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Merged
merged 5 commits into from
Jun 21, 2019
Merged

Reduce gridlink memory footprint #186

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3a9907f
* Reduce gridlink memory footprint for autocorrelations
lgarrison Jun 18, 2019
80d8f5b
Update changelog
lgarrison Jun 18, 2019
68b13a0
Reduced the size of the cell_pair struct
manodeep Jun 18, 2019
c9bbeda
(Hopefully) Made the changelog entry clearer [ci skip]
manodeep Jun 18, 2019
9ed92bc
Fix Python version so Travis will run
lgarrison Jun 18, 2019
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10 changes: 9 additions & 1 deletion CHANGES.rst
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Expand Up @@ -10,9 +10,17 @@ New features
- conda installable package
- GPU version

2.3.0 (upcoming)
2.3.1 (upcoming)
================

Enhancements
------------
- Reduce memory footprint of the cell pairs [#186]


2.3.0 (2019-05-20)
==================

**Breaking Changes**
--------------------

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2 changes: 1 addition & 1 deletion Corrfunc/__init__.py
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Expand Up @@ -10,7 +10,7 @@
unicode_literals)
import os

__version__ = "2.3.0"
__version__ = "2.3.1"
__author__ = "Manodeep Sinha <manodeep@gmail.com>"


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2 changes: 1 addition & 1 deletion common.mk
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Expand Up @@ -41,7 +41,7 @@ OPT += -DUSE_OMP
DISTNAME:=Corrfunc
MAJOR:=2
MINOR:=3
PATCHLEVEL:=0
PATCHLEVEL:=1
VERSION:=$(MAJOR).$(MINOR).$(PATCHLEVEL)
ABI_COMPAT_VERSION:=$(MAJOR).0
# Whenever conda needs to be checked again
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11 changes: 7 additions & 4 deletions mocks/DDrppi_mocks/countpairs_rp_pi_mocks_impl.c.src
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Expand Up @@ -625,10 +625,13 @@ int countpairs_mocks_DOUBLE(const int64_t ND1, DOUBLE *ra1, DOUBLE *dec1, DOUBLE
DOUBLE *this_rpavg = options->need_avg_sep ? rpavg:NULL;
DOUBLE *this_weightavg = need_weightavg ? weightavg:NULL;

const int status = countpairs_rp_pi_mocks_function_DOUBLE(this_cell_pair->N1, this_cell_pair->x1,
this_cell_pair->y1, this_cell_pair->z1, this_cell_pair->weights1,
this_cell_pair->N2, this_cell_pair->x2,
this_cell_pair->y2, this_cell_pair->z2, this_cell_pair->weights2,
const int64_t icell = this_cell_pair->cellindex1;
const int64_t icell2 = this_cell_pair->cellindex2;
const cellarray_mocks_DOUBLE *first = &lattice1[icell];
const cellarray_mocks_DOUBLE *second = &lattice2[icell2];

const int status = countpairs_rp_pi_mocks_function_DOUBLE(first->nelements, first->x, first->y, first->z, &(first->weights),
second->nelements, second->x, second->y, second->z, &(second->weights),
this_cell_pair->same_cell,
options->fast_divide_and_NR_steps,
sqr_rpmax, sqr_rpmin, nrpbin, npibin, rupp_sqr, pimax,
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11 changes: 7 additions & 4 deletions mocks/DDsmu_mocks/countpairs_s_mu_mocks_impl.c.src
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Expand Up @@ -631,10 +631,13 @@ int countpairs_mocks_s_mu_DOUBLE(const int64_t ND1, DOUBLE *ra1, DOUBLE *dec1, D
DOUBLE *this_savg = options->need_avg_sep ? &(savg[0]):NULL;
DOUBLE *this_weightavg = need_weightavg ? weightavg:NULL;

const int status = countpairs_s_mu_mocks_function_DOUBLE(this_cell_pair->N1, this_cell_pair->x1,
this_cell_pair->y1, this_cell_pair->z1, this_cell_pair->weights1,
this_cell_pair->N2, this_cell_pair->x2,
this_cell_pair->y2, this_cell_pair->z2, this_cell_pair->weights2,
const int64_t icell = this_cell_pair->cellindex1;
const int64_t icell2 = this_cell_pair->cellindex2;
const cellarray_mocks_DOUBLE *first = &lattice1[icell];
const cellarray_mocks_DOUBLE *second = &lattice2[icell2];

const int status = countpairs_s_mu_mocks_function_DOUBLE(first->nelements, first->x, first->y, first->z, &(first->weights),
second->nelements, second->x, second->y, second->z, &(second->weights),
this_cell_pair->same_cell,
options->fast_divide_and_NR_steps,
sqr_smax, sqr_smin, nsbin, nmu_bins, supp_sqr, mu_max,
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11 changes: 7 additions & 4 deletions mocks/DDtheta_mocks/countpairs_theta_mocks_impl.c.src
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Expand Up @@ -1007,10 +1007,13 @@ int countpairs_theta_mocks_DOUBLE(const int64_t ND1, DOUBLE *ra1, DOUBLE *dec1,
DOUBLE *this_thetaavg = options->need_avg_sep ? thetaavg:NULL;
DOUBLE *this_weightavg = need_weightavg ? weightavg:NULL;

const int status = countpairs_theta_mocks_function_DOUBLE(this_cell_pair->N1, this_cell_pair->x1,
this_cell_pair->y1, this_cell_pair->z1, this_cell_pair->weights1,
this_cell_pair->N2, this_cell_pair->x2,
this_cell_pair->y2, this_cell_pair->z2, this_cell_pair->weights2,
const int64_t icell = this_cell_pair->cellindex1;
const int64_t icell2 = this_cell_pair->cellindex2;
const cellarray_mocks_DOUBLE *first = &lattice1[icell];
const cellarray_mocks_DOUBLE *second = &lattice2[icell2];

const int status = countpairs_theta_mocks_function_DOUBLE(first->nelements, first->x, first->y, first->z, &(first->weights),
second->nelements, second->x, second->y, second->z, &(second->weights),
this_cell_pair->same_cell,
options->fast_acos,
costhetamax, costhetamin, nthetabin,
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11 changes: 7 additions & 4 deletions theory/DD/countpairs_impl.c.src
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Expand Up @@ -452,10 +452,13 @@ int countpairs_DOUBLE(const int64_t ND1, DOUBLE *X1, DOUBLE *Y1, DOUBLE *Z1,
DOUBLE *this_rpavg = options->need_avg_sep ? rpavg:NULL;
DOUBLE *this_weightavg = need_weightavg ? weightavg:NULL;

const int status = countpairs_function_DOUBLE(this_cell_pair->N1, this_cell_pair->x1,
this_cell_pair->y1, this_cell_pair->z1, this_cell_pair->weights1,
this_cell_pair->N2, this_cell_pair->x2,
this_cell_pair->y2, this_cell_pair->z2, this_cell_pair->weights2,
const int64_t icell = this_cell_pair->cellindex1;
const int64_t icell2 = this_cell_pair->cellindex2;
const cellarray_DOUBLE *first = &lattice1[icell];
const cellarray_DOUBLE *second = &lattice2[icell2];

const int status = countpairs_function_DOUBLE(first->nelements, first->x, first->y, first->z, &(first->weights),
second->nelements, second->x, second->y, second->z, &(second->weights),
this_cell_pair->same_cell,
sqr_rpmax, sqr_rpmin, nrpbin, rupp_sqr, pimax, //pimax is simply rpmax cast to DOUBLE
this_cell_pair->xwrap, this_cell_pair->ywrap, this_cell_pair->zwrap,
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11 changes: 7 additions & 4 deletions theory/DDrppi/countpairs_rp_pi_impl.c.src
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Expand Up @@ -446,10 +446,13 @@ int countpairs_rp_pi_DOUBLE(const int64_t ND1, DOUBLE *X1, DOUBLE *Y1, DOUBLE *Z
DOUBLE *this_rpavg = options->need_avg_sep ? rpavg:NULL;
DOUBLE *this_weightavg = need_weightavg ? weightavg:NULL;

const int status = countpairs_rp_pi_function_DOUBLE(this_cell_pair->N1, this_cell_pair->x1,
this_cell_pair->y1, this_cell_pair->z1, this_cell_pair->weights1,
this_cell_pair->N2, this_cell_pair->x2,
this_cell_pair->y2, this_cell_pair->z2, this_cell_pair->weights2,
const int64_t icell = this_cell_pair->cellindex1;
const int64_t icell2 = this_cell_pair->cellindex2;
const cellarray_DOUBLE *first = &lattice1[icell];
const cellarray_DOUBLE *second = &lattice2[icell2];

const int status = countpairs_rp_pi_function_DOUBLE(first->nelements, first->x, first->y, first->z, &(first->weights),
second->nelements, second->x, second->y, second->z, &(second->weights),
this_cell_pair->same_cell,
sqr_rpmax, sqr_rpmin, nrpbin, npibin, rupp_sqr, pimax,
this_cell_pair->xwrap, this_cell_pair->ywrap, this_cell_pair->zwrap,
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11 changes: 7 additions & 4 deletions theory/DDsmu/countpairs_s_mu_impl.c.src
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Expand Up @@ -466,10 +466,13 @@ int countpairs_s_mu_DOUBLE(const int64_t ND1, DOUBLE *X1, DOUBLE *Y1, DOUBLE *Z1
DOUBLE *this_rpavg = options->need_avg_sep ? savg:NULL;
DOUBLE *this_weightavg = need_weightavg ? weightavg:NULL;

const int status = countpairs_s_mu_function_DOUBLE(this_cell_pair->N1, this_cell_pair->x1,
this_cell_pair->y1, this_cell_pair->z1, this_cell_pair->weights1,
this_cell_pair->N2, this_cell_pair->x2,
this_cell_pair->y2, this_cell_pair->z2, this_cell_pair->weights2,
const int64_t icell = this_cell_pair->cellindex1;
const int64_t icell2 = this_cell_pair->cellindex2;
const cellarray_DOUBLE *first = &lattice1[icell];
const cellarray_DOUBLE *second = &lattice2[icell2];

const int status = countpairs_s_mu_function_DOUBLE(first->nelements, first->x, first->y, first->z, &(first->weights),
second->nelements, second->x, second->y, second->z, &(second->weights),
this_cell_pair->same_cell,
options->fast_divide_and_NR_steps,
sqr_smax, sqr_smin, nsbin, nmu_bins, supp_sqr, mu_max, pimax,
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13 changes: 8 additions & 5 deletions theory/wp/countpairs_wp_impl.c.src
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Expand Up @@ -427,10 +427,13 @@ int countpairs_wp_DOUBLE(const int64_t ND, DOUBLE * restrict X, DOUBLE * restric
current_utc_time(&tcell_start);
}

const int status = wp_function_DOUBLE(this_cell_pair->x1, this_cell_pair->y1, this_cell_pair->z1,
this_cell_pair->weights1, this_cell_pair->N1,
this_cell_pair->x2, this_cell_pair->y2, this_cell_pair->z2,
this_cell_pair->weights2, this_cell_pair->N2,
const int64_t icell = this_cell_pair->cellindex1;
const int64_t icell2 = this_cell_pair->cellindex2;
const cellarray_DOUBLE *first = &lattice[icell];
const cellarray_DOUBLE *second = &lattice[icell2];

const int status = wp_function_DOUBLE(first->x, first->y, first->z, &(first->weights), first->nelements,
second->x, second->y, second->z, &(second->weights), second->nelements,
this_cell_pair->same_cell,
sqr_rpmax, sqr_rpmin, nrpbins, rupp_sqr, pimax,
this_cell_pair->xwrap, this_cell_pair->ywrap, this_cell_pair->zwrap,
Expand All @@ -448,7 +451,7 @@ int countpairs_wp_DOUBLE(const int64_t ND, DOUBLE * restrict X, DOUBLE * restric
current_utc_time(&tcell_end);
double time_in_ns = REALTIME_ELAPSED_NS(tcell_start, tcell_end);
struct api_cell_timings *base_cell = &(options->cell_timings[icellpair]);
ASSIGN_CELL_TIMINGS(base_cell, this_cell_pair->N1, this_cell_pair->N2, time_in_ns,
ASSIGN_CELL_TIMINGS(base_cell, first->nelements, second->nelements, time_in_ns,
tid, this_cell_pair->cellindex1, this_cell_pair->cellindex2);
}
}//abort-status
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11 changes: 7 additions & 4 deletions theory/xi/countpairs_xi_impl.c.src
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Expand Up @@ -395,10 +395,13 @@ int countpairs_xi_DOUBLE(const int64_t ND, DOUBLE * restrict X, DOUBLE * restric
DOUBLE *this_rpavg = options->need_avg_sep ? ravg:NULL;
DOUBLE *this_weightavg = need_weightavg ? weightavg:NULL;

const int status = xi_function_DOUBLE(this_cell_pair->x1, this_cell_pair->y1, this_cell_pair->z1,
this_cell_pair->weights1, this_cell_pair->N1,
this_cell_pair->x2, this_cell_pair->y2, this_cell_pair->z2,
this_cell_pair->weights2, this_cell_pair->N2,
const int64_t icell = this_cell_pair->cellindex1;
const int64_t icell2 = this_cell_pair->cellindex2;
const cellarray_DOUBLE *first = &lattice[icell];
const cellarray_DOUBLE *second = &lattice[icell2];

const int status = xi_function_DOUBLE(first->x, first->y, first->z, &(first->weights), first->nelements,
second->x, second->y, second->z, &(second->weights), second->nelements,
this_cell_pair->same_cell,
sqr_rmax, sqr_rmin, nbins, rupp_sqr,
this_cell_pair->xwrap, this_cell_pair->ywrap, this_cell_pair->zwrap,
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23 changes: 0 additions & 23 deletions utils/cell_pair.h.src
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Expand Up @@ -18,20 +18,7 @@ extern "C" {
#include "weight_defs_DOUBLE.h"

struct cell_pair_DOUBLE{
int64_t N1;
DOUBLE *x1;
DOUBLE *y1;
DOUBLE *z1;
int64_t *orig_index1;
weight_struct_DOUBLE *weights1;
int64_t cellindex1;

int64_t N2;
DOUBLE *x2;
DOUBLE *y2;
DOUBLE *z2;
int64_t *orig_index2;
weight_struct_DOUBLE *weights2;
int64_t cellindex2;

DOUBLE xwrap;
Expand All @@ -47,16 +34,6 @@ struct cell_pair_DOUBLE{
DOUBLE closest_z1;

int8_t same_cell;
union{
int16_t xbin_offset;
int16_t ra_bin_offset;
};
union{
int16_t ybin_offset;
int16_t dec_bin_offset;
};
int16_t zbin_offset;
int8_t unused;//explicitly adding here for alignment
};

#ifdef __cplusplus
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2 changes: 1 addition & 1 deletion utils/defs.h
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Expand Up @@ -19,7 +19,7 @@
extern "C" {
#endif

#define API_VERSION STR("2.3.0")
#define API_VERSION STR("2.3.1")

typedef enum {
DEFAULT=-42,/* present simply to make the enum a signed int*/
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29 changes: 10 additions & 19 deletions utils/gridlink_impl.c.src
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Expand Up @@ -428,9 +428,17 @@ struct cell_pair_DOUBLE * generate_cell_pairs_DOUBLE(struct cellarray_DOUBLE *la
const int64_t nx_ngb = 2*xbin_refine_factor + 1;
const int64_t ny_ngb = 2*ybin_refine_factor + 1;
const int64_t nz_ngb = 2*zbin_refine_factor + 1;
const int64_t max_ngb_cells = nx_ngb * ny_ngb * nz_ngb;
const int64_t max_ngb_cells = nx_ngb * ny_ngb * nz_ngb - 1; // -1 for self

const int64_t max_num_cell_pairs = totncells * max_ngb_cells;

if( ! (autocorr == 0 || autocorr == 1) ) {
fprintf(stderr,"Error: Strange value of autocorr = %d. Expected to receive either 1 (auto-correlations) or 0 (cross-correlations)\n", autocorr);
return NULL;
}
const int64_t num_self_pairs = totncells;
const int64_t num_nonself_pairs = totncells * max_ngb_cells / (1 + autocorr);

const int64_t max_num_cell_pairs = num_self_pairs + num_nonself_pairs;
int64_t num_cell_pairs = 0;
struct cell_pair_DOUBLE *all_cell_pairs = my_malloc(sizeof(*all_cell_pairs), max_num_cell_pairs);
XRETURN(all_cell_pairs != NULL, NULL,
Expand Down Expand Up @@ -542,20 +550,7 @@ struct cell_pair_DOUBLE * generate_cell_pairs_DOUBLE(struct cellarray_DOUBLE *la
//If we have reached here, then this cell *MIGHT* have a pair. We
//need to add a cell-pair to the array of all cell-pairs
struct cell_pair_DOUBLE *this_cell_pair = &all_cell_pairs[num_cell_pairs];
this_cell_pair->N1 = first->nelements;
this_cell_pair->x1 = first->x;
this_cell_pair->y1 = first->y;
this_cell_pair->z1 = first->z;
this_cell_pair->orig_index1 = first->original_index;
this_cell_pair->weights1 = &first->weights;
this_cell_pair->cellindex1 = icell;

this_cell_pair->N2 = second->nelements;
this_cell_pair->x2 = second->x;
this_cell_pair->y2 = second->y;
this_cell_pair->z2 = second->z;
this_cell_pair->orig_index2 = second->original_index;
this_cell_pair->weights2 = &second->weights;
this_cell_pair->cellindex2 = icell2;

this_cell_pair->xwrap = off_xwrap;
Expand All @@ -570,10 +565,6 @@ struct cell_pair_DOUBLE * generate_cell_pairs_DOUBLE(struct cellarray_DOUBLE *la
this_cell_pair->closest_y1 = closest_y1;
this_cell_pair->closest_z1 = closest_z1;

this_cell_pair->xbin_offset = iix;
this_cell_pair->ybin_offset = iiy;
this_cell_pair->zbin_offset = iiz;

this_cell_pair->same_cell = (autocorr == 1 && icell2 == icell) ? 1:0;

num_cell_pairs++;
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