_cfg[1]}\""
         fi
     elif [ "${backend_cfg[0]}" == "serial" ] ; then
-        result+=" -DALPAKA_ACC_CPU_B_SEQ_T_SEQ_ENABLE=ON"
+        result+=" -DALPAKA_ACC_CPU_B_SEQ_T_SEQ_ENABLE=ON -DCUPLA_STREAM_ASYNC_ENABLE=OFF"
         if [ $num_options -eq 2 ] ; then
             result+=" -DPMACC_CPU_ARCH=\"${backend_cfg[1]}\""
         fi
     elif [ "${backend_cfg[0]}" == "tbb" ] ; then
-        result+=" -DALPAKA_ACC_CPU_B_TBB_T_SEQ_ENABLE=ON"
+        result+=" -DALPAKA_ACC_CPU_B_TBB_T_SEQ_ENABLE=ON -DCUPLA_STREAM_ASYNC_ENABLE=OFF"
         if [ $num_options -eq 2 ] ; then
             result+=" -DPMACC_CPU_ARCH=\"${backend_cfg[1]}\""
         fi
     elif [ "${backend_cfg[0]}" == "threads" ] ; then
-        result+=" -DALPAKA_ACC_CPU_B_SEQ_T_THREADS_ENABLE=ON"
+        result+=" -DALPAKA_ACC_CPU_B_SEQ_T_THREADS_ENABLE=ON -DCUPLA_STREAM_ASYNC_ENABLE=OFF"
         if [ $num_options -eq 2 ] ; then
             result+=" -DPMACC_CPU_ARCH=\"${backend_cfg[1]}\""
         fi

bin/pic-create

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2013-2020 Axel Huebl, Rene Widera
+# Copyright 2013-2021 Axel Huebl, Rene Widera
 #
 # This file is part of PIConGPU.
 #

bin/pic-edit

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2017-2020 Axel Huebl
+# Copyright 2017-2021 Axel Huebl
 #
 # This file is part of PIConGPU.
 #

bin/tbg

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2013-2020 Axel Huebl, Rene Widera, Richard Pausch
+# Copyright 2013-2021 Axel Huebl, Rene Widera, Richard Pausch
 #
 # This file is part of PIConGPU.
 #

buildsystem/CompileSuite/autoTests/config.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2013-2020 Axel Huebl
+# Copyright 2013-2021 Axel Huebl
 #
 # This file is part of PIConGPU.
 #

buildsystem/CompileSuite/autoTests/get_work.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2013-2020 Axel Huebl
+# Copyright 2013-2021 Axel Huebl
 #
 # This file is part of PIConGPU.
 #

buildsystem/CompileSuite/autoTests/new_commits.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2013-2020 Axel Huebl
+# Copyright 2013-2021 Axel Huebl
 #
 # This file is part of PIConGPU.
 #

buildsystem/CompileSuite/autoTests/report.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2013-2020 Axel Huebl
+# Copyright 2013-2021 Axel Huebl
 #
 # This file is part of PIConGPU.
 #

buildsystem/CompileSuite/color.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2013-2020 Axel Huebl, Rene Widera
+# Copyright 2013-2021 Axel Huebl, Rene Widera
 #
 # This file is part of PIConGPU.
 #

buildsystem/CompileSuite/compileSet.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2013-2020 Axel Huebl
+# Copyright 2013-2021 Axel Huebl
 #
 # This file is part of PIConGPU.
 #

buildsystem/CompileSuite/exec_helper.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2013-2020 Axel Huebl
+# Copyright 2013-2021 Axel Huebl
 #
 # This file is part of PIConGPU.
 #

buildsystem/CompileSuite/help.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2013-2020 Axel Huebl
+# Copyright 2013-2021 Axel Huebl
 #
 # This file is part of PIConGPU.
 #

buildsystem/CompileSuite/options.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2013-2020 Axel Huebl
+# Copyright 2013-2021 Axel Huebl
 #
 # This file is part of PIConGPU.
 #

buildsystem/CompileSuite/path.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2013-2020 Axel Huebl
+# Copyright 2013-2021 Axel Huebl
 #
 # This file is part of PIConGPU.
 #

docs/TBG_macros.cfg

@@ -1,4 +1,4 @@
-# Copyright 2014-2020 Felix Schmitt, Axel Huebl, Richard Pausch, Heiko Burau,
+# Copyright 2014-2021 Felix Schmitt, Axel Huebl, Richard Pausch, Heiko Burau,
 #                     Franz Poeschel
 #
 # This file is part of PIConGPU.

docs/propose_changelog.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 #
-# Copyright 2017-2020 Axel Huebl
+# Copyright 2017-2021 Axel Huebl
 #
 # License: GPLv3+
 #

docs/source/dev/picongpu.rst

@@ -3,10 +3,10 @@ Important PIConGPU Classes
 
 This is very, very small selection of classes of interest to get you started.
 
-MySimulation
-------------
+Simulation
+----------
 
-.. doxygenclass:: picongpu::MySimulation
+.. doxygenclass:: picongpu::Simulation
    :project: PIConGPU
    :members:
    :undoc-members:

docs/source/models/field_ionization_charge_state_prediction.py

@@ -1,7 +1,7 @@
 """Ionization prediction module and example.
 
 This file is part of the PIConGPU.
-Copyright 2019-2020 PIConGPU contributors
+Copyright 2019-2021 PIConGPU contributors
 Authors: Marco Garten
 License: GPLv3+
 """

docs/source/usage/plugins/openPMD.rst

@@ -9,6 +9,7 @@ External Dependencies
 ^^^^^^^^^^^^^^^^^^^^^
 
 The plugin is available as soon as the :ref:`openPMD API <install-dependencies>` is compiled in.
+If the openPMD API is found in version 0.13.0 or greater, PIConGPU will support streaming IO via openPMD.
 
 .param file
 ^^^^^^^^^^^
@@ -40,15 +41,18 @@ The openPMD API will parse the file name to decide the chosen backend and iterat
 In order to set defaults for these value, two further options control the filename:
 
 * ``--openPMD.ext`` sets the filename extension.
-  Possible extensions include ``.bp`` for the ADIOS backends (default).
+  Possible extensions include ``bp`` for the ADIOS backends (default), ``h5`` for HDF5 and ``sst`` for Streaming via ADIOS2/SST.
   If the openPMD API has been built with support for the ADIOS1 and ADIOS2 backends, ADIOS2 will take precedence over ADIOS1.
   This behavior can be overridden by setting the environment variable ``OPENPMD_BP_BACKEND=ADIOS1``.
-  The extension for the HDF5 backend is ``.h5``.
-  (The version of ADIOS will depend on the compile-time configuration of the openPMD API.)
 * ``--openPMD.infix`` sets the filename pattern that controls the iteration layout, default is "_06T" for a six-digit number specifying the iteration.
   Leave empty to pick group-based iteration layout.
   Since passing an empty string may be tricky in some workflows, specifying ``--openPMD.infix=NULL`` is also possible.
 
+  Note that streaming IO requires group-based iteration layout in openPMD, i.e. ``--openPMD.infix=NULL`` is mandatory.
+  If PIConGPU detects a streaming backend (e.g. by ``--openPMD.ext=sst``), it will automatically set ``--openPMD.infix=NULL``, overriding the user's choice.
+  Note however that the ADIOS2 backend can also be selected via ``--openPMD.json`` and via environment variables which PIConGPU does not check.
+  It is hence recommended to set ``--openPMD.infix=NULL`` explicitly.
+
 For example, ``--openPMD.period 128 --openPMD.file simData --openPMD.source 'species_all'`` will write only the particle species data to files of the form ``simData_000000.bp``, ``simData_000128.bp`` in the default simulation output directory every 128 steps.
 Note that this plugin will only be available if the openPMD API is found during compile configuration.
 

docs/source/usage/workflows/memoryPerDevice.py

@@ -3,7 +3,7 @@
 """
 This file is part of PIConGPU.
 
-Copyright 2018-2020 PIConGPU contributors
+Copyright 2018-2021 PIConGPU contributors
 Authors: Marco Garten, Pawel Ordyna
 License: GPLv3+
 """

etc/picongpu/aris-grnet/gpu.tpl

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Copyright 2013-2020 Axel Huebl, Richard Pausch, Rene Widera, Sergei Bastrakov,
+# Copyright 2013-2021 Axel Huebl, Richard Pausch, Rene Widera, Sergei Bastrakov,
 #                     Jian Fuh Ong
 #
 # This file is part of PIConGPU.

etc/picongpu/bash/mpiexec.tpl

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Copyright 2013-2020 Axel Huebl, Anton Helm, Rene Widera
+# Copyright 2013-2021 Axel Huebl, Anton Helm, Rene Widera
 #
 # This file is part of PIConGPU.
 #

etc/picongpu/bash/mpirun.tpl

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Copyright 2013-2020 Axel Huebl, Anton Helm, Rene Widera
+# Copyright 2013-2021 Axel Huebl, Anton Helm, Rene Widera
 #
 # This file is part of PIConGPU.
 #

etc/picongpu/cori-nersc/knl.tpl

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Copyright 2013-2020 Axel Huebl, Richard Pausch, Alexander Matthes
+# Copyright 2013-2021 Axel Huebl, Richard Pausch, Alexander Matthes
 #
 # This file is part of PIConGPU.
 #

etc/picongpu/cpuNumaStarter.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright 2017-2020 Rene Widera, Alexander Matthes
+# Copyright 2017-2021 Rene Widera, Alexander Matthes
 #
 # This file is part of PIConGPU.
 #

etc/picongpu/davide-cineca/gpu.tpl

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Copyright 2013-2020 Axel Huebl, Richard Pausch, Rene Widera
+# Copyright 2013-2021 Axel Huebl, Richard Pausch, Rene Widera
 #
 # This file is part of PIConGPU.
 #

etc/picongpu/davinci-rice/picongpu.tpl

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Copyright 2013-2020 Axel Huebl, Rene Widera, Richard Pausch
+# Copyright 2013-2021 Axel Huebl, Rene Widera, Richard Pausch
 #
 # This file is part of PIConGPU.
 #

etc/picongpu/draco-mpcdf/general.tpl

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Copyright 2013-2020 Axel Huebl, Richard Pausch, Rene Widera
+# Copyright 2013-2021 Axel Huebl, Richard Pausch, Rene Widera
 #
 # This file is part of PIConGPU.
 #

etc/picongpu/hemera-hzdr/defq.tpl

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Copyright 2013-2020 Axel Huebl, Richard Pausch, Rene Widera
+# Copyright 2013-2021 Axel Huebl, Richard Pausch, Rene Widera
 #
 # This file is part of PIConGPU.
 #

etc/picongpu/hemera-hzdr/defq_picongpu.profile.example

@@ -30,7 +30,6 @@ module load adios/1.13.1
 module load hdf5-parallel/1.8.20
 module load libsplash/1.7.0
 module load python/3.6.5
-module load openpmd/0.11.1
 
 module load libpng/1.6.35
 module load pngwriter/0.7.0

etc/picongpu/hemera-hzdr/fwkt_v100.tpl

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Copyright 2013-2020 Axel Huebl, Richard Pausch, Rene Widera,
+# Copyright 2013-2021 Axel Huebl, Richard Pausch, Rene Widera,
 #                     Marco Garten, Alexander Debus
 #
 # This file is part of PIConGPU.

etc/picongpu/hemera-hzdr/gpu.tpl

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Copyright 2013-2020 Axel Huebl, Richard Pausch, Rene Widera, Marco Garten
+# Copyright 2013-2021 Axel Huebl, Richard Pausch, Rene Widera, Marco Garten
 #
 # This file is part of PIConGPU.
 #

etc/picongpu/hemera-hzdr/k20.tpl

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Copyright 2013-2020 Axel Huebl, Anton Helm, Richard Pausch, Rene Widera,
+# Copyright 2013-2021 Axel Huebl, Anton Helm, Richard Pausch, Rene Widera,
 #                     Marco Garten
 #
 # This file is part of PIConGPU.

etc/picongpu/hemera-hzdr/k20_restart.tpl

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Copyright 2013-2020 Axel Huebl, Anton Helm, Rene Widera, Richard Pausch,
+# Copyright 2013-2021 Axel Huebl, Anton Helm, Rene Widera, Richard Pausch,
 #                     Bifeng Lei, Marco Garten
 #
 # This file is part of PIConGPU.

etc/picongpu/hemera-hzdr/k80.tpl

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Copyright 2013-2020 Axel Huebl, Anton Helm, Richard Pausch, Rene Widera,
+# Copyright 2013-2021 Axel Huebl, Anton Helm, Richard Pausch, Rene Widera,
 #                     Marco Garten
 #
 # This file is part of PIConGPU.

etc/picongpu/hemera-hzdr/k80_restart.tpl

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Copyright 2013-2020 Axel Huebl, Anton Helm, Rene Widera, Richard Pausch,
+# Copyright 2013-2021 Axel Huebl, Anton Helm, Rene Widera, Richard Pausch,
 #                     Bifeng Lei, Marco Garten
 #
 # This file is part of PIConGPU.