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Merged in io_improvement_20190924 (pull request #11)

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Io improvement 20190924
This commit is contained in:
Miikka Väisälä
2019-10-02 13:12:25 +00:00
committed by jpekkila
parent 7d76250f70 f8e82d41af
commit 15cc71895d
4 changed files with 123 additions and 51 deletions
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2
acc/mhd_solver/stencil_definition.sdh
View File

@@ -14,9 +14,11 @@ uniform int AC_max_steps;
uniform int AC_save_steps;
uniform int AC_bin_steps;
uniform int AC_bc_type;
uniform int AC_start_step;
// Real params
uniform Scalar AC_dt;
uniform Scalar AC_max_time;
// Spacing
uniform Scalar AC_dsx;
uniform Scalar AC_dsy;

22
analysis/python/astar/data/read.py
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@@ -21,20 +21,33 @@
import numpy as np
def set_dtype(endian, AcRealSize):
if endian == 0:
en = '>'
elif endian == 1:
en = '<'
type_instruction = en + 'f' + str(AcRealSize)
print("type_instruction", type_instruction)
my_dtype = np.dtype(type_instruction)
return my_dtype
def read_bin(fname, fdir, fnum, minfo, numtype=np.longdouble):
'''Read in a floating point array'''
filename = fdir + fname + '_' + fnum + '.mesh'
datas = np.DataSource()
read_ok = datas.exists(filename)
my_dtype = set_dtype(minfo.contents['endian'], minfo.contents['AcRealSize'])
if read_ok:
print(filename)
array = np.fromfile(filename, dtype=numtype)
array = np.fromfile(filename, dtype=my_dtype)
timestamp = array[0]
array = np.reshape(array[1:], (minfo.contents['AC_mx'],
minfo.contents['AC_my'],
minfo.contents['AC_mz']), order='F')
minfo.contents['AC_my'],
minfo.contents['AC_mz']), order='F')
else:
array = None
timestamp = None
@@ -52,6 +65,9 @@ def read_meshtxt(fdir, fname):
if line[0] == 'int':
contents[line[1]] = np.int(line[2])
print(line[1], contents[line[1]])
elif line[0] == 'size_t':
contents[line[1]] = np.int(line[2])
print(line[1], contents[line[1]])
elif line[0] == 'int3':
contents[line[1]] = [np.int(line[2]), np.int(line[3]), np.int(line[4])]
print(line[1], contents[line[1]])

7
config/astaroth.conf
View File

@@ -23,6 +23,13 @@ AC_save_steps = 10
AC_bin_steps = 1000
AC_bin_save_t = 1e666
// Set to 0 if you want to run the simulation from the beginning, or just a new
// simulation. If continuing from a saved step, specify the step number here.
AC_start_step = 0
// Maximum time in code units. If negative, there is no time limit
AC_max_time = -1.0
// Hydro
AC_cdt = 0.4
AC_cdtv = 0.3

143
src/standalone/simulation.cc
View File

@@ -60,8 +60,17 @@ write_mesh_info(const AcMeshInfo* config)
infotxt = fopen("mesh_info.list", "w");
// Determine endianness
unsigned int EE = 1;
char *CC = (char*) &EE;
const int endianness = (int) *CC;
// endianness = 0 -> big endian
// endianness = 1 -> little endian
fprintf(infotxt, "size_t %s %lu \n", "AcRealSize", sizeof(AcReal));
fprintf(infotxt, "int %s %i \n", "endian", endianness);
// JP: this could be done shorter and with smaller chance for errors with the following
// (modified from acPrintMeshInfo() in astaroth.cu)
// MV: Now adapted into working condition. E.g. removed useless / harmful formatting.
@@ -86,9 +95,7 @@ write_mesh_info(const AcMeshInfo* config)
fclose(infotxt);
}
// This funtion writes a run state into a set of C binaries. For the sake of
// accuracy, all floating point numbers are to be saved in long double precision
// regardless of the choise of accuracy during runtime.
// This funtion writes a run state into a set of C binaries.
static inline void
save_mesh(const AcMesh& save_mesh, const int step, const AcReal t_step)
{
@@ -115,18 +122,61 @@ save_mesh(const AcMesh& save_mesh, const int step, const AcReal t_step)
save_ptr = fopen(bin_filename, "wb");
// Start file with time stamp
long double write_long_buf = (long double)t_step;
fwrite(&write_long_buf, sizeof(long double), 1, save_ptr);
AcReal write_long_buf = (AcReal)t_step;
fwrite(&write_long_buf, sizeof(AcReal), 1, save_ptr);
// Grid data
for (size_t i = 0; i < n; ++i) {
const AcReal point_val = save_mesh.vertex_buffer[VertexBufferHandle(w)][i];
long double write_long_buf = (long double)point_val;
fwrite(&write_long_buf, sizeof(long double), 1, save_ptr);
AcReal write_long_buf = (AcReal)point_val;
fwrite(&write_long_buf, sizeof(AcReal), 1, save_ptr);
}
fclose(save_ptr);
}
}
// This funtion reads a run state from a set of C binaries.
static inline void
read_mesh(AcMesh& read_mesh, const int step, AcReal* t_step)
{
FILE* read_ptr;
for (int w = 0; w < NUM_VTXBUF_HANDLES; ++w) {
const size_t n = acVertexBufferSize(read_mesh.info);
const char* buffername = vtxbuf_names[w];
char cstep[11];
char bin_filename[80] = "\0";
// sprintf(bin_filename, "");
sprintf(cstep, "%d", step);
strcat(bin_filename, buffername);
strcat(bin_filename, "_");
strcat(bin_filename, cstep);
strcat(bin_filename, ".mesh");
printf("Reading savefile %s \n", bin_filename);
read_ptr = fopen(bin_filename, "rb");
// Start file with time stamp
size_t result;
result = fread(t_step, sizeof(AcReal), 1, read_ptr);
// Read grid data
AcReal read_buf;
for (size_t i = 0; i < n; ++i) {
result = fread(&read_buf, sizeof(AcReal), 1, read_ptr);
read_mesh.vertex_buffer[VertexBufferHandle(w)][i] = read_buf;
if (int(result) != 1) {
fprintf(stderr, "Reading error in %s, element %i\n", vtxbuf_names[w], int(i));
fprintf(stderr, "Result = %i, \n", int(result));
}
}
fclose(read_ptr);
}
}
// This function prints out the diagnostic values to std.out and also saves and
// appends an ascii file to contain all the result.
static inline void
@@ -190,19 +240,27 @@ run_simulation(const char* config_path)
vertex_buffer_set(VTXBUF_ACCRETION, 0.0, mesh);
#endif
// Read old binary if we want to continue from an existing snapshot
// WARNING: Explicit specification of step needed!
const int start_step = mesh_info.int_params[AC_start_step];
AcReal t_step = 0.0;
if (start_step > 0) {
read_mesh(*mesh, start_step, &t_step);
}
acInit(mesh_info);
acLoad(*mesh);
FILE* diag_file;
diag_file = fopen("timeseries.ts", "a");
// TODO Get time from earlier state.
AcReal t_step = 0.0;
// Generate the title row.
fprintf(diag_file, "step t_step dt uu_total_min uu_total_rms uu_total_max ");
for (int i = 0; i < NUM_VTXBUF_HANDLES; ++i) {
fprintf(diag_file, "%s_min %s_rms %s_max ", vtxbuf_names[i], vtxbuf_names[i],
vtxbuf_names[i]);
if (start_step == 0) {
fprintf(diag_file, "step t_step dt uu_total_min uu_total_rms uu_total_max ");
for (int i = 0; i < NUM_VTXBUF_HANDLES; ++i) {
fprintf(diag_file, "%s_min %s_rms %s_max ", vtxbuf_names[i], vtxbuf_names[i],
vtxbuf_names[i]);
}
}
#if LSINK
fprintf(diag_file, "sink_mass accreted_mass ");
@@ -210,38 +268,36 @@ run_simulation(const char* config_path)
fprintf(diag_file, "\n");
write_mesh_info(&mesh_info);
if (start_step == 0) {
#if LSINK
print_diagnostics(0, AcReal(.0), t_step, diag_file, mesh_info.real_params[AC_M_sink_init], 0.0);
print_diagnostics(0, AcReal(.0), t_step, diag_file, mesh_info.real_params[AC_M_sink_init], 0.0);
#else
print_diagnostics(0, AcReal(.0), t_step, diag_file, -1.0, -1.0);
print_diagnostics(0, AcReal(.0), t_step, diag_file, -1.0, -1.0);
#endif
}
acBoundcondStep();
acStore(mesh);
save_mesh(*mesh, 0, t_step);
if (start_step == 0) {
save_mesh(*mesh, 0, t_step);
}
const int max_steps = mesh_info.int_params[AC_max_steps];
const int save_steps = mesh_info.int_params[AC_save_steps];
const int bin_save_steps = mesh_info.int_params[AC_bin_steps]; // TODO Get from mesh_info
const int bin_save_steps = mesh_info.int_params[AC_bin_steps];
AcReal bin_save_t = mesh_info.real_params[AC_bin_save_t];
const AcReal max_time = mesh_info.real_params[AC_max_time];
const AcReal bin_save_t = mesh_info.real_params[AC_bin_save_t];
AcReal bin_crit_t = bin_save_t;
/* initialize random seed: */
srand(312256655);
// TODO_SINK. init_sink_particle()
// Initialize the basic variables of the sink particle to a suitable initial value.
// 1. Location of the particle
// 2. Mass of the particle
// (3. Velocity of the particle)
// This at the level of Host in this case.
// acUpdate_sink_particle() will do the similar trick to the device.
/* Step the simulation */
AcReal accreted_mass = 0.0;
AcReal sink_mass = 0.0;
for (int i = 1; i < max_steps; ++i) {
for (int i = start_step + 1; i < max_steps; ++i) {
const AcReal umax = acReduceVec(RTYPE_MAX, VTXBUF_UUX, VTXBUF_UUY, VTXBUF_UUZ);
const AcReal dt = host_timestep(umax, mesh_info);
@@ -262,18 +318,6 @@ run_simulation(const char* config_path)
on_off_switch = 1;
}
acLoadDeviceConstant(AC_switch_accretion, on_off_switch);
// MV: Old TODOs to remind of eventual future directions.
// TODO_SINK acUpdate_sink_particle()
// 3. Velocity of the particle)
// TODO_SINK acAdvect_sink_particle()
// 1. Calculate the equation of motion for the sink particle.
// NOTE: Might require embedding with acIntegrate(dt).
// TODO_SINK acAccrete_sink_particle()
// 2. Transfer momentum into sink particle
// (OPTIONAL: Affection the motion of the particle)
// NOTE: Might require embedding with acIntegrate(dt).
// This is the hardest part. Please see Lee et al. ApJ 783 (2014) for reference.
#else
accreted_mass = -1.0;
sink_mass = -1.0;
@@ -288,6 +332,8 @@ run_simulation(const char* config_path)
t_step += dt;
/* Save the simulation state and print diagnostics */
if ((i % save_steps) == 0) {
@@ -316,15 +362,6 @@ run_simulation(const char* config_path)
This loop saves the data into simple C binaries which can be
used for analysing the data snapshots closely.
Saving simulation state should happen in a separate stage. We do
not want to save it as often as diagnostics. The file format
should IDEALLY be HDF5 which has become a well supported, portable and
reliable data format when it comes to HPC applications.
However, implementing it will have to for more simpler approach
to function. (TODO?)
*/
/*
The updated mesh will be located on the GPU. Also all calls
to the astaroth interface (functions beginning with ac*) are
assumed to be asynchronous, so the meshes must be also synchronized
@@ -340,6 +377,16 @@ run_simulation(const char* config_path)
bin_crit_t += bin_save_t;
}
// End loop if max time reached.
if (max_time > AcReal(0.0)) {
if (t_step >= max_time) {
printf("Time limit reached! at t = %e \n", double(t_step));
break;
}
}
}
//////Save the final snapshot