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Merge branch 'master' into node_device_interface_revision_07-23

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jpekkila
2019-08-07 16:25:33 +03:00
parent a930864f42 5432d20b1b
commit 10200e4dd5
7 changed files with 134 additions and 86 deletions
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27
acc/mhd_solver/stencil_assembly.sas
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@@ -21,9 +21,12 @@ der6x_upwd(in Scalar vertex)
return (Scalar){ Scalar(1.0/60.0)*inv_ds* (
- Scalar(20.0)* vertex[vertexIdx.x, vertexIdx.y, vertexIdx.z]
+ Scalar(15.0)*(vertex[vertexIdx.x+1, vertexIdx.y, vertexIdx.z] + vertex[vertexIdx.x-1, vertexIdx.y, vertexIdx.z])
- Scalar( 6.0)*(vertex[vertexIdx.x+2, vertexIdx.y, vertexIdx.z] + vertex[vertexIdx.x-2, vertexIdx.y, vertexIdx.z])
+ vertex[vertexIdx.x+3, vertexIdx.y, vertexIdx.z] + vertex[vertexIdx.x-3, vertexIdx.y, vertexIdx.z])};
+ Scalar(15.0)*(vertex[vertexIdx.x+1, vertexIdx.y, vertexIdx.z]
+ vertex[vertexIdx.x-1, vertexIdx.y, vertexIdx.z])
- Scalar( 6.0)*(vertex[vertexIdx.x+2, vertexIdx.y, vertexIdx.z]
+ vertex[vertexIdx.x-2, vertexIdx.y, vertexIdx.z])
+ vertex[vertexIdx.x+3, vertexIdx.y, vertexIdx.z]
+ vertex[vertexIdx.x-3, vertexIdx.y, vertexIdx.z])};
}
Preprocessed Scalar
@@ -33,9 +36,12 @@ der6y_upwd(in Scalar vertex)
return (Scalar){ Scalar(1.0/60.0)*inv_ds* (
-Scalar( 20.0)* vertex[vertexIdx.x, vertexIdx.y, vertexIdx.z]
+Scalar( 15.0)*(vertex[vertexIdx.x, vertexIdx.y+1, vertexIdx.z] + vertex[vertexIdx.x, vertexIdx.y-1, vertexIdx.z])
-Scalar( 6.0)*(vertex[vertexIdx.x, vertexIdx.y+2, vertexIdx.z] + vertex[vertexIdx.x, vertexIdx.y-2, vertexIdx.z])
+ vertex[vertexIdx.x, vertexIdx.y+3, vertexIdx.z] + vertex[vertexIdx.x, vertexIdx.y-3, vertexIdx.z])};
+Scalar( 15.0)*(vertex[vertexIdx.x, vertexIdx.y+1, vertexIdx.z]
+ vertex[vertexIdx.x, vertexIdx.y-1, vertexIdx.z])
-Scalar( 6.0)*(vertex[vertexIdx.x, vertexIdx.y+2, vertexIdx.z]
+ vertex[vertexIdx.x, vertexIdx.y-2, vertexIdx.z])
+ vertex[vertexIdx.x, vertexIdx.y+3, vertexIdx.z]
+ vertex[vertexIdx.x, vertexIdx.y-3, vertexIdx.z])};
}
Preprocessed Scalar
@@ -45,9 +51,12 @@ der6z_upwd(in Scalar vertex)
return (Scalar){ Scalar(1.0/60.0)*inv_ds* (
-Scalar( 20.0)* vertex[vertexIdx.x, vertexIdx.y, vertexIdx.z]
+Scalar( 15.0)*(vertex[vertexIdx.x, vertexIdx.y, vertexIdx.z+1] + vertex[vertexIdx.x, vertexIdx.y, vertexIdx.z-1])
-Scalar( 6.0)*(vertex[vertexIdx.x, vertexIdx.y, vertexIdx.z+2] + vertex[vertexIdx.x, vertexIdx.y, vertexIdx.z-2])
+ vertex[vertexIdx.x, vertexIdx.y, vertexIdx.z+3] + vertex[vertexIdx.x, vertexIdx.y, vertexIdx.z-3])};
+Scalar( 15.0)*(vertex[vertexIdx.x, vertexIdx.y, vertexIdx.z+1]
+ vertex[vertexIdx.x, vertexIdx.y, vertexIdx.z-1])
-Scalar( 6.0)*(vertex[vertexIdx.x, vertexIdx.y, vertexIdx.z+2]
+ vertex[vertexIdx.x, vertexIdx.y, vertexIdx.z-2])
+ vertex[vertexIdx.x, vertexIdx.y, vertexIdx.z+3]
+ vertex[vertexIdx.x, vertexIdx.y, vertexIdx.z-3])};
}
#endif

2
acc/mhd_solver/stencil_defines.h
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@@ -31,7 +31,7 @@
#define LENTROPY (1)
#define LTEMPERATURE (0)
#define LFORCING (1)
#define LUPWD (0)
#define LUPWD (1)
#define AC_THERMAL_CONDUCTIVITY (AcReal(0.001)) // TODO: make an actual config parameter

21
acc/mhd_solver/stencil_process.sps
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@@ -222,23 +222,26 @@ helical_forcing(Scalar magnitude, Vector k_force, Vector xx, Vector ff_re, Vecto
// JP: This looks wrong:
// 1) Should it be dsx * nx instead of dsx * ny?
// 2) Should you also use globalGrid.n instead of the local n?
// MV: You are rigth. Made a quickfix. I did not see the error because multigpu is split
// in z direction not y direction.
// 3) Also final point: can we do this with vectors/quaternions instead?
// Tringonometric functions are much more expensive and inaccurate/
// MV: Good idea. No an immediate priority.
// Fun related article:
// https://randomascii.wordpress.com/2014/10/09/intel-underestimates-error-bounds-by-1-3-quintillion/
xx.x = xx.x*(2.0*M_PI/(dsx*(DCONST_INT(AC_ny_max) - DCONST_INT(AC_ny_min))));
xx.y = xx.y*(2.0*M_PI/(dsy*(DCONST_INT(AC_ny_max) - DCONST_INT(AC_ny_min))));
xx.z = xx.z*(2.0*M_PI/(dsz*(DCONST_INT(AC_ny_max) - DCONST_INT(AC_ny_min))));
xx.x = xx.x*(2.0*M_PI/(dsx*globalGrid.n.x));
xx.y = xx.y*(2.0*M_PI/(dsy*globalGrid.n.y));
xx.z = xx.z*(2.0*M_PI/(dsz*globalGrid.n.z));
Scalar cos_phi = cos(phi);
Scalar sin_phi = sin(phi);
Scalar cos_k_dox_x = cos(dot(k_force, xx));
Scalar sin_k_dox_x = sin(dot(k_force, xx));
Scalar cos_k_dot_x = cos(dot(k_force, xx));
Scalar sin_k_dot_x = sin(dot(k_force, xx));
// Phase affect only the x-component
//Scalar real_comp = cos_k_dox_x;
//Scalar imag_comp = sin_k_dox_x;
Scalar real_comp_phase = cos_k_dox_x*cos_phi - sin_k_dox_x*sin_phi;
Scalar imag_comp_phase = cos_k_dox_x*sin_phi + sin_k_dox_x*cos_phi;
//Scalar real_comp = cos_k_dot_x;
//Scalar imag_comp = sin_k_dot_x;
Scalar real_comp_phase = cos_k_dot_x*cos_phi - sin_k_dot_x*sin_phi;
Scalar imag_comp_phase = cos_k_dot_x*sin_phi + sin_k_dot_x*cos_phi;
Vector force = (Vector){ ff_re.x*real_comp_phase - ff_im.x*imag_comp_phase,

2
doc/manual/.gitignore vendored Normal file
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@@ -0,0 +1,2 @@
*.html
*.pdf

51
scripts/auto_optimize.sh
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@@ -1,51 +0,0 @@
#!/bin/bash
# Run this in your build directory (cd build && ../scripts/auto_optimize.sh)
# Generates a ${BENCHMARK_FILE} which contains the threadblock dims and other
# constants used in the integration in addition to the time used.
MAX_THREADS=1024 # Max size of the thread block, depends on hardware
BENCHMARK_FILE="benchmark.out"
TBCONFCREATOR_SRC_PATH="../scripts/gen_rk3_threadblockconf.c"
TBCONFFILE_DST_PATH="../src/core/kernels"
C_COMPILER_NAME="gcc"
rm ${BENCHMARK_FILE}
for (( tz=2; tz<=8; tz*=2))
do
for (( ty=1; ty<=1; ty+=1))
do
for (( tx=16; tx<=64; tx*=2))
do
if ( (${tx}*${ty}*${tz}) > ${MAX_THREADS})
then break
fi
for (( launch_bound=1; launch_bound<=8; launch_bound*=2))
do
for (( elems_per_thread=1; elems_per_thread<=128; elems_per_thread*=2))
do
# Generate the threadblock configuration
${C_COMPILER_NAME} ${TBCONFCREATOR_SRC_PATH} -o gen_rk3_threadblockconf
./gen_rk3_threadblockconf ${tx} ${ty} ${tz} ${elems_per_thread} ${launch_bound}
rm gen_rk3_threadblockconf
mv rk3_threadblock.conf ${TBCONFFILE_DST_PATH}
# Compile and run the test build
cmake -DBUILD_DEBUG=OFF -DDOUBLE_PRECISION=OFF -DAUTO_OPTIMIZE=ON .. && make -j
#if ./ac_run -t; then
# echo Success
./ac_run -b
#else
# echo fail!
#fi
done
done
done
done
done

5
scripts/autotest.sh
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@@ -5,10 +5,13 @@
# source ./sourceme.sh
# autotest.sh
#
# If you need slurm or to pass something before ./ac_run, set the variable
# If you need slurm or to pass something before ./ac_run, export the variable
# SRUN_COMMAND before calling this script.
#
# F.ex. on Taito SRUN_COMMAND="srun --gres=gpu:k80:4 --mem=24000 -t 00:14:59 -p gputest --cpus-per-task 1 -n 1"
# export SRUN_COMMAND
# autotest.sh
echo "SRUN_COMMAND: " ${SRUN_COMMAND}
results=()

106
src/standalone/model/model_rk3.cc
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@@ -43,6 +43,9 @@ typedef struct {
ModelScalar value;
ModelVector gradient;
ModelMatrix hessian;
#if LUPWD
ModelVector upwind;
#endif
} ModelScalarData;
typedef struct {
@@ -273,6 +276,53 @@ derzz(const int i, const int j, const int k, const ModelScalar* arr)
return second_derivative(pencil, get(AC_inv_dsz));
}
#if LUPWD
static inline ModelScalar
der6x_upwd(const int i, const int j, const int k, const ModelScalar* arr)
{
ModelScalar inv_ds = get(AC_inv_dsx);
return ModelScalar(1.0/60.0)*inv_ds* (
-ModelScalar( 20.0)* arr[IDX(i, j, k)]
+ModelScalar( 15.0)*(arr[IDX(i+1, j, k)]
+ arr[IDX(i-1, j, k)])
-ModelScalar( 6.0)*(arr[IDX(i+2, j, k)]
+ arr[IDX(i-2, j, k)])
+ arr[IDX(i+3, j, k)]
+ arr[IDX(i-3, j, k)]);
}
static inline ModelScalar
der6y_upwd(const int i, const int j, const int k, const ModelScalar* arr)
{
ModelScalar inv_ds = get(AC_inv_dsy);
return ModelScalar(1.0/60.0)*inv_ds* (
-ModelScalar( 20.0)* arr[IDX(i, j, k)]
+ModelScalar( 15.0)*(arr[IDX(i, j+1, k)]
+ arr[IDX(i, j-1, k)])
-ModelScalar( 6.0)*(arr[IDX(i, j+2, k)]
+ arr[IDX(i, j-2, k)])
+ arr[IDX(i, j+3, k)]
+ arr[IDX(i, j-3, k)]);
}
static inline ModelScalar
der6z_upwd(const int i, const int j, const int k, const ModelScalar* arr)
{
ModelScalar inv_ds = get(AC_inv_dsz);
return ModelScalar(1.0/60.0)*inv_ds* (
-ModelScalar( 20.0)* arr[IDX(i, j, k )]
+ModelScalar( 15.0)*(arr[IDX(i, j, k+1)]
+ arr[IDX(i, j, k-1)])
-ModelScalar( 6.0)*(arr[IDX(i, j, k+2)]
+ arr[IDX(i, j, k-2)])
+ arr[IDX(i, j, k+3)]
+ arr[IDX(i, j, k-3)]);
}
#endif
static inline ModelScalar
compute_value(const int i, const int j, const int k, const ModelScalar* arr)
{
@@ -285,6 +335,14 @@ compute_gradient(const int i, const int j, const int k, const ModelScalar* arr)
return (ModelVector){derx(i, j, k, arr), dery(i, j, k, arr), derz(i, j, k, arr)};
}
#if LUPWD
static inline ModelVector
compute_upwind(const int i, const int j, const int k, const ModelScalar* arr)
{
return (ModelVector){der6x_upwd(i, j, k, arr), der6y_upwd(i, j, k, arr), der6z_upwd(i, j, k, arr)};
}
#endif
static inline ModelMatrix
compute_hessian(const int i, const int j, const int k, const ModelScalar* arr)
{
@@ -309,6 +367,10 @@ read_data(const int i, const int j, const int k, ModelScalar* buf[], const int h
// diagonals with all arrays
data.hessian = compute_hessian(i, j, k, buf[handle]);
#if LUPWD
data.upwind = compute_upwind(i, j, k, buf[handle]);
#endif
return data;
}
@@ -354,6 +416,8 @@ gradients(const ModelVectorData& data)
return (ModelMatrix){gradient(data.x), gradient(data.y), gradient(data.z)};
}
/*
* =============================================================================
* Level 0.3 (Built-in functions available during the Stencil Processing Stage)
@@ -502,10 +566,27 @@ contract(const ModelMatrix& mat)
* Stencil Processing Stage (equations)
* =============================================================================
*/
#if LUPWD
ModelScalar
upwd_der6(const ModelVectorData& uu, const ModelScalarData& lnrho)
{
ModelScalar uux = fabs(value(uu).x);
ModelScalar uuy = fabs(value(uu).y);
ModelScalar uuz = fabs(value(uu).z);
return uux*lnrho.upwind.x + uuy*lnrho.upwind.y + uuz*lnrho.upwind.z;
}
#endif
static inline ModelScalar
continuity(const ModelVectorData& uu, const ModelScalarData& lnrho)
{
return -dot(value(uu), gradient(lnrho)) - divergence(uu);
return -dot(value(uu), gradient(lnrho))
#if LUPWD
//This is a corrective hyperdiffusion term for upwinding.
+ upwd_der6(uu, lnrho)
#endif
- divergence(uu);
}
static inline ModelScalar
@@ -679,19 +760,20 @@ helical_forcing(ModelScalar magnitude, ModelVector k_force, ModelVector xx, Mode
ModelVector ff_im, ModelScalar phi)
{
(void)magnitude; // WARNING: unused
xx.x = xx.x * (2.0l * M_PI / (get(AC_dsx) * (get(AC_ny_max) - get(AC_ny_min))));
xx.y = xx.y * (2.0l * M_PI / (get(AC_dsy) * (get(AC_ny_max) - get(AC_ny_min))));
xx.z = xx.z * (2.0l * M_PI / (get(AC_dsz) * (get(AC_ny_max) - get(AC_ny_min))));
xx.x = xx.x*(2.0*M_PI/(get(AC_dsx)*get(AC_nx)));
xx.y = xx.y*(2.0*M_PI/(get(AC_dsy)*get(AC_ny)));
xx.z = xx.z*(2.0*M_PI/(get(AC_dsz)*get(AC_nz)));
ModelScalar cosl_phi = cosl(phi);
ModelScalar sinl_phi = sinl(phi);
ModelScalar cosl_k_dox_x = cosl(dot(k_force, xx));
ModelScalar sinl_k_dox_x = sinl(dot(k_force, xx));
ModelScalar cos_phi = cosl(phi);
ModelScalar sin_phi = sinl(phi);
ModelScalar cos_k_dot_x = cosl(dot(k_force, xx));
ModelScalar sin_k_dot_x = sinl(dot(k_force, xx));
// Phase affect only the x-component
// ModelScalar real_comp = cosl_k_dox_x;
// ModelScalar imag_comp = sinl_k_dox_x;
ModelScalar real_comp_phase = cosl_k_dox_x * cosl_phi - sinl_k_dox_x * sinl_phi;
ModelScalar imag_comp_phase = cosl_k_dox_x * sinl_phi + sinl_k_dox_x * cosl_phi;
//Scalar real_comp = cos_k_dot_x;
//Scalar imag_comp = sin_k_dot_x;
ModelScalar real_comp_phase = cos_k_dot_x*cos_phi - sin_k_dot_x*sin_phi;
ModelScalar imag_comp_phase = cos_k_dot_x*sin_phi + sin_k_dot_x*cos_phi;
ModelVector force = (ModelVector){ ff_re.x*real_comp_phase - ff_im.x*imag_comp_phase,
ff_re.y*real_comp_phase - ff_im.y*imag_comp_phase,