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Add template args to DataBox #47

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merged 9 commits into from
Jan 22, 2024
Merged

Add template args to DataBox #47

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a34e356
Add template args
brryan Dec 8, 2023
95905d1
update spiner, try to fix CI
jonahm-LANL Dec 8, 2023
b5fa194
portability path
jonahm-LANL Dec 8, 2023
c1fcfc8
come on...
jonahm-LANL Dec 8, 2023
f597c8b
ok add ports-of-call submodule and that seems to fix things
jonahm-LANL Dec 8, 2023
d5115e1
well it works with HDF5 turned off now at least...
jonahm-LANL Dec 8, 2023
52fa0df
OK FINALLY
jonahm-LANL Dec 8, 2023
46a6dde
brryan fix
jonahm-LANL Dec 9, 2023
34de0ed
One more using statement
brryan Jan 22, 2024
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8 changes: 5 additions & 3 deletions .github/workflows/tests.yml
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Expand Up @@ -13,13 +13,15 @@ jobs:

steps:
- name: Checkout code
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
submodules: true
submodules: recursive
- name: Set system to non-interactive mode
run: export DEBIAN_FRONTEND=noninteractive
- name: install dependencies
run: sudo apt-get install -y --force-yes -qq build-essential libhdf5-serial-dev
run: |
sudo apt-get update -y -qq
sudo apt-get install -y --force-yes -qq build-essential libhdf5-serial-dev
- name: build and run tests
run: |
mkdir -p bin
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3 changes: 3 additions & 0 deletions .gitmodules
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Expand Up @@ -10,3 +10,6 @@
[submodule "utils/kokkos"]
path = utils/kokkos
url = https://github.com/kokkos/kokkos.git
[submodule "utils/ports-of-call"]
path = utils/ports-of-call
url = [email protected]:lanl/ports-of-call.git
14 changes: 12 additions & 2 deletions CMakeLists.txt
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@@ -1,4 +1,4 @@
# © 2021. Triad National Security, LLC. All rights reserved. This
# © 2023. Triad National Security, LLC. All rights reserved. This
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# program was produced under U.S. Government contract
# 89233218CNA000001 for Los Alamos National Laboratory (LANL), which
# is operated by Triad National Security, LLC for the U.S. Department
Expand Down Expand Up @@ -53,11 +53,21 @@ target_include_directories(singularity-opac::flags
INTERFACE
$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}>)

include (SetupDeps)
include (SetupOptions)
include (SetupDeps)
include (SetupCompilers)
include (SetupFlags)

if (SINGULARITY_USE_HDF5)
message(STATUS "HDF5 enabled. Requesting it in spiner")
set(SPINER_USE_HDF ON CACHE BOOL "")
else()
message(STATUS "HDF5 not enabled. Turning it off in spiner")
set(SPINER_USE_HDF OFF CACHE BOOL "")
endif()
add_subdirectory(utils/spiner)
target_link_libraries(singularity-opac::flags INTERFACE spiner)

include(GNUInstallDirs)
include(CTest)

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2 changes: 1 addition & 1 deletion cmake/SetupCompilers.cmake
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Expand Up @@ -6,7 +6,7 @@
enable_language(CXX)
include(CMakeDetermineCXXCompiler)

set(CMAKE_CXX_STANDARD 14)
set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)

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17 changes: 16 additions & 1 deletion cmake/SetupDeps.cmake
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Expand Up @@ -33,7 +33,9 @@ endif()
#=======================================
# Can't play the target games above unless using
# cmake 3.20+, so leave this one for now.
find_package(HDF5 COMPONENTS C HL QUIET)
# JMM: DO NOT SEARCH FOR HDF5 IF WE DON'T NEED IT
if (SINGULARITY_USE_HDF5)
find_package(HDF5 COMPONENTS C HL)

# findpackage doesnt export an interface for HDF5,
# so create one
Expand Down Expand Up @@ -64,9 +66,22 @@ if (HDF5_FOUND)
else()
message("MPI::MPI_CXX provided by parent package")
endif()
else()
message(status "HDF5 is not parallel")
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message(STATUS?

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case-senstivity is weird in CMake but I think in this case it's insensitive

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@brryan brryan Dec 8, 2023 •
edited
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I briefly googled this out of curiosity and the first example was message(status of all things and apparently it actually does matter in this case: https://stackoverflow.com/a/35034125

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It looks like that stack overflow is about the case of the thing the message is about, not the STATUS flag? The rest of the code is using lower-case, which is why I kept doing it

endif()
else()
message(STATUS "No HDF5")
endif()
endif()

# JMM: I'm putting this here, as it depends on what happens with HDF5,
# and I want that to be set AFTER we set all our options, so we don't
# set HDF5 unnecessarily.
cmake_dependent_option(SINGULARITY_USE_MPI
"Link to MPI"
ON "${SINGULARITY_USE_MPI};${HDF5_IS_PARALLEL}"
OFF)

#=======================================
# Setup Catch2
# - provides Catch2::Catch2
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10 changes: 6 additions & 4 deletions singularity-opac/base/indexers.hpp
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Expand Up @@ -46,6 +46,7 @@ struct Identity {

class Linear {
public:
using DataBox = Spiner::DataBox<Real>;
Linear() = default;

PORTABLE_INLINE_FUNCTION
Expand All @@ -58,7 +59,7 @@ class Linear {
SetRange_(numin, numax, N);
}

PORTABLE_INLINE_FUNCTION Linear(const Spiner::DataBox &data, Real numin,
PORTABLE_INLINE_FUNCTION Linear(const DataBox &data, Real numin,
Real numax, int N)
: data_(data) {
SetRange_(numin, numax, N);
Expand All @@ -79,11 +80,12 @@ class Linear {
void SetRange_(Real numin, Real numax, int N) {
data_.setRange(0, numin, numax, N);
}
Spiner::DataBox data_;
DataBox data_;
};

class LogLinear {
public:
using DataBox = Spiner::DataBox<Real>;
LogLinear() = default;

PORTABLE_INLINE_FUNCTION
Expand All @@ -97,7 +99,7 @@ class LogLinear {
}

PORTABLE_INLINE_FUNCTION
LogLinear(const Spiner::DataBox &data, Real numin, Real numax, int N)
LogLinear(const DataBox &data, Real numin, Real numax, int N)
: data_(data) {
SetRange_(numin, numax, N);
}
Expand All @@ -119,7 +121,7 @@ class LogLinear {
void SetRange_(Real numin, Real numax, int N) {
data_.setRange(0, BDMath::log10(numin), BDMath::log10(numax), N);
}
Spiner::DataBox data_;
DataBox data_;
};

template <int N, typename Data_t>
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4 changes: 2 additions & 2 deletions singularity-opac/neutrinos/mean_opacity_neutrinos.hpp
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Expand Up @@ -210,8 +210,8 @@ class MeanOpacity {
PORTABLE_INLINE_FUNCTION Real fromLog_(const Real lx) const {
return std::pow(10., lx);
}
Spiner::DataBox lkappaPlanck_;
Spiner::DataBox lkappaRosseland_;
Spiner::DataBox<Real> lkappaPlanck_;
Spiner::DataBox<Real> lkappaRosseland_;
const char *filename_;
};

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5 changes: 3 additions & 2 deletions singularity-opac/neutrinos/mean_s_opacity_neutrinos.hpp
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Expand Up @@ -41,6 +41,7 @@ namespace impl {
template <typename ThermalDistribution, typename pc = PhysicalConstantsCGS>
class MeanSOpacity {
public:
using DataBox = Spiner::DataBox<Real>;
MeanSOpacity() = default;
template <typename SOpacity>
MeanSOpacity(const SOpacity &s_opac, const Real lRhoMin, const Real lRhoMax,
Expand Down Expand Up @@ -211,8 +212,8 @@ class MeanSOpacity {
PORTABLE_INLINE_FUNCTION Real fromLog_(const Real lx) const {
return std::pow(10., lx);
}
Spiner::DataBox lkappaPlanck_;
Spiner::DataBox lkappaRosseland_;
DataBox lkappaPlanck_;
DataBox lkappaRosseland_;
const char *filename_;
};

Expand Down
7 changes: 4 additions & 3 deletions singularity-opac/neutrinos/spiner_opac_neutrinos.hpp
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Expand Up @@ -61,6 +61,7 @@ enum class DataStatus { Deallocated, OnDevice, OnHost };
template <typename ThermalDistribution, typename pc = PhysicalConstantsCGS>
class SpinerOpacity {
public:
using DataBox = Spiner::DataBox<Real>;
static constexpr Real EPS = 10.0 * std::numeric_limits<Real>::min();
static constexpr Real Hz2MeV = pc::h / (1e6 * pc::eV);
static constexpr Real MeV2Hz = 1 / Hz2MeV;
Expand Down Expand Up @@ -130,8 +131,8 @@ class SpinerOpacity {

// DataBox constructor. Note that this constructor *shallow* copies
// the databoxes, so they must be managed externally.
SpinerOpacity(const Spiner::DataBox &lalphanu, const Spiner::DataBox ljnu,
const Spiner::DataBox lJ, const Spiner::DataBox lJYe)
SpinerOpacity(const DataBox &lalphanu, const DataBox ljnu,
const DataBox lJ, const DataBox lJYe)
: memoryStatus_(impl::DataStatus::OnHost), lalphanu_(lalphanu),
ljnu_(ljnu), lJ_(lJ), lJYe_(lJYe) {}

Expand Down Expand Up @@ -391,7 +392,7 @@ class SpinerOpacity {
impl::DataStatus memoryStatus_ = impl::DataStatus::Deallocated;
// TODO(JMM): Integrating J and JYe seems wise.
// We can add more things here as needed.
Spiner::DataBox lalphanu_, ljnu_, lJ_, lJYe_;
DataBox lalphanu_, ljnu_, lJ_, lJYe_;
// TODO(JMM): Should we add table bounds? Given they're recorded in
// each spiner table, I lean towards no, but could be convinced
// otherwise if we need to do extrapolation, etc.
Expand Down
4 changes: 2 additions & 2 deletions singularity-opac/photons/mean_opacity_photons.hpp
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Expand Up @@ -186,8 +186,8 @@ class MeanOpacity {
PORTABLE_INLINE_FUNCTION Real fromLog_(const Real lx) const {
return std::pow(10., lx);
}
Spiner::DataBox lkappaPlanck_;
Spiner::DataBox lkappaRosseland_;
Spiner::DataBox<Real> lkappaPlanck_;
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Thanks for fixing the mean_s_opacity functions as well -- should we move these original changes to the using Databox = pattern you have elsewhere for consistency? I can do this if you want to hand the PR back to me

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Sure, that sounds good. Thanks!

Spiner::DataBox<Real> lkappaRosseland_;
const char *filename_;
};

Expand Down
6 changes: 4 additions & 2 deletions singularity-opac/photons/mean_s_opacity_photons.hpp
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Expand Up @@ -42,6 +42,8 @@ template <typename ThermalDistribution, typename pc = PhysicalConstantsCGS>
class MeanSOpacity {

public:
using DataBox = Spiner::DataBox<Real>;

MeanSOpacity() = default;
template <typename SOpacity>
MeanSOpacity(const SOpacity &s_opac, const Real lRhoMin, const Real lRhoMax,
Expand Down Expand Up @@ -192,8 +194,8 @@ class MeanSOpacity {
PORTABLE_INLINE_FUNCTION Real fromLog_(const Real lx) const {
return std::pow(10., lx);
}
Spiner::DataBox lkappaPlanck_;
Spiner::DataBox lkappaRosseland_;
DataBox lkappaPlanck_;
DataBox lkappaRosseland_;
const char *filename_;
};

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5 changes: 4 additions & 1 deletion test/CMakeLists.txt
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Expand Up @@ -29,6 +29,8 @@ message(STATUS "Configuring unit tests")
add_library(catch2_define)
target_sources(catch2_define PUBLIC catch2_define.cpp)
target_link_libraries(catch2_define PUBLIC
${PROJECT_NAME}
singularity-opac::flags
Catch2::Catch2)

add_executable(${PROJECT_NAME}_unit_tests)
Expand All @@ -50,7 +52,8 @@ PRIVATE
target_link_libraries(${PROJECT_NAME}_unit_tests
PRIVATE
catch2_define
${PROJECT_NAME})
${PROJECT_NAME}
singularity-opac::flags)

# Ensure code works with C++11 and earlier
# TODO(MM): Remove this later when it's not needed.
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2 changes: 1 addition & 1 deletion test/catch2_define.cpp
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Expand Up @@ -13,7 +13,7 @@
// publicly, and to permit others to do so.
// ======================================================================

#include "../utils/ports-of-call/portability.hpp"
#include <ports-of-call/portability.hpp>

#define CATCH_CONFIG_RUNNER
#include <catch2/catch.hpp>
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3 changes: 2 additions & 1 deletion test/test_brt_opacities.cpp
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Expand Up @@ -32,6 +32,7 @@
using namespace singularity;

using pc = PhysicalConstantsCGS;
using DataBox = Spiner::DataBox<Real>;

#ifdef PORTABILITY_STRATEGY_KOKKOS
using atomic_view = Kokkos::MemoryTraits<Kokkos::Atomic>;
Expand Down Expand Up @@ -169,7 +170,7 @@ TEST_CASE("BRT neutrino opacities", "[BRTNeutrinos]") {
nu_coeffs, nu_min, nu_max);
opac.EmissivityPerNu(rho, temp, Ye, type, nu_bins, J_cheb, nbins);
Real Jtrue = opac.EmissivityPerNu(rho, temp, Ye, type, nu);
J_cheb.SetInterpCoeffs(Spiner::DataBox(vm9, 9, 9));
J_cheb.SetInterpCoeffs(DataBox(vm9, 9, 9));
if (std::isnan(J_cheb(nu)) ||
((std::abs(Jtrue) >= 1e-14 || J_cheb(nu) >= 1e-14) &&
FractionalDifference(J_cheb(nu), Jtrue) > EPS_TEST)) {
Expand Down
4 changes: 3 additions & 1 deletion test/test_chebyshev.cpp
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Expand Up @@ -23,6 +23,8 @@
#include <singularity-opac/chebyshev/chebyshev.hpp>
using namespace singularity::chebyshev;

using DataBox = Spiner::DataBox<Real>;

#ifdef PORTABILITY_STRATEGY_KOKKOS
using atomic_view = Kokkos::MemoryTraits<Kokkos::Atomic>;
#endif
Expand Down Expand Up @@ -62,7 +64,7 @@ TEST_CASE("Chebyshev Polynomials", "[Chebyshev]") {
Real *ycoeffs = (Real *)PORTABLE_MALLOC(sizeof(Real) * N);
portableFor(
"Compute Cheb polynomial", 0, 1, PORTABLE_LAMBDA(const int &i) {
MatMultiply(Spiner::DataBox(vm9, 9, 9), y, ycoeffs, N);
MatMultiply(DataBox(vm9, 9, 9), y, ycoeffs, N);
});
AND_THEN("The chebyshev polynomials fit") {
int n_wrong_h = 0;
Expand Down
3 changes: 2 additions & 1 deletion test/test_epbremsstrahlung_opacities.cpp
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Expand Up @@ -31,6 +31,7 @@
using namespace singularity;

using pc = PhysicalConstantsCGS;
using DataBox = Spiner::DataBox<Real>;

#ifdef PORTABILITY_STRATEGY_KOKKOS
using atomic_view = Kokkos::MemoryTraits<Kokkos::Atomic>;
Expand Down Expand Up @@ -132,7 +133,7 @@ TEST_CASE("E-P bremsstrahlung photon opacities", "[EPBremsstrahlungPhotons]") {

Real *nu_bins = (Real *)PORTABLE_MALLOC(nbins * sizeof(Real));
Real *temp_bins = (Real *)PORTABLE_MALLOC(ntemps * sizeof(Real));
Spiner::DataBox loglin_bins(Spiner::AllocationTarget::Device, ntemps,
DataBox loglin_bins(Spiner::AllocationTarget::Device, ntemps,
nbins);

portableFor(
Expand Down
5 changes: 3 additions & 2 deletions test/test_gray_opacities.cpp
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Expand Up @@ -32,6 +32,7 @@
using namespace singularity;

using pc = PhysicalConstantsCGS;
using DataBox = Spiner::DataBox<Real>;

#ifdef PORTABILITY_STRATEGY_KOKKOS
using atomic_view = Kokkos::MemoryTraits<Kokkos::Atomic>;
Expand Down Expand Up @@ -167,7 +168,7 @@ TEST_CASE("Gray neutrino opacities", "[GrayNeutrinos]") {
nu_coeffs, nu_min, nu_max);
opac.EmissivityPerNu(rho, temp, Ye, type, nu_bins, J_cheb, nbins);
Real Jtrue = opac.EmissivityPerNu(rho, temp, Ye, type, nu);
J_cheb.SetInterpCoeffs(Spiner::DataBox(vm9, 9, 9));
J_cheb.SetInterpCoeffs(DataBox(vm9, 9, 9));
if (std::isnan(J_cheb(nu)) ||
((std::abs(Jtrue) >= 1e-14 || J_cheb(nu) >= 1e-14) &&
FractionalDifference(J_cheb(nu), Jtrue) > EPS_TEST)) {
Expand Down Expand Up @@ -282,7 +283,7 @@ TEST_CASE("Gray photon opacities", "[GrayPhotons]") {

Real *nu_bins = (Real *)PORTABLE_MALLOC(nbins * sizeof(Real));
Real *temp_bins = (Real *)PORTABLE_MALLOC(ntemps * sizeof(Real));
Spiner::DataBox loglin_bins(Spiner::AllocationTarget::Device, ntemps,
DataBox loglin_bins(Spiner::AllocationTarget::Device, ntemps,
nbins);

portableFor(
Expand Down
2 changes: 1 addition & 1 deletion test/test_spiner_opac_neutrinos.cpp
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Expand Up @@ -73,7 +73,7 @@ TEST_CASE("Spiner opacities, filled with gray data",
const std::string grayname = "gray.sp5";

WHEN("We initialize a gray neutrino opacity and tabulate it") {
using Grid_t = Spiner::RegularGrid1D;
using Grid_t = Spiner::RegularGrid1D<Real>;

// Offset the frequencies to hopefully get over the point
// where the power laws transition
Expand Down
1 change: 0 additions & 1 deletion utils/ports-of-call
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This file was deleted.

1 change: 1 addition & 0 deletions utils/ports-of-call
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Submodule ports-of-call added at 993d82
2 changes: 1 addition & 1 deletion utils/spiner
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Submodule spiner updated 54 files
+2 −1 .github/PULL_REQUEST_TEMPLATE.md
+46 −0 .github/workflows/deps.yml
+40 −0 .github/workflows/docs.yml
+24 −0 .github/workflows/formatting.yml
+36 −0 .github/workflows/install.yml
+11 −6 .github/workflows/tests.yml
+5 −0 .gitignore
+157 −0 .gitlab-ci.yml
+5 −0 .gitlab-ci/config/spack/upstreams.yaml
+3 −4 .gitmodules
+213 −0 CMakeLists.txt
+0 −1 Catch2
+93 −32 README.md
+66 −0 cmake/Format.cmake
+232 −0 cmake/content.cmake
+22 −0 cmake/spinerConfig.cmake.in
+10 −0 doc/index.html
+1 −0 doc/sphinx/.gitignore
+27 −0 doc/sphinx/Makefile
+3 −0 doc/sphinx/README
+1 −0 doc/sphinx/_static/placeholder
+27 −0 doc/sphinx/_templates/versions.html
+57 −0 doc/sphinx/conf.py
+68 −0 doc/sphinx/index.rst
+35 −0 doc/sphinx/make.bat
+93 −0 doc/sphinx/src/building.rst
+503 −0 doc/sphinx/src/databox.rst
+54 −0 doc/sphinx/src/getting-started.rst
+178 −0 doc/sphinx/src/interpolation.rst
+102 −0 doc/sphinx/src/sphinx-howto.rst
+70 −0 doc/sphinx/src/statement-of-need.rst
+ − figs/spiner_interpolation_benchmark.png
+1 −0 installtest/.gitignore
+43 −0 installtest/CMakeLists.txt
+7 −0 installtest/libtest.cpp
+0 −79 ports-of-call/README.md
+0 −232 ports-of-call/portability.hpp
+0 −492 ports-of-call/portable_arrays.hpp
+50 −0 spack-repo/packages/ports-of-call/package.py
+106 −0 spack-repo/packages/spiner/package.py
+6 −0 spack-repo/repo.yaml
+206 −162 spiner/databox.hpp
+21 −0 spiner/interpolation.hpp
+221 −0 spiner/piecewise_grid_1d.hpp
+57 −34 spiner/regular_grid_1d.hpp
+5 −0 spiner/sp5.hpp
+0 −0 spiner/spiner_types.hpp
+112 −0 test/CMakeLists.txt
+0 −71 test/Makefile
+0 −78 test/Makefile.kokkos
+135 −0 test/benchmark.cpp
+8 −7 test/convergence.cpp
+7 −9 test/plot_convergence.py
+196 −22 test/test.cpp