move things

lanl · Sep 20, 2023 · d27d77d · d27d77d
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diff --git a/doc/sphinx/0_intro/introduction.rst → doc/sphinx/00_intro/introduction.rst b/doc/sphinx/0_intro/introduction.rst → doc/sphinx/00_intro/introduction.rst
@@ -14,7 +14,10 @@ benchmarks prior to RFP.
 
 To use these benchmarks please refer to the ATS-5 benchmarks repository `ATS-5 repo <https://github.com/lanl/benchmarks>`_
 
-Benchmark changes from Crossroads
+The benchmarks will, eventually, be generated atop Crossroads as the reference
+system (see :ref:`ReferenceCrossroads` for more information).
+
+Benchmark Changes from Crossroads
 =================================
 
 The key differences from Crossroads benchmarks and ATS-5 benchmarks are as summarized below: 

diff --git a/doc/sphinx/1_branson/branson.rst → doc/sphinx/01_branson/branson.rst b/doc/sphinx/1_branson/branson.rst → doc/sphinx/01_branson/branson.rst
diff --git a/doc/sphinx/1_branson/cpu.gp → doc/sphinx/01_branson/cpu.gp b/doc/sphinx/1_branson/cpu.gp → doc/sphinx/01_branson/cpu.gp
diff --git a/doc/sphinx/1_branson/cpu_10M.csv → doc/sphinx/01_branson/cpu_10M.csv b/doc/sphinx/1_branson/cpu_10M.csv → doc/sphinx/01_branson/cpu_10M.csv
diff --git a/doc/sphinx/1_branson/cpu_133M.csv → doc/sphinx/01_branson/cpu_133M.csv b/doc/sphinx/1_branson/cpu_133M.csv → doc/sphinx/01_branson/cpu_133M.csv
diff --git a/doc/sphinx/1_branson/cpu_200M.csv → doc/sphinx/01_branson/cpu_200M.csv b/doc/sphinx/1_branson/cpu_200M.csv → doc/sphinx/01_branson/cpu_200M.csv
diff --git a/doc/sphinx/1_branson/cpu_200M_bdw.csv → doc/sphinx/01_branson/cpu_200M_bdw.csv b/doc/sphinx/1_branson/cpu_200M_bdw.csv → doc/sphinx/01_branson/cpu_200M_bdw.csv
diff --git a/doc/sphinx/1_branson/cpu_66M.csv → doc/sphinx/01_branson/cpu_66M.csv b/doc/sphinx/1_branson/cpu_66M.csv → doc/sphinx/01_branson/cpu_66M.csv
diff --git a/doc/sphinx/1_branson/cpu_66M_bdw.csv → doc/sphinx/01_branson/cpu_66M_bdw.csv b/doc/sphinx/1_branson/cpu_66M_bdw.csv → doc/sphinx/01_branson/cpu_66M_bdw.csv
diff --git a/doc/sphinx/1_branson/gpu.csv → doc/sphinx/01_branson/gpu.csv b/doc/sphinx/1_branson/gpu.csv → doc/sphinx/01_branson/gpu.csv
diff --git a/doc/sphinx/1_branson/gpu.gp → doc/sphinx/01_branson/gpu.gp b/doc/sphinx/1_branson/gpu.gp → doc/sphinx/01_branson/gpu.gp
diff --git a/doc/sphinx/2_amg/amg.rst → doc/sphinx/02_amg/amg.rst b/doc/sphinx/2_amg/amg.rst → doc/sphinx/02_amg/amg.rst
diff --git a/doc/sphinx/2_amg/cpu.gp → doc/sphinx/02_amg/cpu.gp b/doc/sphinx/2_amg/cpu.gp → doc/sphinx/02_amg/cpu.gp
diff --git a/doc/sphinx/2_amg/cpu1_120.csv → doc/sphinx/02_amg/cpu1_120.csv b/doc/sphinx/2_amg/cpu1_120.csv → doc/sphinx/02_amg/cpu1_120.csv
diff --git a/doc/sphinx/2_amg/cpu1_160.csv → doc/sphinx/02_amg/cpu1_160.csv b/doc/sphinx/2_amg/cpu1_160.csv → doc/sphinx/02_amg/cpu1_160.csv
diff --git a/doc/sphinx/2_amg/cpu1_200.csv → doc/sphinx/02_amg/cpu1_200.csv b/doc/sphinx/2_amg/cpu1_200.csv → doc/sphinx/02_amg/cpu1_200.csv
diff --git a/doc/sphinx/2_amg/cpu2_200.csv → doc/sphinx/02_amg/cpu2_200.csv b/doc/sphinx/2_amg/cpu2_200.csv → doc/sphinx/02_amg/cpu2_200.csv
diff --git a/doc/sphinx/2_amg/cpu2_256.csv → doc/sphinx/02_amg/cpu2_256.csv b/doc/sphinx/2_amg/cpu2_256.csv → doc/sphinx/02_amg/cpu2_256.csv
diff --git a/doc/sphinx/2_amg/cpu2_320.csv → doc/sphinx/02_amg/cpu2_320.csv b/doc/sphinx/2_amg/cpu2_320.csv → doc/sphinx/02_amg/cpu2_320.csv
diff --git a/doc/sphinx/2_amg/gpu.gp → doc/sphinx/02_amg/gpu.gp b/doc/sphinx/2_amg/gpu.gp → doc/sphinx/02_amg/gpu.gp
diff --git a/doc/sphinx/2_amg/gpu1.csv → doc/sphinx/02_amg/gpu1.csv b/doc/sphinx/2_amg/gpu1.csv → doc/sphinx/02_amg/gpu1.csv
diff --git a/doc/sphinx/2_amg/gpu2.csv → doc/sphinx/02_amg/gpu2.csv b/doc/sphinx/2_amg/gpu2.csv → doc/sphinx/02_amg/gpu2.csv
diff --git a/doc/sphinx/2_amg/plots/CPU-FOM-1.png → doc/sphinx/02_amg/plots/CPU-FOM-1.png b/doc/sphinx/2_amg/plots/CPU-FOM-1.png → doc/sphinx/02_amg/plots/CPU-FOM-1.png
diff --git a/doc/sphinx/2_amg/plots/CPU-FOM-2.png → doc/sphinx/02_amg/plots/CPU-FOM-2.png b/doc/sphinx/2_amg/plots/CPU-FOM-2.png → doc/sphinx/02_amg/plots/CPU-FOM-2.png
diff --git a/doc/sphinx/2_amg/plots/amg-J1.png → doc/sphinx/02_amg/plots/amg-J1.png b/doc/sphinx/2_amg/plots/amg-J1.png → doc/sphinx/02_amg/plots/amg-J1.png
diff --git a/doc/sphinx/2_amg/plots/amg-J2.png → doc/sphinx/02_amg/plots/amg-J2.png b/doc/sphinx/2_amg/plots/amg-J2.png → doc/sphinx/02_amg/plots/amg-J2.png
diff --git a/doc/sphinx/2_amg/plots/mem-J1.png → doc/sphinx/02_amg/plots/mem-J1.png b/doc/sphinx/2_amg/plots/mem-J1.png → doc/sphinx/02_amg/plots/mem-J1.png
diff --git a/doc/sphinx/2_amg/plots/mem-J2.png → doc/sphinx/02_amg/plots/mem-J2.png b/doc/sphinx/2_amg/plots/mem-J2.png → doc/sphinx/02_amg/plots/mem-J2.png
diff --git a/doc/sphinx/3_vibe/cpu.gp → doc/sphinx/03_vibe/cpu.gp b/doc/sphinx/3_vibe/cpu.gp → doc/sphinx/03_vibe/cpu.gp
diff --git a/doc/sphinx/3_vibe/cpu_20.csv → doc/sphinx/03_vibe/cpu_20.csv b/doc/sphinx/3_vibe/cpu_20.csv → doc/sphinx/03_vibe/cpu_20.csv
diff --git a/doc/sphinx/3_vibe/cpu_40.csv → doc/sphinx/03_vibe/cpu_40.csv b/doc/sphinx/3_vibe/cpu_40.csv → doc/sphinx/03_vibe/cpu_40.csv
diff --git a/doc/sphinx/3_vibe/cpu_60.csv → doc/sphinx/03_vibe/cpu_60.csv b/doc/sphinx/3_vibe/cpu_60.csv → doc/sphinx/03_vibe/cpu_60.csv
diff --git a/doc/sphinx/3_vibe/do_gpu_throughput.sh → doc/sphinx/03_vibe/do_gpu_throughput.sh b/doc/sphinx/3_vibe/do_gpu_throughput.sh → doc/sphinx/03_vibe/do_gpu_throughput.sh
diff --git a/doc/sphinx/3_vibe/do_strong_scaling_cpu.sh → doc/sphinx/03_vibe/do_strong_scaling_cpu.sh b/doc/sphinx/3_vibe/do_strong_scaling_cpu.sh → doc/sphinx/03_vibe/do_strong_scaling_cpu.sh
diff --git a/doc/sphinx/3_vibe/gpu.csv → doc/sphinx/03_vibe/gpu.csv b/doc/sphinx/3_vibe/gpu.csv → doc/sphinx/03_vibe/gpu.csv
diff --git a/doc/sphinx/3_vibe/gpu.gp → doc/sphinx/03_vibe/gpu.gp b/doc/sphinx/3_vibe/gpu.gp → doc/sphinx/03_vibe/gpu.gp
diff --git a/...rthenon-ats5_spr-hbm128-intel-classic.csv → ...rthenon-ats5_spr-hbm128-intel-classic.csv b/...rthenon-ats5_spr-hbm128-intel-classic.csv → ...rthenon-ats5_spr-hbm128-intel-classic.csv
diff --git a/...rthenon-ats5_spr-hbm160-intel-classic.csv → ...rthenon-ats5_spr-hbm160-intel-classic.csv b/...rthenon-ats5_spr-hbm160-intel-classic.csv → ...rthenon-ats5_spr-hbm160-intel-classic.csv
diff --git a/doc/sphinx/3_vibe/plots/cpu-strong.png → doc/sphinx/03_vibe/plots/cpu-strong.png b/doc/sphinx/3_vibe/plots/cpu-strong.png → doc/sphinx/03_vibe/plots/cpu-strong.png
diff --git a/doc/sphinx/3_vibe/plots/gpu-throughput.png → doc/sphinx/03_vibe/plots/gpu-throughput.png b/doc/sphinx/3_vibe/plots/gpu-throughput.png → doc/sphinx/03_vibe/plots/gpu-throughput.png
diff --git a/doc/sphinx/3_vibe/vibe.rst → doc/sphinx/03_vibe/vibe.rst b/doc/sphinx/3_vibe/vibe.rst → doc/sphinx/03_vibe/vibe.rst
@@ -1,6 +1,6 @@
-******
+******************
 Parthenon-VIBE
-******
+******************
 
 This is the documentation for the ATS-5 Benchmark, Parthenon-VIBE.
 
@@ -25,7 +25,7 @@ and evolves one or more passive scalar quantities :math:`q^i` according to
    \partial_t q^i + \nabla \cdot \left( q^i \mathbf{u} \right) = 0
 
 
-as well as computing an auxiliary quantity :math:`d`` that resemebles a kinetic energy
+as well as computing an auxiliary quantity :math:`d` that resemebles a kinetic energy
 
 .. math::
    d = \frac{1}{2} q^0 \mathbf{u}\cdot\mathbf{u}.
@@ -124,8 +124,33 @@ Results from Parthenon are provided on the following systems:
 * Commodity Technology System 1 (CTS-1) (Snow) with Intel Broadwell processors,
 * An Nvidia A100 GPU hosted on an [Nvidia Arm HPC Developer Kit](https://developer.nvidia.com/arm-hpc-devkit)
 
-CTS-1
---------
+ATS-3 Rocinante HBM
+-------------------
+
+.. csv-table:: VIBE Throughput Performance on ATS-3 Rocinante HBM nodes 40% Memory
+   :file: parthenon-ats5_spr-hbm128-intel-classic.csv
+   :align: center
+   :widths: 10, 10
+   :header-rows: 1
+
+.. figure:: ats3_40.png
+   :align: center
+   :scale: 50%
+   :alt: VIBE Throughput Performance on ATS-3 Rocinante HBM nodes
+
+.. csv-table:: VIBE Throughput Performance on ATS-3 Rocinante HBM nodes 60% Memory
+   :file: parthenon-ats5_spr-hbm160-intel-classic.csv
+   :align: center
+   :widths: 10, 10
+   :header-rows: 1
+
+.. figure:: ats3_60.png
+   :align: center
+   :scale: 50%
+   :alt: VIBE Throughput Performance on ATS-3 Rocinante HBM nodes
+
+CTS-1 Snow
+-----------
 
 The mesh and meshblock size parameters are chosen to balance
 realism/performance with memory footprint. For the following tests we
@@ -196,31 +221,6 @@ Throughput performance of Parthenon-VIBE on a 40GB A100 is provided within the f
    :scale: 50%
    :alt: VIBE Throughput Performance on A100
 
-ATS-3
-------
-
-.. csv-table:: VIBE Throughput Performance on ATS-3 Rocinante HBM nodes 40% Memory
-   :file: parthenon-ats5_spr-hbm128-intel-classic.csv
-   :align: center
-   :widths: 10, 10
-   :header-rows: 1
-
-.. figure:: ats3_40.png
-   :align: center
-   :scale: 50%
-   :alt: VIBE Throughput Performance on ATS-3 Rocinante HBM nodes
-
-.. csv-table:: VIBE Throughput Performance on ATS-3 Rocinante HBM nodes 60% Memory
-   :file: parthenon-ats5_spr-hbm160-intel-classic.csv
-   :align: center
-   :widths: 10, 10
-   :header-rows: 1
-
-.. figure:: ats3_60.png
-   :align: center
-   :scale: 50%
-   :alt: VIBE Throughput Performance on ATS-3 Rocinante HBM nodes
-
 Verification of Results
 =======================
 

diff --git a/doc/sphinx/4_spatter/a100.gp → doc/sphinx/04_spatter/a100.gp b/doc/sphinx/4_spatter/a100.gp → doc/sphinx/04_spatter/a100.gp
diff --git a/doc/sphinx/4_spatter/a100_throughput_001.csv → ...sphinx/04_spatter/a100_throughput_001.csv b/doc/sphinx/4_spatter/a100_throughput_001.csv → ...sphinx/04_spatter/a100_throughput_001.csv
diff --git a/...phinx/4_spatter/a100_throughput_001fp.csv → ...hinx/04_spatter/a100_throughput_001fp.csv b/...phinx/4_spatter/a100_throughput_001fp.csv → ...hinx/04_spatter/a100_throughput_001fp.csv
diff --git a/...nx/4_spatter/a100_throughput_001nonfp.csv → ...x/04_spatter/a100_throughput_001nonfp.csv b/...nx/4_spatter/a100_throughput_001nonfp.csv → ...x/04_spatter/a100_throughput_001nonfp.csv
diff --git a/...nx/4_spatter/a100_throughput_asteroid.csv → ...x/04_spatter/a100_throughput_asteroid.csv b/...nx/4_spatter/a100_throughput_asteroid.csv → ...x/04_spatter/a100_throughput_asteroid.csv
diff --git a/doc/sphinx/4_spatter/cts1.gp → doc/sphinx/04_spatter/cts1.gp b/doc/sphinx/4_spatter/cts1.gp → doc/sphinx/04_spatter/cts1.gp
diff --git a/...phinx/4_spatter/cts1_weak_average_001.csv → ...hinx/04_spatter/cts1_weak_average_001.csv b/...phinx/4_spatter/cts1_weak_average_001.csv → ...hinx/04_spatter/cts1_weak_average_001.csv
diff --git a/...inx/4_spatter/cts1_weak_average_001fp.csv → ...nx/04_spatter/cts1_weak_average_001fp.csv b/...inx/4_spatter/cts1_weak_average_001fp.csv → ...nx/04_spatter/cts1_weak_average_001fp.csv
diff --git a/.../4_spatter/cts1_weak_average_001nonfp.csv → ...04_spatter/cts1_weak_average_001nonfp.csv b/.../4_spatter/cts1_weak_average_001nonfp.csv → ...04_spatter/cts1_weak_average_001nonfp.csv
diff --git a/.../4_spatter/cts1_weak_average_asteroid.csv → ...04_spatter/cts1_weak_average_asteroid.csv b/.../4_spatter/cts1_weak_average_asteroid.csv → ...04_spatter/cts1_weak_average_asteroid.csv
diff --git a/doc/sphinx/4_spatter/cts1_weak_total_001.csv → ...sphinx/04_spatter/cts1_weak_total_001.csv b/doc/sphinx/4_spatter/cts1_weak_total_001.csv → ...sphinx/04_spatter/cts1_weak_total_001.csv
diff --git a/...phinx/4_spatter/cts1_weak_total_001fp.csv → ...hinx/04_spatter/cts1_weak_total_001fp.csv b/...phinx/4_spatter/cts1_weak_total_001fp.csv → ...hinx/04_spatter/cts1_weak_total_001fp.csv
diff --git a/...nx/4_spatter/cts1_weak_total_001nonfp.csv → ...x/04_spatter/cts1_weak_total_001nonfp.csv b/...nx/4_spatter/cts1_weak_total_001nonfp.csv → ...x/04_spatter/cts1_weak_total_001nonfp.csv
diff --git a/...nx/4_spatter/cts1_weak_total_asteroid.csv → ...x/04_spatter/cts1_weak_total_asteroid.csv b/...nx/4_spatter/cts1_weak_total_asteroid.csv → ...x/04_spatter/cts1_weak_total_asteroid.csv
diff --git a/doc/sphinx/4_spatter/skylake.gp → doc/sphinx/04_spatter/skylake.gp b/doc/sphinx/4_spatter/skylake.gp → doc/sphinx/04_spatter/skylake.gp
diff --git a/...nx/4_spatter/skylake_weak_average_001.csv → ...x/04_spatter/skylake_weak_average_001.csv b/...nx/4_spatter/skylake_weak_average_001.csv → ...x/04_spatter/skylake_weak_average_001.csv
diff --git a/.../4_spatter/skylake_weak_average_001fp.csv → ...04_spatter/skylake_weak_average_001fp.csv b/.../4_spatter/skylake_weak_average_001fp.csv → ...04_spatter/skylake_weak_average_001fp.csv
diff --git a/...spatter/skylake_weak_average_001nonfp.csv → ...spatter/skylake_weak_average_001nonfp.csv b/...spatter/skylake_weak_average_001nonfp.csv → ...spatter/skylake_weak_average_001nonfp.csv
diff --git a/...spatter/skylake_weak_average_asteroid.csv → ...spatter/skylake_weak_average_asteroid.csv b/...spatter/skylake_weak_average_asteroid.csv → ...spatter/skylake_weak_average_asteroid.csv
diff --git a/...hinx/4_spatter/skylake_weak_total_001.csv → ...inx/04_spatter/skylake_weak_total_001.csv b/...hinx/4_spatter/skylake_weak_total_001.csv → ...inx/04_spatter/skylake_weak_total_001.csv
diff --git a/...nx/4_spatter/skylake_weak_total_001fp.csv → ...x/04_spatter/skylake_weak_total_001fp.csv b/...nx/4_spatter/skylake_weak_total_001fp.csv → ...x/04_spatter/skylake_weak_total_001fp.csv
diff --git a/...4_spatter/skylake_weak_total_001nonfp.csv → ...4_spatter/skylake_weak_total_001nonfp.csv b/...4_spatter/skylake_weak_total_001nonfp.csv → ...4_spatter/skylake_weak_total_001nonfp.csv
diff --git a/...4_spatter/skylake_weak_total_asteroid.csv → ...4_spatter/skylake_weak_total_asteroid.csv b/...4_spatter/skylake_weak_total_asteroid.csv → ...4_spatter/skylake_weak_total_asteroid.csv
diff --git a/doc/sphinx/4_spatter/spatter.rst → doc/sphinx/04_spatter/spatter.rst b/doc/sphinx/4_spatter/spatter.rst → doc/sphinx/04_spatter/spatter.rst
diff --git a/doc/sphinx/4_spatter/v100.gp → doc/sphinx/04_spatter/v100.gp b/doc/sphinx/4_spatter/v100.gp → doc/sphinx/04_spatter/v100.gp
diff --git a/doc/sphinx/4_spatter/v100_throughput_001.csv → ...sphinx/04_spatter/v100_throughput_001.csv b/doc/sphinx/4_spatter/v100_throughput_001.csv → ...sphinx/04_spatter/v100_throughput_001.csv
diff --git a/...phinx/4_spatter/v100_throughput_001fp.csv → ...hinx/04_spatter/v100_throughput_001fp.csv b/...phinx/4_spatter/v100_throughput_001fp.csv → ...hinx/04_spatter/v100_throughput_001fp.csv
diff --git a/...nx/4_spatter/v100_throughput_001nonfp.csv → ...x/04_spatter/v100_throughput_001nonfp.csv b/...nx/4_spatter/v100_throughput_001nonfp.csv → ...x/04_spatter/v100_throughput_001nonfp.csv
diff --git a/...nx/4_spatter/v100_throughput_asteroid.csv → ...x/04_spatter/v100_throughput_asteroid.csv b/...nx/4_spatter/v100_throughput_asteroid.csv → ...x/04_spatter/v100_throughput_asteroid.csv
diff --git a/doc/sphinx/5_mlmd/gpu.csv → doc/sphinx/05_mlmd/gpu.csv b/doc/sphinx/5_mlmd/gpu.csv → doc/sphinx/05_mlmd/gpu.csv
diff --git a/doc/sphinx/5_mlmd/gpu.gp → doc/sphinx/05_mlmd/gpu.gp b/doc/sphinx/5_mlmd/gpu.gp → doc/sphinx/05_mlmd/gpu.gp
diff --git a/doc/sphinx/5_mlmd/mlmd.rst → doc/sphinx/05_mlmd/mlmd.rst b/doc/sphinx/5_mlmd/mlmd.rst → doc/sphinx/05_mlmd/mlmd.rst
diff --git a/doc/sphinx/5_mlmd/plots/StrongSingle-s.png → doc/sphinx/05_mlmd/plots/StrongSingle-s.png b/doc/sphinx/5_mlmd/plots/StrongSingle-s.png → doc/sphinx/05_mlmd/plots/StrongSingle-s.png
diff --git a/doc/sphinx/5_mlmd/plots/StrongSingle-t.png → doc/sphinx/05_mlmd/plots/StrongSingle-t.png b/doc/sphinx/5_mlmd/plots/StrongSingle-t.png → doc/sphinx/05_mlmd/plots/StrongSingle-t.png
diff --git a/doc/sphinx/5_mlmd/plots/WeakParallel-s.png → doc/sphinx/05_mlmd/plots/WeakParallel-s.png b/doc/sphinx/5_mlmd/plots/WeakParallel-s.png → doc/sphinx/05_mlmd/plots/WeakParallel-s.png
diff --git a/doc/sphinx/5_mlmd/plots/WeakParallel-t.png → doc/sphinx/05_mlmd/plots/WeakParallel-t.png b/doc/sphinx/5_mlmd/plots/WeakParallel-t.png → doc/sphinx/05_mlmd/plots/WeakParallel-t.png
diff --git a/...sphinx/6_umt/spp1_strong_scaling_cts2.csv → ...phinx/06_umt/spp1_strong_scaling_cts2.csv b/...sphinx/6_umt/spp1_strong_scaling_cts2.csv → ...phinx/06_umt/spp1_strong_scaling_cts2.csv
diff --git a/doc/sphinx/6_umt/spp1_strong_scaling_cts2.gp → ...sphinx/06_umt/spp1_strong_scaling_cts2.gp b/doc/sphinx/6_umt/spp1_strong_scaling_cts2.gp → ...sphinx/06_umt/spp1_strong_scaling_cts2.gp
diff --git a/...umt/spp1_strong_scaling_cts2_abridged.csv → ...umt/spp1_strong_scaling_cts2_abridged.csv b/...umt/spp1_strong_scaling_cts2_abridged.csv → ...umt/spp1_strong_scaling_cts2_abridged.csv
diff --git a/doc/sphinx/6_umt/spp1_throughput_V100.csv → doc/sphinx/06_umt/spp1_throughput_V100.csv b/doc/sphinx/6_umt/spp1_throughput_V100.csv → doc/sphinx/06_umt/spp1_throughput_V100.csv
diff --git a/doc/sphinx/6_umt/spp1_throughput_V100.gp → doc/sphinx/06_umt/spp1_throughput_V100.gp b/doc/sphinx/6_umt/spp1_throughput_V100.gp → doc/sphinx/06_umt/spp1_throughput_V100.gp
diff --git a/doc/sphinx/6_umt/umt.rst → doc/sphinx/06_umt/umt.rst b/doc/sphinx/6_umt/umt.rst → doc/sphinx/06_umt/umt.rst
diff --git a/...phinx/6_umt/umtsp2_strong_scaling_cpu.csv → ...hinx/06_umt/umtsp2_strong_scaling_cpu.csv b/...phinx/6_umt/umtsp2_strong_scaling_cpu.csv → ...hinx/06_umt/umtsp2_strong_scaling_cpu.csv
diff --git a/doc/sphinx/6_umt/umtsp2_throughput_gpu.csv → doc/sphinx/06_umt/umtsp2_throughput_gpu.csv b/doc/sphinx/6_umt/umtsp2_throughput_gpu.csv → doc/sphinx/06_umt/umtsp2_throughput_gpu.csv
diff --git a/doc/sphinx/7_miniem/ats2.csv → doc/sphinx/07_miniem/ats2.csv b/doc/sphinx/7_miniem/ats2.csv → doc/sphinx/07_miniem/ats2.csv
diff --git a/doc/sphinx/7_miniem/ats2.gp → doc/sphinx/07_miniem/ats2.gp b/doc/sphinx/7_miniem/ats2.gp → doc/sphinx/07_miniem/ats2.gp
diff --git a/doc/sphinx/7_miniem/ats2mem.gp → doc/sphinx/07_miniem/ats2mem.gp b/doc/sphinx/7_miniem/ats2mem.gp → doc/sphinx/07_miniem/ats2mem.gp
diff --git a/doc/sphinx/7_miniem/cts1-0.25.csv → doc/sphinx/07_miniem/cts1-0.25.csv b/doc/sphinx/7_miniem/cts1-0.25.csv → doc/sphinx/07_miniem/cts1-0.25.csv
diff --git a/doc/sphinx/7_miniem/cts1-0.25.gp → doc/sphinx/07_miniem/cts1-0.25.gp b/doc/sphinx/7_miniem/cts1-0.25.gp → doc/sphinx/07_miniem/cts1-0.25.gp
diff --git a/doc/sphinx/7_miniem/cts1-0.50.csv → doc/sphinx/07_miniem/cts1-0.50.csv b/doc/sphinx/7_miniem/cts1-0.50.csv → doc/sphinx/07_miniem/cts1-0.50.csv
diff --git a/doc/sphinx/7_miniem/cts1-0.50.gp → doc/sphinx/07_miniem/cts1-0.50.gp b/doc/sphinx/7_miniem/cts1-0.50.gp → doc/sphinx/07_miniem/cts1-0.50.gp
diff --git a/doc/sphinx/7_miniem/cts1-1.00.csv → doc/sphinx/07_miniem/cts1-1.00.csv b/doc/sphinx/7_miniem/cts1-1.00.csv → doc/sphinx/07_miniem/cts1-1.00.csv
diff --git a/doc/sphinx/7_miniem/cts1-1.00.gp → doc/sphinx/07_miniem/cts1-1.00.gp b/doc/sphinx/7_miniem/cts1-1.00.gp → doc/sphinx/07_miniem/cts1-1.00.gp
diff --git a/doc/sphinx/7_miniem/cts1-2.00.csv → doc/sphinx/07_miniem/cts1-2.00.csv b/doc/sphinx/7_miniem/cts1-2.00.csv → doc/sphinx/07_miniem/cts1-2.00.csv
diff --git a/doc/sphinx/7_miniem/cts1-2.00.gp → doc/sphinx/07_miniem/cts1-2.00.gp b/doc/sphinx/7_miniem/cts1-2.00.gp → doc/sphinx/07_miniem/cts1-2.00.gp
diff --git a/doc/sphinx/7_miniem/cts1.csv → doc/sphinx/07_miniem/cts1.csv b/doc/sphinx/7_miniem/cts1.csv → doc/sphinx/07_miniem/cts1.csv
diff --git a/doc/sphinx/7_miniem/cts1.gp → doc/sphinx/07_miniem/cts1.gp b/doc/sphinx/7_miniem/cts1.gp → doc/sphinx/07_miniem/cts1.gp
diff --git a/doc/sphinx/7_miniem/cts1mem-0.25.gp → doc/sphinx/07_miniem/cts1mem-0.25.gp b/doc/sphinx/7_miniem/cts1mem-0.25.gp → doc/sphinx/07_miniem/cts1mem-0.25.gp
diff --git a/doc/sphinx/7_miniem/cts1mem-0.50.gp → doc/sphinx/07_miniem/cts1mem-0.50.gp b/doc/sphinx/7_miniem/cts1mem-0.50.gp → doc/sphinx/07_miniem/cts1mem-0.50.gp
diff --git a/doc/sphinx/7_miniem/cts1mem-1.00.gp → doc/sphinx/07_miniem/cts1mem-1.00.gp b/doc/sphinx/7_miniem/cts1mem-1.00.gp → doc/sphinx/07_miniem/cts1mem-1.00.gp
diff --git a/doc/sphinx/7_miniem/cts1mem-2.00.gp → doc/sphinx/07_miniem/cts1mem-2.00.gp b/doc/sphinx/7_miniem/cts1mem-2.00.gp → doc/sphinx/07_miniem/cts1mem-2.00.gp
diff --git a/doc/sphinx/7_miniem/cts1mem.gp → doc/sphinx/07_miniem/cts1mem.gp b/doc/sphinx/7_miniem/cts1mem.gp → doc/sphinx/07_miniem/cts1mem.gp
diff --git a/doc/sphinx/7_miniem/miniem.rst → doc/sphinx/07_miniem/miniem.rst b/doc/sphinx/7_miniem/miniem.rst → doc/sphinx/07_miniem/miniem.rst
diff --git a/doc/sphinx/7_miniem/output.log → doc/sphinx/07_miniem/output.log b/doc/sphinx/7_miniem/output.log → doc/sphinx/07_miniem/output.log
diff --git a/doc/sphinx/7_miniem/recipe.sh → doc/sphinx/07_miniem/recipe.sh b/doc/sphinx/7_miniem/recipe.sh → doc/sphinx/07_miniem/recipe.sh
diff --git a/doc/sphinx/8_sparta/Makefile.manzano_kokkos → doc/sphinx/08_sparta/Makefile.manzano_kokkos b/doc/sphinx/8_sparta/Makefile.manzano_kokkos → doc/sphinx/08_sparta/Makefile.manzano_kokkos
diff --git a/doc/sphinx/8_sparta/ats2.csv → doc/sphinx/08_sparta/ats2.csv b/doc/sphinx/8_sparta/ats2.csv → doc/sphinx/08_sparta/ats2.csv
diff --git a/doc/sphinx/8_sparta/ats2.gp → doc/sphinx/08_sparta/ats2.gp b/doc/sphinx/8_sparta/ats2.gp → doc/sphinx/08_sparta/ats2.gp
diff --git a/doc/sphinx/8_sparta/build-manzano.sh → doc/sphinx/08_sparta/build-manzano.sh b/doc/sphinx/8_sparta/build-manzano.sh → doc/sphinx/08_sparta/build-manzano.sh
diff --git a/doc/sphinx/8_sparta/cts1-0.25.csv → doc/sphinx/08_sparta/cts1-0.25.csv b/doc/sphinx/8_sparta/cts1-0.25.csv → doc/sphinx/08_sparta/cts1-0.25.csv
diff --git a/doc/sphinx/8_sparta/cts1-0.25.gp → doc/sphinx/08_sparta/cts1-0.25.gp b/doc/sphinx/8_sparta/cts1-0.25.gp → doc/sphinx/08_sparta/cts1-0.25.gp
diff --git a/doc/sphinx/8_sparta/cts1-0.50.csv → doc/sphinx/08_sparta/cts1-0.50.csv b/doc/sphinx/8_sparta/cts1-0.50.csv → doc/sphinx/08_sparta/cts1-0.50.csv
diff --git a/doc/sphinx/8_sparta/cts1-0.50.gp → doc/sphinx/08_sparta/cts1-0.50.gp b/doc/sphinx/8_sparta/cts1-0.50.gp → doc/sphinx/08_sparta/cts1-0.50.gp
diff --git a/doc/sphinx/8_sparta/cts1-1.00.csv → doc/sphinx/08_sparta/cts1-1.00.csv b/doc/sphinx/8_sparta/cts1-1.00.csv → doc/sphinx/08_sparta/cts1-1.00.csv
diff --git a/doc/sphinx/8_sparta/cts1-1.00.gp → doc/sphinx/08_sparta/cts1-1.00.gp b/doc/sphinx/8_sparta/cts1-1.00.gp → doc/sphinx/08_sparta/cts1-1.00.gp
diff --git a/doc/sphinx/8_sparta/cts1-2.00.csv → doc/sphinx/08_sparta/cts1-2.00.csv b/doc/sphinx/8_sparta/cts1-2.00.csv → doc/sphinx/08_sparta/cts1-2.00.csv
diff --git a/doc/sphinx/8_sparta/cts1-2.00.gp → doc/sphinx/08_sparta/cts1-2.00.gp b/doc/sphinx/8_sparta/cts1-2.00.gp → doc/sphinx/08_sparta/cts1-2.00.gp
diff --git a/doc/sphinx/8_sparta/cts1.csv → doc/sphinx/08_sparta/cts1.csv b/doc/sphinx/8_sparta/cts1.csv → doc/sphinx/08_sparta/cts1.csv
diff --git a/doc/sphinx/8_sparta/cts1.gp → doc/sphinx/08_sparta/cts1.gp b/doc/sphinx/8_sparta/cts1.gp → doc/sphinx/08_sparta/cts1.gp
diff --git a/doc/sphinx/8_sparta/cts1mem-0.25.gp → doc/sphinx/08_sparta/cts1mem-0.25.gp b/doc/sphinx/8_sparta/cts1mem-0.25.gp → doc/sphinx/08_sparta/cts1mem-0.25.gp
diff --git a/doc/sphinx/8_sparta/cts1mem-0.50.gp → doc/sphinx/08_sparta/cts1mem-0.50.gp b/doc/sphinx/8_sparta/cts1mem-0.50.gp → doc/sphinx/08_sparta/cts1mem-0.50.gp
diff --git a/doc/sphinx/8_sparta/cts1mem-1.00.gp → doc/sphinx/08_sparta/cts1mem-1.00.gp b/doc/sphinx/8_sparta/cts1mem-1.00.gp → doc/sphinx/08_sparta/cts1mem-1.00.gp
diff --git a/doc/sphinx/8_sparta/cts1mem-2.00.gp → doc/sphinx/08_sparta/cts1mem-2.00.gp b/doc/sphinx/8_sparta/cts1mem-2.00.gp → doc/sphinx/08_sparta/cts1mem-2.00.gp
diff --git a/doc/sphinx/8_sparta/log.sparta → doc/sphinx/08_sparta/log.sparta b/doc/sphinx/8_sparta/log.sparta → doc/sphinx/08_sparta/log.sparta
diff --git a/doc/sphinx/08_sparta/manzano_era/Makefile.manzano_kokkos b/doc/sphinx/08_sparta/manzano_era/Makefile.manzano_kokkos
@@ -0,0 +1,104 @@
+# kokkos_mpi_only = KOKKOS package with Serial backend (no OpenMP support), MPI compiler, default MPI
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC =		mpicxx
+CCFLAGS =	-g -O3 -DSPARTA_BIGBIG
+SHFLAGS =	-fPIC
+DEPFLAGS =	-M
+
+LINK =		mpicxx
+LINKFLAGS =	-g -O3
+LIB = 
+SIZE =		size
+
+ARCHIVE =	ar
+ARFLAGS =	-rc
+SHLIBFLAGS =	-shared
+KOKKOS_DEVICES = Serial
+KOKKOS_ARCH = SKX
+
+# ---------------------------------------------------------------------
+# SPARTA-specific settings
+# specify settings for SPARTA features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# SPARTA ifdef settings, OPTIONAL
+# see possible settings in doc/Section_start.html#2_2 (step 4)
+
+SPARTA_INC =	-DSPARTA_GZIP
+
+# MPI library, REQUIRED
+# see discussion in doc/Section_start.html#2_2 (step 5)
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =       -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1
+MPI_PATH =      
+MPI_LIB =	
+
+# JPEG library, OPTIONAL
+# see discussion in doc/Section_start.html#2_2 (step 7)
+# only needed if -DSPARTA_JPEG listed with SPARTA_INC
+# INC = path for jpeglib.h
+# PATH = path for JPEG library
+# LIB = name of JPEG library
+
+JPG_INC =       
+JPG_PATH = 	
+JPG_LIB =	
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# no need to edit this section
+
+include	Makefile.package.settings
+include	Makefile.package
+
+EXTRA_INC = $(SPARTA_INC) $(PKG_INC) $(MPI_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(JPG_LIB) $(PKG_SYSLIB)
+EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
+EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE):	$(OBJ) $(EXTRA_LINK_DEPENDS)
+	$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+	$(SIZE) $(EXE)
+
+# Library targets
+
+lib:	$(OBJ) $(EXTRA_LINK_DEPENDS)
+	$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
+shlib:	$(OBJ) $(EXTRA_LINK_DEPENDS)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
+        $(OBJ) $(EXTRA_LIB) $(LIB)
+
+# Compilation rules
+
+%.o:%.cpp $(EXTRA_CPP_DEPENDS)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp $(EXTRA_CPP_DEPENDS)
+	$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+
+%.o:%.cu $(EXTRA_CPP_DEPENDS)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+# Individual dependencies
+
+DEPENDS = $(OBJ:.o=.d)
+sinclude $(DEPENDS)
diff --git a/doc/sphinx/08_sparta/manzano_era/ats2.csv b/doc/sphinx/08_sparta/manzano_era/ats2.csv
@@ -0,0 +1,8 @@
+No. Particles,Actual
+7142385,436.3179
+14287466,575.0493
+28571551,751.5044
+35712209,840.5981
+42855549,873.2238
+49999941,894.6309
+57143091,921.2964
diff --git a/doc/sphinx/08_sparta/manzano_era/ats2.gp-noauto b/doc/sphinx/08_sparta/manzano_era/ats2.gp-noauto
@@ -0,0 +1,25 @@
+#!/usr/bin/gnuplot
+set terminal pngcairo enhanced size 1024, 768 dashed font 'Helvetica,18'
+set output "ats2.png"
+
+set title "SPARTA Throughput Performance on ATS-2/Vortex" font "serif,22"
+set xlabel "No. Particles"
+set ylabel "Figure of Merit (M-particle-steps/sec)"
+
+# set xrange [1:64]
+set key left top
+
+# set logscale x 2
+# set logscale y 2
+
+set grid
+show grid
+
+set datafile separator comma
+set key autotitle columnheader
+
+set style line 1 linetype 6 dashtype 1 linecolor rgb "#FF0000" linewidth 2 pointtype 6 pointsize 3
+set style line 2 linetype 1 dashtype 2 linecolor rgb "#FF0000" linewidth 2
+set style line 3 linetype 6 dashtype 1 linecolor rgb "#0000FF" linewidth 2 pointtype 6 pointsize 3
+
+plot "ats2.csv" using 1:2 with linespoints linestyle 3
diff --git a/doc/sphinx/08_sparta/manzano_era/build-manzano.sh b/doc/sphinx/08_sparta/manzano_era/build-manzano.sh
@@ -0,0 +1,30 @@
+#!/bin/sh
+
+umask 022
+set -e
+set -x
+
+dir_root=`git rev-parse --show-toplevel`
+dir_src="${dir_root}/sparta"
+
+module unload intel
+module unload openmpi-intel
+module use /apps/modules/modulefiles-apps/cde/v3/
+module load cde/v3/devpack/intel-ompi
+module list
+
+pushd "${dir_src}"
+git clean -fdx
+git reset --hard
+popd
+cp -a Makefile.manzano_kokkos "${dir_src}/src/MAKE"
+
+pushd "${dir_src}/src"
+make yes-kokkos
+make -j 16 manzano_kokkos
+echo "Resultant build info:"
+ls -lh `pwd -P`/spa_manzano_kokkos
+popd
+
+
+exit 0
diff --git a/doc/sphinx/08_sparta/manzano_era/cts1-0.25.csv b/doc/sphinx/08_sparta/manzano_era/cts1-0.25.csv
@@ -0,0 +1,8 @@
+No. Cores,Actual,Ideal,Memory (GiB)
+1,27.083,27.083,11.23
+2,48.984,54.166,11.23
+4,86.519,108.332,11.37
+8,147.291,216.664,11.47
+16,245.349,433.328,11.71
+32,347.010,866.656,12.34
+48,406.431,1299.984,12.76
diff --git a/doc/sphinx/08_sparta/manzano_era/cts1-0.25.gp-noauto b/doc/sphinx/08_sparta/manzano_era/cts1-0.25.gp-noauto
@@ -0,0 +1,24 @@
+#!/usr/bin/gnuplot
+set terminal pngcairo enhanced size 1024, 768 dashed font 'Helvetica,18'
+set output "cts1-0.25.png"
+
+set title "SPARTA Strong Scaling Performance on CTS-1/Manzano (0.25 GiB/PE)" font "serif,22"
+set xlabel "No. Processing Elements"
+set ylabel "Figure of Merit (time steps/sec)"
+
+set xrange [1:64]
+set key left top
+
+set logscale x 2
+set logscale y 2
+
+set grid
+show grid
+
+set datafile separator comma
+set key autotitle columnheader
+
+set style line 1 linetype 6 dashtype 1 linecolor rgb "#FF0000" linewidth 2 pointtype 6 pointsize 3
+set style line 2 linetype 1 dashtype 2 linecolor rgb "#FF0000" linewidth 2
+
+plot "cts1-0.25.csv" using 1:2 with linespoints linestyle 1, "" using 1:3 with line linestyle 2
diff --git a/doc/sphinx/08_sparta/manzano_era/cts1-0.50.csv b/doc/sphinx/08_sparta/manzano_era/cts1-0.50.csv
@@ -0,0 +1,8 @@
+No. Cores,Actual,Ideal,Memory (GiB)
+1,29.078,29.078,18.42
+2,55.678,58.156,18.41
+4,100.193,116.312,18.55
+8,173.462,232.624,18.65
+16,287.659,465.248,18.89
+32,395.545,930.496,19.52
+48,454.229,1395.744,20.01
diff --git a/doc/sphinx/08_sparta/manzano_era/cts1-0.50.gp-noauto b/doc/sphinx/08_sparta/manzano_era/cts1-0.50.gp-noauto
@@ -0,0 +1,24 @@
+#!/usr/bin/gnuplot
+set terminal pngcairo enhanced size 1024, 768 dashed font 'Helvetica,18'
+set output "cts1-0.50.png"
+
+set title "SPARTA Strong Scaling Performance on CTS-1/Manzano (0.50 GiB/PE)" font "serif,22"
+set xlabel "No. Processing Elements"
+set ylabel "Figure of Merit (time steps/sec)"
+
+set xrange [1:64]
+set key left top
+
+set logscale x 2
+set logscale y 2
+
+set grid
+show grid
+
+set datafile separator comma
+set key autotitle columnheader
+
+set style line 1 linetype 6 dashtype 1 linecolor rgb "#FF0000" linewidth 2 pointtype 6 pointsize 3
+set style line 2 linetype 1 dashtype 2 linecolor rgb "#FF0000" linewidth 2
+
+plot "cts1-0.50.csv" using 1:2 with linespoints linestyle 1, "" using 1:3 with line linestyle 2
diff --git a/doc/sphinx/08_sparta/manzano_era/cts1-1.00.csv b/doc/sphinx/08_sparta/manzano_era/cts1-1.00.csv
@@ -0,0 +1,8 @@
+No. Cores,Actual,Ideal,Memory (GiB)
+1,32.306,32.306,33.51
+2,60.208,64.612,33.50
+4,111.753,129.224,33.63
+8,200.736,258.448,33.73
+16,328.496,516.896,33.98
+32,440.688,1033.792,34.55
+48,504.080,1550.688,35.03
diff --git a/doc/sphinx/08_sparta/manzano_era/cts1-1.00.gp-noauto b/doc/sphinx/08_sparta/manzano_era/cts1-1.00.gp-noauto
@@ -0,0 +1,24 @@
+#!/usr/bin/gnuplot
+set terminal pngcairo enhanced size 1024, 768 dashed font 'Helvetica,18'
+set output "cts1-1.00.png"
+
+set title "SPARTA Strong Scaling Performance on CTS-1/Manzano (1.00 GiB/PE)" font "serif,22"
+set xlabel "No. Processing Elements"
+set ylabel "Figure of Merit (time steps/sec)"
+
+set xrange [1:64]
+set key left top
+
+set logscale x 2
+set logscale y 2
+
+set grid
+show grid
+
+set datafile separator comma
+set key autotitle columnheader
+
+set style line 1 linetype 6 dashtype 1 linecolor rgb "#FF0000" linewidth 2 pointtype 6 pointsize 3
+set style line 2 linetype 1 dashtype 2 linecolor rgb "#FF0000" linewidth 2
+
+plot "cts1-1.00.csv" using 1:2 with linespoints linestyle 1, "" using 1:3 with line linestyle 2
diff --git a/doc/sphinx/08_sparta/manzano_era/cts1-2.00.csv b/doc/sphinx/08_sparta/manzano_era/cts1-2.00.csv
@@ -0,0 +1,8 @@
+No. Cores,Actual,Ideal,Memory (GiB)
+1,33.259,33.259,93.86
+2,65.506,66.519,93.85
+4,119.683,133.038,93.98
+8,230.232,266.075,94.08
+16,363.815,532.151,94.29
+32,477.281,1064.302,94.81
+48,535.983,1596.453,95.23