Merge branch 'master' into forcing

2019-07-02 16:43:10 +08:00
parent d0eb308f17 9a87053f26
commit 03689709df
17 changed files with 152 additions and 113 deletions
--- a/README.md
+++ b/README.md
@@ -2,13 +2,13 @@

 # Astaroth - A Multi-GPU library for generic stencil computations

-Astaroth is a single-node multi-GPU library for multiphysics and other problems, which involve stencil computations in a discrete mesh. It's licenced under the terms of the GNU General Public Licence, version 3, or later (see [LICENCE.txt](https://bitbucket.org/miikkavaisala/astaroth-code/src/master/astaroth_2.0/LICENCE.txt)). Astaroth ships with a domain-specific language, that can be used to translate high-level representation of the stencil computations into a heavily inlined GPU pipeline.
+Astaroth is a single-node multi-GPU library for multiphysics and other problems, which involve stencil computations in a discrete mesh. It's licenced under the terms of the GNU General Public Licence, version 3, or later (see [LICENCE.txt](https://bitbucket.org/miikkavaisala/astaroth-code/src/master/astaroth_2.0/LICENCE.txt)). Astaroth ships with a domain-specific language that can be used to translate high-level representations of various stencil operations into efficient CUDA kernels.

 ## System requirements

 NVIDIA GPU with >= 3.0 compute capability. See https://en.wikipedia.org/wiki/CUDA#GPUs_supported.

-## Building (3rd party libraries)
+## Building (3rd party libraries for real-time visualization)

 1. `cd 3rdparty`
 1. `./setup_dependencies.sh` Note: this may take some time.
@@ -60,6 +60,43 @@ Run `doxygen doxyfile` in astaroth_2.0 directory. The generated files can be fou
 If you have clang-format, you may run `scripts/fix_style.sh`. This script will recursively fix style of all the source files down from the current working directory. The script will ask for a confirmation before making any changes. 

 ## Directory structure
+TODO
+
+## Contributing
+
+0. **Do not break existing functionality.** Do not modify the interface functions declared in astaroth.h and device.cuh in any way. Bug fixes are exceptions. If you need new functionality, create a new function.
+
+0. **Do not rename or redefine variables or constants declared in astaroth.h** without consulting everyone involved with the project.
+
+0. **Ensure that the code compiles and the automated tests pass** by running `./ac_run -t` before pushing changes to master. If you want to implement a feature that consists of multiple commits, see Managing feature branches below.
+
+### Managing feature branches 
+
+0. Ensure that you're on the latest version of master. `git checkout master && git pull`
+
+0. Create a feature branch with `git checkout -b <feature_name_year-month-date>`, f.ex. `git checkout -b forcingtests_2019-01-01`
+
+0. Do your commits in that branch until your new feature works
+
+0. Merge master with your feature branch `git merge master`
+
+0. Resolve the conflicts and test that the code compiles and still works by running `./ac_run -t`
+
+0. If everything is OK, commit your final changes to the feature branch and merge it to master `git commit && git checkout master && git merge <your feature branch> && git push`
+
+0. Unless you really have to keep your feature branch around for historical/other reasons, remove it from remote by calling `git push origin --delete <your feature branch>`
+
+A flowchart is available at [doc/commitflowchart.png](https://bitbucket.org/jpekkila/astaroth/src/2d91df19dcb3/doc/commitflowchart.png?at=master).
+
+### About branches in general
+
+* Unused branches should not kept around after merging them into master in order to avoid cluttering the repository. 
+
+* `git branch -a --merged` shows a list of branches that have been merged to master and are likely not needed any more.
+
+* `git push origin --delete <feature branch>` deletes a remote branch while `git branch -d <feature branch>` deletes a local branch
+
+* If you think that you have messed up and lost work, run `git reflog` which lists the latests commits. All work that has been committed should be accessible with the hashes listed by this command with `git checkout <reflog hash>`.

 ## Coding style.

--- a/acc/mhd_solver/stencil_process.sps
+++ b/acc/mhd_solver/stencil_process.sps
@@ -1,4 +1,4 @@
-#define LINDUCTION (1)
+#define LMAGNETIC (1)
 #define LENTROPY (1)
 #define LTEMPERATURE (0)
 #define LGRAVITY (0)
@@ -295,7 +295,7 @@ in Vector uu = (int3) {VTXBUF_UUX, VTXBUF_UUY, VTXBUF_UUZ};
 out Vector out_uu = (int3) {VTXBUF_UUX,VTXBUF_UUY,VTXBUF_UUZ};


-#if LINDUCTION
+#if LMAGNETIC
 in Vector aa = (int3) {VTXBUF_AX,VTXBUF_AY,VTXBUF_AZ};
 out Vector out_aa = (int3) {VTXBUF_AX,VTXBUF_AY,VTXBUF_AZ};
 #endif
@@ -314,7 +314,7 @@ Kernel void
 solve(Scalar dt) {
    out_lnrho = rk3(out_lnrho, lnrho, continuity(uu, lnrho), dt);

-    #if LINDUCTION
+    #if LMAGNETIC
    out_aa = rk3(out_aa, aa, induction(uu, aa), dt);
    #endif

--- a/acc/pseudodisk/stencil_process_gravx.sps
+++ b/acc/pseudodisk/stencil_process_gravx.sps
@@ -1,4 +1,4 @@
-#define LINDUCTION (1)
+#define LMAGNETIC (1)
 #define LENTROPY (1)


@@ -200,7 +200,7 @@ in Vector uu = (int3) {VTXBUF_UUX, VTXBUF_UUY, VTXBUF_UUZ};
 out Vector out_uu = (int3) {VTXBUF_UUX,VTXBUF_UUY,VTXBUF_UUZ};


-#if LINDUCTION
+#if LMAGNETIC
 in Vector aa = (int3) {VTXBUF_AX,VTXBUF_AY,VTXBUF_AZ};
 out Vector out_aa = (int3) {VTXBUF_AX,VTXBUF_AY,VTXBUF_AZ};
 #endif
@@ -214,7 +214,7 @@ Kernel void
 solve(Scalar dt) {
    WRITE(out_lnrho, RK3(out_lnrho, lnrho, continuity(uu, lnrho), dt));

-    #if LINDUCTION
+    #if LMAGNETIC
        WRITE(out_aa,    RK3(out_aa, aa, induction(uu, aa), dt));
    #endif

--- a/acc/pseudodisk/stencil_process_isotherm_gravx.sps
+++ b/acc/pseudodisk/stencil_process_isotherm_gravx.sps
@@ -117,7 +117,7 @@ out Scalar out_lnrho = VTXBUF_LNRHO;
 in Vector uu = (int3) {VTXBUF_UUX, VTXBUF_UUY, VTXBUF_UUZ};
 out Vector out_uu = (int3) {VTXBUF_UUX,VTXBUF_UUY,VTXBUF_UUZ};

-#if LINDUCTION
+#if LMAGNETIC
 in Vector aa = (int3) {VTXBUF_AX,VTXBUF_AY,VTXBUF_AZ};
 out Vector out_aa = (int3) {VTXBUF_AX,VTXBUF_AY,VTXBUF_AZ};
 #endif
@@ -126,7 +126,7 @@ Kernel void
 solve(Scalar dt) {
  WRITE(out_lnrho, RK3(out_lnrho, lnrho, continuity(uu, lnrho), dt));

-  #if LINDUCTION
+  #if LMAGNETIC
  WRITE(out_aa,    RK3(out_aa, aa, induction(uu, aa), dt));
  #endif

--- a/acc/pseudodisk/stencil_process_isotherm_linegrav.sps
+++ b/acc/pseudodisk/stencil_process_isotherm_linegrav.sps
@@ -122,7 +122,7 @@ out Scalar out_lnrho = VTXBUF_LNRHO;
 in Vector uu = (int3) {VTXBUF_UUX, VTXBUF_UUY, VTXBUF_UUZ};
 out Vector out_uu = (int3) {VTXBUF_UUX,VTXBUF_UUY,VTXBUF_UUZ};

-#if LINDUCTION
+#if LMAGNETIC
 in Vector aa = (int3) {VTXBUF_AX,VTXBUF_AY,VTXBUF_AZ};
 out Vector out_aa = (int3) {VTXBUF_AX,VTXBUF_AY,VTXBUF_AZ};
 #endif
@@ -131,7 +131,7 @@ Kernel void
 solve(Scalar dt) {
  WRITE(out_lnrho, RK3(out_lnrho, lnrho, continuity(uu, lnrho), dt));

-  #if LINDUCTION
+  #if LMAGNETIC
  WRITE(out_aa,    RK3(out_aa, aa, induction(uu, aa), dt));
  #endif

--- a/acc/pseudodisk/stencil_process_linegrav.sps
+++ b/acc/pseudodisk/stencil_process_linegrav.sps
@@ -1,4 +1,4 @@
-#define LINDUCTION (1)
+#define LMAGNETIC (1)
 #define LENTROPY (1)


@@ -205,7 +205,7 @@ in Vector uu = (int3) {VTXBUF_UUX, VTXBUF_UUY, VTXBUF_UUZ};
 out Vector out_uu = (int3) {VTXBUF_UUX,VTXBUF_UUY,VTXBUF_UUZ};


-#if LINDUCTION
+#if LMAGNETIC
 in Vector aa = (int3) {VTXBUF_AX,VTXBUF_AY,VTXBUF_AZ};
 out Vector out_aa = (int3) {VTXBUF_AX,VTXBUF_AY,VTXBUF_AZ};
 #endif
@@ -219,7 +219,7 @@ Kernel void
 solve(Scalar dt) {
    WRITE(out_lnrho, RK3(out_lnrho, lnrho, continuity(uu, lnrho), dt));

-    #if LINDUCTION
+    #if LMAGNETIC
        WRITE(out_aa,    RK3(out_aa, aa, induction(uu, aa), dt));
    #endif

--- a/acc/samples/common_header.h
+++ b/acc/samples/common_header.h
@@ -76,7 +76,7 @@ extern "C" {
 // L-prefix inherited from the old Astaroth, no idea what it means
 // MV: L means a Logical switch variale, something having true of false value.
 #define LFORCING (0) // Note: forcing is disabled currently in the files generated by acc (compiler of our DSL)
-#define LINDUCTION (1)
+#define LMAGNETIC (1)
 #define LENTROPY (1)
 #define LTEMPERATURE (0)

@@ -185,13 +185,13 @@ extern "C" {
        FUNC(VTXBUF_UUZ), \
        // FUNC(VTXBUF_DYE),

-#if LINDUCTION
-#define AC_FOR_INDUCTION_VTXBUF_HANDLES(FUNC)\
+#if LMAGNETIC
+#define AC_FOR_MAGNETIC_VTXBUF_HANDLES(FUNC)\
        FUNC(VTXBUF_AX), \
        FUNC(VTXBUF_AY), \
        FUNC(VTXBUF_AZ),
 #else
-#define AC_FOR_INDUCTION_VTXBUF_HANDLES(FUNC)
+#define AC_FOR_MAGNETIC_VTXBUF_HANDLES(FUNC)
 #endif

 #if LENTROPY
@@ -210,7 +210,7 @@ extern "C" {

 #define AC_FOR_VTXBUF_HANDLES(FUNC)\
        AC_FOR_HYDRO_VTXBUF_HANDLES(FUNC)\
-        AC_FOR_INDUCTION_VTXBUF_HANDLES(FUNC)\
+        AC_FOR_MAGNETIC_VTXBUF_HANDLES(FUNC)\
        AC_FOR_ENTROPY_VTXBUF_HANDLES(FUNC)\
        AC_FOR_TEMPERATURE_VTXBUF_HANDLES(FUNC)
 // clang-format on
--- a/doc/commitflowchart.drawio
+++ b/doc/commitflowchart.drawio
@@ -0,0 +1 @@
+<mxfile modified="2019-07-01T13:02:52.345Z" host="www.draw.io" agent="Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:67.0) Gecko/20100101 Firefox/67.0" etag="hgMGwkDtdVmJ2zmkpNJe" version="10.8.4" type="device"><diagram id="buiN-QRA47Ge1Fg0ieOi" name="Page-1">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</diagram></mxfile>
--- a/doc/commitflowchart.png
+++ b/doc/commitflowchart.png
--- a/include/astaroth.h
+++ b/include/astaroth.h
@@ -67,17 +67,18 @@ extern "C" {
 // logical switches
 #include "user.h"

+// clang-format off
 #ifndef USER_PROVIDED_DEFINES
-  #define STENCIL_ORDER (6)
-  #define NGHOST (STENCIL_ORDER/2)
-  #define LHYDRO (1)
-  #define LDENSITY (1)
-  #define LFORCING (1)
-  #define LINDUCTION (1)
-  #define LENTROPY (1)
-  #define LTEMPERATURE (0)
-  #define LMAGNETIC LINDUCTION
+    #define STENCIL_ORDER (6)
+    #define NGHOST (STENCIL_ORDER / 2)
+    #define LDENSITY (1)
+    #define LHYDRO (1)
+    #define LMAGNETIC (1)
+    #define LENTROPY (1)
+    #define LTEMPERATURE (0)
+    #define LFORCING (1)
 #endif
+// clang-format on

 #define AC_THERMAL_CONDUCTIVITY (AcReal(0.001)) // TODO: make an actual config parameter

@@ -193,6 +194,13 @@ extern "C" {
 * =============================================================================
 */
 // clang-format off
+#ifdef LDENSITY
+#define AC_FOR_DENSITY_VTXBUF_HANDLES(FUNC) \
+        FUNC(VTXBUF_LNRHO),
+#else
+#define AC_FOR_DENSITY_VTXBUF_HANDLES(FUNC)
+#endif
+
 #ifdef LHYDRO
 #define AC_FOR_HYDRO_VTXBUF_HANDLES(FUNC) \
        FUNC(VTXBUF_UUX), \
@@ -202,11 +210,13 @@ extern "C" {
 #define AC_FOR_HYDRO_VTXBUF_HANDLES(FUNC)
 #endif

-#ifdef LDENSITY 
-#define AC_FOR_DENSITY_VTXBUF_HANDLES(FUNC) \
-        FUNC(VTXBUF_LNRHO), 
+#ifdef LMAGNETIC
+#define AC_FOR_MAGNETIC_VTXBUF_HANDLES(FUNC) \
+        FUNC(VTXBUF_AX), \
+        FUNC(VTXBUF_AY), \
+        FUNC(VTXBUF_AZ),
 #else
-#define AC_FOR_DENSITY_VTXBUF_HANDLES(FUNC)
+#define AC_FOR_MAGNETIC_VTXBUF_HANDLES(FUNC)
 #endif

 #ifdef LENTROPY
@@ -216,31 +226,19 @@ extern "C" {
 #define AC_FOR_ENTROPY_VTXBUF_HANDLES(FUNC)
 #endif

-#ifdef LMAGNETIC
-#define AC_FOR_INDUCTION_VTXBUF_HANDLES(FUNC) \
-        FUNC(VTXBUF_AX), \
-        FUNC(VTXBUF_AY), \
-        FUNC(VTXBUF_AZ),
+//MR: Temperature must not have an additional variable slot, but should sit on the
+//    same as entropy.
+#if LTEMPERATURE
+    #define AC_FOR_TEMPERATURE_VTXBUF_HANDLES(FUNC)\
+          FUNC(VTXBUF_TEMPERATURE),
 #else
-#define AC_FOR_INDUCTION_VTXBUF_HANDLES(FUNC)
+    #define AC_FOR_TEMPERATURE_VTXBUF_HANDLES(FUNC)
 #endif

 #define AC_FOR_VTXBUF_HANDLES(FUNC) AC_FOR_HYDRO_VTXBUF_HANDLES(FUNC) \
                                    AC_FOR_DENSITY_VTXBUF_HANDLES(FUNC) \
                                    AC_FOR_ENTROPY_VTXBUF_HANDLES(FUNC) \
-                                    AC_FOR_INDUCTION_VTXBUF_HANDLES(FUNC) \
-
-//MR: Temperature must not have an additional variable slot, but should sit on the 
-//    same as entropy.
-#ifndef USER_PROVIDED
-  #if LTEMPERATURE
-    #define AC_FOR_TEMPERATURE_VTXBUF_HANDLES(FUNC)\
-          FUNC(VTXBUF_TEMPERATURE),
-  #else
-    #define AC_FOR_TEMPERATURE_VTXBUF_HANDLES(FUNC)
-  #endif
-#endif
-
+                                    AC_FOR_MAGNETIC_VTXBUF_HANDLES(FUNC) \
 // clang-format on

 /*
@@ -248,19 +246,21 @@ extern "C" {
 * Single/double precision switch
 * =============================================================================
 */
+// clang-format off
 #if AC_DOUBLE_PRECISION == 1
-typedef double AcReal;
-typedef double3 AcReal3;
-#define AC_REAL_MAX (DBL_MAX)
-#define AC_REAL_MIN (DBL_MIN)
-#define AC_REAL_EPSILON (DBL_EPSILON)
+    typedef double AcReal;
+    typedef double3 AcReal3;
+    #define AC_REAL_MAX (DBL_MAX)
+    #define AC_REAL_MIN (DBL_MIN)
+    #define AC_REAL_EPSILON (DBL_EPSILON)
 #else
-typedef float AcReal;
-typedef float3 AcReal3;
-#define AC_REAL_MAX (FLT_MAX)
-#define AC_REAL_MIN (FLT_MIN)
-#define AC_REAL_EPSILON (FLT_EPSILON)
+    typedef float AcReal;
+    typedef float3 AcReal3;
+    #define AC_REAL_MAX (FLT_MAX)
+    #define AC_REAL_MIN (FLT_MIN)
+    #define AC_REAL_EPSILON (FLT_EPSILON)
 #endif
+// clang-format on

 typedef struct {
    AcReal3 row[3];
@@ -296,7 +296,7 @@ typedef enum { RTYPE_MAX, RTYPE_MIN, RTYPE_RMS, RTYPE_RMS_EXP, NUM_REDUCTION_TYP
 typedef enum { AC_FOR_INT_PARAM_TYPES(AC_GEN_ID), NUM_INT_PARAM_TYPES } AcIntParam;

 typedef enum { AC_FOR_REAL_PARAM_TYPES(AC_GEN_ID), NUM_REAL_PARAM_TYPES } AcRealParam;
-//typedef enum { AC_FOR_VEC_PARAM_TYPES(AC_GEN_ID), NUM_VEC_PARAM_TYPES } AcVecParam;
+// typedef enum { AC_FOR_VEC_PARAM_TYPES(AC_GEN_ID), NUM_VEC_PARAM_TYPES } AcVecParam;

 extern const char* intparam_names[];  // Defined in astaroth.cu
 extern const char* realparam_names[]; // Defined in astaroth.cu
@@ -304,7 +304,7 @@ extern const char* realparam_names[]; // Defined in astaroth.cu
 typedef struct {
    int int_params[NUM_INT_PARAM_TYPES];
    AcReal real_params[NUM_REAL_PARAM_TYPES];
-    //AcReal* vec_params[NUM_VEC_PARAM_TYPES];
+    // AcReal* vec_params[NUM_VEC_PARAM_TYPES];
 } AcMeshInfo;

 /*
@@ -418,35 +418,3 @@ AcResult acForcingVec(const AcReal forcing_magnitude, const AcReal3 k_force, con
 #ifdef __cplusplus
 }
 #endif
-
-/*
- * =============================================================================
- * Notes
- * =============================================================================
- */
-/*
-typedef enum {
-    VTX_BUF_LNRHO,
-    VTX_BUF_UUX,
-    VTX_BUF_UUY,
-    VTX_BUF_UUZ,
-    NUM_VERTEX_BUFFER_HANDLES
-} VertexBufferHandle
-
-// LNRHO etc
-typedef struct {
-    AcReal* data;
-} VertexBuffer;
-
-// Host
-typedef struct {
-    VertexBuffer vertex_buffers[NUM_VERTEX_BUFFER_HANDLES];
-    MeshInfo info;
-} Mesh;
-
-// Device
-typedef struct {
-    VertexBuffer in[NUM_VERTEX_BUFFER_HANDLES];
-    VertexBuffer out[NUM_VERTEX_BUFFER_HANDLES];
-} VertexBufferArray;
-*/
--- a/include/user.h
+++ b/include/user.h
@@ -1,3 +1,4 @@
+// clang-format off
 #ifdef PENCIL_ASTAROTH

  #include "../cparam.inc_c.h"
@@ -11,6 +12,11 @@
  #else
    #define AC_DOUBLE_PRECISION 0
  #endif
+
+  #define LENTROPY (1) // TODO above
+  #define LFORCING (1) // TODO above
+  #define STENCIL_ORDER (6) // nghost is not 1, 2 or 3 (as it is not fetched from fortran yet). This causes the compilation to fail. TODO remove this line
+
  #define USER_PROVIDED_DEFINES
 #endif
-
+// clang-format on
--- a/src/core/astaroth.cu
+++ b/src/core/astaroth.cu
@@ -120,12 +120,14 @@ acInit(const AcMeshInfo& config)
    ERRCHK_ALWAYS(subgrid.n.y >= STENCIL_ORDER);
    ERRCHK_ALWAYS(subgrid.n.z >= STENCIL_ORDER);

+#if VERBOSE_PRINTING
    // clang-format off
    printf("Grid m ");   printInt3(grid.m);    printf("\n");
    printf("Grid n ");   printInt3(grid.n);    printf("\n");
    printf("Subrid m "); printInt3(subgrid.m); printf("\n");
    printf("Subrid n "); printInt3(subgrid.n); printf("\n");
    // clang-format on
+#endif

    // Initialize the devices
    for (int i = 0; i < num_devices; ++i) {
@@ -271,8 +273,7 @@ AcResult
 acIntegrateStep(const int& isubstep, const AcReal& dt)
 {
    const int3 start = (int3){NGHOST, NGHOST, NGHOST};
-    const int3 end   = (int3){NGHOST + subgrid.n.x, NGHOST + subgrid.n.y,
-                              NGHOST + subgrid.n.z};
+    const int3 end   = (int3){NGHOST + subgrid.n.x, NGHOST + subgrid.n.y, NGHOST + subgrid.n.z};
    for (int i = 0; i < num_devices; ++i) {
        rkStep(devices[i], STREAM_PRIMARY, isubstep, start, end, dt);
    }
--- a/src/core/device.cu
+++ b/src/core/device.cu
@@ -42,6 +42,10 @@ __constant__ Grid globalGrid;
 #define DEVICE_1D_COMPDOMAIN_IDX(i, j, k) ((i) + (j)*DCONST_INT(AC_nx) + (k)*DCONST_INT(AC_nxy))
 #include "kernels/kernels.cuh"

+#if PACKED_DATA_TRANSFERS // Defined in device.cuh
+// #include "kernels/pack_unpack.cuh"
+#endif
+
 struct device_s {
    int id;
    AcMeshInfo local_config;
@@ -53,6 +57,11 @@ struct device_s {
    VertexBufferArray vba;
    AcReal* reduce_scratchpad;
    AcReal* reduce_result;
+
+#if PACKED_DATA_TRANSFERS
+// Declare memory for buffers needed for packed data transfers here
+// AcReal* data_packing_buffer;
+#endif
 };

 AcResult
@@ -154,6 +163,10 @@ createDevice(const int id, const AcMeshInfo device_config, Device* device_handle
        cudaMalloc(&device->reduce_scratchpad, AC_VTXBUF_COMPDOMAIN_SIZE_BYTES(device_config)));
    ERRCHK_CUDA_ALWAYS(cudaMalloc(&device->reduce_result, sizeof(AcReal)));

+#if PACKED_DATA_TRANSFERS
+// Allocate data required for packed transfers here (cudaMalloc)
+#endif
+
    // Device constants
    ERRCHK_CUDA_ALWAYS(cudaMemcpyToSymbol(d_mesh_info, &device_config, sizeof(device_config), 0,
                                          cudaMemcpyHostToDevice));
@@ -184,6 +197,10 @@ destroyDevice(Device device)
    cudaFree(device->reduce_scratchpad);
    cudaFree(device->reduce_result);

+#if PACKED_DATA_TRANSFERS
+// Free data required for packed tranfers here (cudaFree)
+#endif
+
    // Concurrency
    for (int i = 0; i < NUM_STREAM_TYPES; ++i)
        cudaStreamDestroy(device->streams[i]);
@@ -373,3 +390,7 @@ loadGlobalGrid(const Device device, const Grid grid)
        cudaMemcpyToSymbol(globalGrid, &grid, sizeof(grid), 0, cudaMemcpyHostToDevice));
    return AC_SUCCESS;
 }
+
+#if PACKED_DATA_TRANSFERS
+// Functions for calling packed data transfers
+#endif
--- a/src/core/device.cuh
+++ b/src/core/device.cuh
@@ -98,3 +98,8 @@ AcResult loadDeviceConstant(const Device device, const AcRealParam param, const

 /** */
 AcResult loadGlobalGrid(const Device device, const Grid grid);
+
+// #define PACKED_DATA_TRANSFERS (1) %JP: placeholder for optimized ghost zone packing and transfers
+#if PACKED_DATA_TRANSFERS
+// Declarations used for packed data transfers
+#endif
--- a/src/core/kernels/kernels.cuh
+++ b/src/core/kernels/kernels.cuh
@@ -426,7 +426,7 @@ cross(const AcReal3& a, const AcReal3& b)
 }

 static __host__ __device__ __forceinline__ bool
-is_valid(const AcReal a)
+is_valid(const AcReal& a)
 {
    return !isnan(a) && !isinf(a);
 }
--- a/src/standalone/config_loader.cc
+++ b/src/standalone/config_loader.cc
@@ -152,7 +152,7 @@ update_config(AcMeshInfo* config)
                                      config->real_params[AC_G_CONST];
    config->real_params[AC_sq2GM_star] = AcReal(sqrt(AcReal(2) * config->real_params[AC_GM_star]));

-#if VERBOSE_PRINTING
+#if VERBOSE_PRINTING // Defined in astaroth.h
    printf("###############################################################\n");
    printf("Config dimensions recalculated:\n");
    print(*config);
--- a/src/standalone/model/model_rk3.cc
+++ b/src/standalone/model/model_rk3.cc
@@ -745,7 +745,7 @@ solve_alpha_step(const int step_number, const ModelScalar dt, const int i, const
    ModelScalar rate_of_change[NUM_VTXBUF_HANDLES] = {0};
    rate_of_change[VTXBUF_LNRHO]                   = continuity(uu, lnrho);

-#if LINDUCTION
+#if LMAGNETIC
    const ModelVectorData aa  = read_data(i, j, k, in.vertex_buffer,
                                         (int3){VTXBUF_AX, VTXBUF_AY, VTXBUF_AZ});
    const ModelVector aa_res  = induction(uu, aa);
				`@@ -0,0 +1 @@`
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