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Matthieu Schaller authoredMatthieu Schaller authored
debug.c 18.86 KiB
/*******************************************************************************
* This file is part of SWIFT.
* Copyright (c) 2013- 2015:
* Matthieu Schaller (matthieu.schaller@durham.ac.uk),
* Pedro Gonnet (pedro.gonnet@durham.ac.uk),
* Peter W. Draper (p.w.draper@durham.ac.uk).
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
/* Config parameters. */
/* This object's header. */
#include "debug.h"
/* Some standard headers. */
#include <float.h>
#include <stdio.h>
#include <unistd.h>
/* Local includes. */
#include "active.h"
#include "cell.h"
#include "engine.h"
#include "hydro.h"
#include "inline.h"
#include "part.h"
#include "space.h"
/* Import the right hydro definition */
#if defined(MINIMAL_SPH)
#include "./hydro/Minimal/hydro_debug.h"
#elif defined(GADGET2_SPH)
#include "./hydro/Gadget2/hydro_debug.h"
#elif defined(HOPKINS_PE_SPH)
#include "./hydro/PressureEntropy/hydro_debug.h"
#elif defined(DEFAULT_SPH)
#include "./hydro/Default/hydro_debug.h"
#elif defined(GIZMO_SPH)
#include "./hydro/Gizmo/hydro_debug.h"
#elif defined(SHADOWFAX_SPH)
#include "./hydro/Shadowswift/hydro_debug.h"
#else
#error "Invalid choice of SPH variant"
#endif
#include "./gravity/Default/gravity_debug.h"
/**
* @brief Looks for the particle with the given id and prints its information to
*the standard output.
*
* @param parts The array of particles.
* @param xparts The array of particle extended data.
* @param id The id too look for.
* @param N The size of the array of particles.
*
* (Should be used for debugging only as it runs in O(N).) */
void printParticle(const struct part *parts, const struct xpart *xparts,
long long int id, size_t N) {
int found = 0;
/* Look for the particle. */
for (size_t i = 0; i < N; i++)
if (parts[i].id == id) {
printf("## Particle[%zu]:\n id=%lld ", i, parts[i].id);
hydro_debug_particle(&parts[i], &xparts[i]);
found = 1;
break;
}
if (!found) printf("## Particles[???] id=%lld not found\n", id);
}
/**
* @brief Looks for the g-particle with the given id and prints its information
* to
* the standard output.
*
* @param gparts The array of g-particles.
* @param parts The array of particles.
* @param id The id too look for.
* @param N The size of the array of g-particles.
*
* (Should be used for debugging only as it runs in O(N).)
*/
void printgParticle(const struct gpart *gparts, const struct part *parts,
long long int id, size_t N) {
int found = 0;
/* Look for the particle. */
for (size_t i = 0; i < N; i++)
if (gparts[i].id_or_neg_offset == id) {
printf("## gParticle[%zu] (DM) :\n id=%lld", i, id);
gravity_debug_particle(&gparts[i]);
found = 1;
break;
} else if (gparts[i].id_or_neg_offset < 0 &&
parts[-gparts[i].id_or_neg_offset].id == id) {
printf("## gParticle[%zu] (hydro) :\n id=%lld", i, id);
gravity_debug_particle(&gparts[i]);
found = 1;
break;
}
if (!found) printf("## Particles[???] id=%lld not found\n", id);
}
/**
* @brief Prints the details of a given particle to stdout
*
* @param p The particle to print
* @param xp The extended data ot the particle to print
*/
void printParticle_single(const struct part *p, const struct xpart *xp) {
printf("## Particle: id=%lld ", p->id);
hydro_debug_particle(p, xp);
printf("\n");
}
/**
* @brief Prints the details of a given particle to stdout
*
* @param gp The g-particle to print */
void printgParticle_single(struct gpart *gp) {
printf("## g-Particle: id=%lld ", gp->id_or_neg_offset);
gravity_debug_particle(gp);
printf("\n");
}
/**
* @brief Check that the cells and particles of a space have consistent h_max
* values.
*
* @param s the space.
* @result 1 or 0
*/
int checkSpacehmax(struct space *s) {
/* Loop over local cells. */
float cell_h_max = 0.0f;
for (int k = 0; k < s->nr_cells; k++) {
if (s->cells_top[k].nodeID == s->e->nodeID &&
s->cells_top[k].h_max > cell_h_max) {
cell_h_max = s->cells_top[k].h_max;
}
}
/* Now all particles. */
float part_h_max = 0.0f;
for (size_t k = 0; k < s->nr_parts; k++) {
if (s->parts[k].h > part_h_max) {
part_h_max = s->parts[k].h;
}
}
/* If within some epsilon we are OK. */
if (fabsf(cell_h_max - part_h_max) <= FLT_EPSILON) return 1;
/* There is a problem. Hunt it down. */
for (int k = 0; k < s->nr_cells; k++) {
if (s->cells_top[k].nodeID == s->e->nodeID) {
if (s->cells_top[k].h_max > part_h_max) {
message("cell %d is inconsistent (%f > %f)", k, s->cells_top[k].h_max,
part_h_max);
}
}
}
for (size_t k = 0; k < s->nr_parts; k++) {
if (s->parts[k].h > cell_h_max) {
message("part %lld is inconsistent (%f > %f)", s->parts[k].id,
s->parts[k].h, cell_h_max);
}
}
return 0;
}
/**
* @brief Check if the h_max and dx_max values of a cell's hierarchy are
* consistent with the particles. Also checks if particles are correctly
* in a cell. Report verbosely if not.
*
* @param c the top cell of the hierarchy.
* @param depth the recursion depth for use in messages. Set to 0 initially.
* @result 1 or 0
*/
int checkCellhdxmax(const struct cell *c, int *depth) {
*depth = *depth + 1;
float h_max = 0.0f;
float dx_max = 0.0f;
int result = 1;
const double loc_min[3] = {c->loc[0], c->loc[1], c->loc[2]};
const double loc_max[3] = {c->loc[0] + c->width[0], c->loc[1] + c->width[1],
c->loc[2] + c->width[2]};
const size_t nr_parts = c->count;
struct part *parts = c->parts;
struct xpart *xparts = c->xparts;
for (size_t k = 0; k < nr_parts; k++) {
struct part *const p = &parts[k];
struct xpart *const xp = &xparts[k];
if (p->x[0] < loc_min[0] || p->x[0] >= loc_max[0] || p->x[1] < loc_min[1] ||
p->x[1] >= loc_max[1] || p->x[2] < loc_min[2] ||
p->x[2] >= loc_max[2]) {
message(
"Inconsistent part position p->x=[%e %e %e], c->loc=[%e %e %e] "
"c->width=[%e %e %e]",
p->x[0], p->x[1], p->x[2], c->loc[0], c->loc[1], c->loc[2],
c->width[0], c->width[1], c->width[2]);
result = 0;
}
const float dx2 = xp->x_diff[0] * xp->x_diff[0] +
xp->x_diff[1] * xp->x_diff[1] +
xp->x_diff[2] * xp->x_diff[2];
h_max = max(h_max, p->h);
dx_max = max(dx_max, sqrt(dx2));
}
if (c->split) {
for (int k = 0; k < 8; k++) {
if (c->progeny[k] != NULL) {
struct cell *cp = c->progeny[k];
checkCellhdxmax(cp, depth);
}
}
}
/* Check. */
if (c->h_max != h_max) {
message("%d Inconsistent h_max: cell %f != parts %f", *depth, c->h_max,
h_max);
message("location: %f %f %f", c->loc[0], c->loc[1], c->loc[2]);
result = 0;
}
if (c->dx_max_part != dx_max) {
message("%d Inconsistent dx_max: %f != %f", *depth, c->dx_max_part, dx_max);
message("location: %f %f %f", c->loc[0], c->loc[1], c->loc[2]);
result = 0;
}
return result;
}
/**
* @brief map function for dumping cells. In MPI mode locally active cells
* only.
*/
static void dumpCells_map(struct cell *c, void *data) {
size_t *ldata = (size_t *)data;
FILE *file = (FILE *)ldata[0];
struct engine *e = (struct engine *)ldata[1]; float ntasks = c->nr_tasks;
int active = (int)ldata[2];
int mpiactive = (int)ldata[3];
int pactive = (int)ldata[4];
#if SWIFT_DEBUG_CHECKS
/* The c->nr_tasks field does not include all the tasks. So let's check this
* the hard way. Note pairs share the task 50/50 with the other cell. */
ntasks = 0.0f;
struct task *tasks = e->sched.tasks;
int nr_tasks = e->sched.nr_tasks;
for (int k = 0; k < nr_tasks; k++) {
if (tasks[k].cj == NULL) {
if (c == tasks[k].ci) {
ntasks = ntasks + 1.0f;
}
} else {
if (c == tasks[k].ci || c == tasks[k].cj) {
ntasks = ntasks + 0.5f;
}
}
}
#endif
/* Only cells with particles are dumped. */
if (c->count > 0 || c->gcount > 0 || c->scount > 0) {
/* In MPI mode we may only output cells with foreign partners.
* These define the edges of the partitions. */
#if WITH_MPI
if (mpiactive)
mpiactive = (c->send_xv != NULL);
else
mpiactive = 1;
#else
mpiactive = 1;
#endif
/* Active cells, otherwise all. */
if (active)
active = cell_is_active_hydro(c, e);
else
active = 1;
/* So output local super cells that are active and have MPI tasks as
* requested. */
if (c->nodeID == e->nodeID && (c->super == c) && active && mpiactive) {
/* If requested we work out how many particles are active in this cell. */
int pactcount = 0;
if (pactive) {
const struct part *parts = c->parts;
for (int k = 0; k < c->count; k++)
if (part_is_active(&parts[k], e)) pactcount++;
struct gpart *gparts = c->gparts;
for (int k = 0; k < c->gcount; k++)
if (gpart_is_active(&gparts[k], e)) pactcount++;
struct spart *sparts = c->sparts;
for (int k = 0; k < c->scount; k++)
if (spart_is_active(&sparts[k], e)) pactcount++;
}
fprintf(file,
" %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %6d %6d %6d %6d %6d %6d "
"%6.1f %20lld %6d %6d %6d %6d %6d\n",
c->loc[0], c->loc[1], c->loc[2], c->width[0], c->width[1],
c->width[2], e->step, c->count, c->gcount, c->scount, pactcount,
c->depth, ntasks, c->ti_hydro_end_min,
get_time_bin(c->ti_hydro_end_min), (c->super == c),
cell_is_active_hydro(c, e), c->nodeID, c->nodeID == e->nodeID); }
}
}
/**
* @brief Dump the location, depth, task counts and timebins and active state,
* for all cells to a simple text file. A more costly count of the active
* particles in a cell can also be output.
*
* @param prefix base output filename, result is written to
* %prefix%_%rank%_%step%.dat
* @param active just output active cells.
* @param mpiactive just output MPI active cells, i.e. those with foreign cells.
* @param pactive also output a count of active particles.
* @param s the space holding the cells to dump.
* @param rank node ID of MPI rank, or 0 if not relevant.
* @param step the current engine step, or some unique integer.
*/
void dumpCells(const char *prefix, int active, int mpiactive, int pactive,
struct space *s, int rank, int step) {
FILE *file = NULL;
/* Name of output file. */
char fname[200];
sprintf(fname, "%s_%03d_%03d.dat", prefix, rank, step);
file = fopen(fname, "w");
/* Header. */
fprintf(file,
"# %6s %6s %6s %6s %6s %6s %6s %6s %6s %6s %6s %6s %6s "
"%20s %6s %6s %6s %6s %6s\n",
"x", "y", "z", "xw", "yw", "zw", "step", "count", "gcount", "scount",
"actcount", "depth", "tasks", "ti_end_min", "timebin", "issuper",
"active", "rank", "local");
size_t data[5];
data[0] = (size_t)file;
data[1] = (size_t)s->e;
data[2] = (size_t)active;
data[3] = (size_t)mpiactive;
data[4] = (size_t)pactive;
space_map_cells_pre(s, 1, dumpCells_map, &data);
fclose(file);
}
#if defined(WITH_MPI) && defined(HAVE_METIS)
/**
* @brief Dump the METIS graph in standard format, simple format and weights
* only, to a file.
*
* The standard format output can be read into the METIS
* command-line tools. The simple format is just the cell connectivity (this
* should not change between calls). The weights format is the standard one,
* minus the cell connectivity.
*
* The output filenames are generated from the prefix and the sequence number
* of calls. So the first is called {prefix}_std_001.dat,
*{prefix}_simple_001.dat,
* {prefix}_weights_001.dat, etc.
*
* @param prefix base output filename
* @param nvertices the number of vertices
* @param nvertexweights the number vertex weights
* @param cellconruns first part of cell connectivity info (CSR)
* @param cellcon second part of cell connectivity info (CSR)
* @param vertexweights weights of vertices
* @param vertexsizes size of vertices
* @param edgeweights weights of edges */
void dumpMETISGraph(const char *prefix, idx_t nvertices, idx_t nvertexweights,
idx_t *cellconruns, idx_t *cellcon, idx_t *vertexweights,
idx_t *vertexsizes, idx_t *edgeweights) {
FILE *stdfile = NULL;
FILE *simplefile = NULL;
FILE *weightfile = NULL;
char fname[200];
int haveedgeweight = 0;
int havevertexsize = 0;
int havevertexweight = 0;
static int nseq = 0;
nseq++;
if (vertexweights != NULL) {
for (idx_t i = 0; i < nvertices * nvertexweights; i++) {
if (vertexweights[i] != 1) {
havevertexweight = 1;
break;
}
}
}
if (vertexsizes != NULL) {
for (idx_t i = 0; i < nvertices; i++) {
if (vertexsizes[i] != 1) {
havevertexsize = 1;
break;
}
}
}
if (edgeweights != NULL) {
for (idx_t i = 0; i < cellconruns[nvertices]; i++) {
if (edgeweights[i] != 1) {
haveedgeweight = 1;
break;
}
}
}
/* Open output files. */
sprintf(fname, "%s_std_%03d.dat", prefix, nseq);
stdfile = fopen(fname, "w");
sprintf(fname, "%s_simple_%03d.dat", prefix, nseq);
simplefile = fopen(fname, "w");
if (havevertexweight || havevertexsize || haveedgeweight) {
sprintf(fname, "%s_weights_%03d.dat", prefix, nseq);
weightfile = fopen(fname, "w");
}
/* Write the header lines. */
fprintf(stdfile, "%" PRIDX " %" PRIDX, nvertices, cellconruns[nvertices] / 2);
fprintf(simplefile, "%" PRIDX " %" PRIDX, nvertices,
cellconruns[nvertices] / 2);
if (havevertexweight || havevertexsize || haveedgeweight) {
fprintf(weightfile, "%" PRIDX " %" PRIDX, nvertices,
cellconruns[nvertices] / 2);
fprintf(stdfile, " %d%d%d", havevertexsize, havevertexweight,
haveedgeweight);
fprintf(weightfile, " %d%d%d", havevertexsize, havevertexweight,
haveedgeweight);
if (havevertexweight) {
fprintf(stdfile, " %d", (int)nvertexweights);
fprintf(weightfile, " %d", (int)nvertexweights);
} }
/* Write the rest of the graph. */
for (idx_t i = 0; i < nvertices; i++) {
fprintf(stdfile, "\n");
fprintf(simplefile, "\n");
if (weightfile != NULL) {
fprintf(weightfile, "\n");
}
if (havevertexsize) {
fprintf(stdfile, " %" PRIDX, vertexsizes[i]);
fprintf(weightfile, " %" PRIDX, vertexsizes[i]);
}
if (havevertexweight) {
for (idx_t j = 0; j < nvertexweights; j++) {
fprintf(stdfile, " %" PRIDX, vertexweights[i * nvertexweights + j]);
fprintf(weightfile, " %" PRIDX, vertexweights[i * nvertexweights + j]);
}
}
for (idx_t j = cellconruns[i]; j < cellconruns[i + 1]; j++) {
fprintf(stdfile, " %" PRIDX, cellcon[j] + 1);
fprintf(simplefile, " %" PRIDX, cellcon[j] + 1);
if (haveedgeweight) {
fprintf(stdfile, " %" PRIDX, edgeweights[j]);
fprintf(weightfile, " %" PRIDX, edgeweights[j]);
}
}
}
fprintf(stdfile, "\n");
fprintf(simplefile, "\n");
if (weightfile != NULL) {
fprintf(weightfile, "\n");
}
fclose(stdfile);
fclose(simplefile);
if (weightfile != NULL) {
fclose(weightfile);
}
}
#endif /* HAVE_METIS */
#ifdef HAVE_MPI
/**
* @brief Dump the positions and MPI ranks of the given top-level cells
* to a simple text file.
*
* Can be used to visualise the partitioning of an MPI run. Note should
* be used immediately after repartitioning when the top-level cells
* have been assigned their nodes. Each time this is called a new file
* with the given prefix, a unique integer and type of .dat is created.
*
* @param prefix base output filename
* @param cells_top the top-level cells.
* @param nr_cells the number of cells.
*/
void dumpCellRanks(const char *prefix, struct cell *cells_top, int nr_cells) {
FILE *file = NULL;
/* Name of output file. */
static int nseq = 0;
char fname[200];
sprintf(fname, "%s_%03d.dat", prefix, nseq);
nseq++;
file = fopen(fname, "w");
/* Header. */
fprintf(file, "# %6s %6s %6s %6s %6s %6s %6s\n", "x", "y", "z", "xw", "yw",
"zw", "rank");
/* Output */
for (int i = 0; i < nr_cells; i++) {
struct cell *c = &cells_top[i];
fprintf(file, " %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %6d\n", c->loc[0],
c->loc[1], c->loc[2], c->width[0], c->width[1], c->width[2],
c->nodeID);
}
fclose(file);
}
#endif /* HAVE_MPI */
/**
* @brief parse the process /proc/self/statm file to get the process
* memory use (in KB). Top field in ().
*
* @param size total virtual memory (VIRT)
* @param resident resident non-swapped memory (RES)
* @param share shared (mmap'd) memory (SHR)
* @param trs text (exe) resident set (CODE)
* @param lrs library resident set
* @param drs data+stack resident set (DATA)
* @param dt dirty pages (nDRT)
*/
void getProcMemUse(long *size, long *resident, long *share, long *trs,
long *lrs, long *drs, long *dt) {
/* Open the file. */
FILE *file = fopen("/proc/self/statm", "r");
if (file != NULL) {
int nscan = fscanf(file, "%ld %ld %ld %ld %ld %ld %ld", size, resident,
share, trs, lrs, drs, dt);
if (nscan == 7) {
/* Convert pages into bytes. Usually 4096, but could be 512 on some
* systems so take care in conversion to KB. */
long sz = sysconf(_SC_PAGESIZE);
*size *= sz;
*resident *= sz;
*share *= sz;
*trs *= sz;
*lrs *= sz;
*drs *= sz;
*dt *= sz;
*size /= 1024;
*resident /= 1024;
*share /= 1024;
*trs /= 1024;
*lrs /= 1024;
*drs /= 1024;
*dt /= 1024;
} else {
error("Failed to read sufficient fields from /proc/self/statm");
}
fclose(file);
} else {
error("Failed to open /proc/self/statm");
}
}
/**
* @brief Print the current memory use of the process. A la "top". */
void printProcMemUse() {
long size;
long resident;
long share;
long trs;
long lrs;
long drs;
long dt;
getProcMemUse(&size, &resident, &share, &trs, &lrs, &drs, &dt);
printf("## VIRT = %ld , RES = %ld , SHR = %ld , CODE = %ld, DATA = %ld\n",
size, resident, share, trs, drs);
fflush(stdout);
}