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Merge pull request #19 from sfiligoi/igor_deprecate_n_2
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Rename some of the variables to clarify semantics. No change in behavior
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@sfiligoi
sfiligoi authored Nov 30, 2022
2 parents d66fda3 + 8189e80 commit c7783a8
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Showing 2 changed files with 26 additions and 23 deletions.
17 changes: 10 additions & 7 deletions src/api.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,9 @@
#define MMAP_FD_MASK 0x0fff
#define MMAP_FLAG 0x1000

// Note: Threading is now full controlled by OpenMP.
// Any threads variable is really referring to n_substeps.
// The old naming was retained to minimize code refactoring.

#define SETUP_TDBG(method) const char *tdbg_method=method; \
bool print_tdbg = false;\
Expand Down Expand Up @@ -358,7 +361,7 @@ void set_tasks(std::vector<su::task_parameters> &tasks,
unsigned int stripe_start,
unsigned int stripe_stop,
bool bypass_tips,
unsigned int nthreads) {
unsigned int n_tasks) {

// compute from start to the max possible stripe if stop doesn't make sense
if(stripe_stop <= stripe_start)
Expand All @@ -369,16 +372,16 @@ void set_tasks(std::vector<su::task_parameters> &tasks,
*
* we use the remaining the chunksize for bins which cannot be full maximally
*/
unsigned int fullchunk = ((stripe_stop - stripe_start) + nthreads - 1) / nthreads; // this computes the ceiling
unsigned int smallchunk = (stripe_stop - stripe_start) / nthreads;
unsigned int fullchunk = ((stripe_stop - stripe_start) + n_tasks - 1) / n_tasks; // this computes the ceiling
unsigned int smallchunk = (stripe_stop - stripe_start) / n_tasks;

unsigned int n_fullbins = (stripe_stop - stripe_start) % nthreads;
unsigned int n_fullbins = (stripe_stop - stripe_start) % n_tasks;
if(n_fullbins == 0)
n_fullbins = nthreads;
n_fullbins = n_tasks;

unsigned int start = stripe_start;

for(unsigned int tid = 0; tid < nthreads; tid++) {
for(unsigned int tid = 0; tid < n_tasks; tid++) {
tasks[tid].tid = tid;
tasks[tid].start = start; // stripe start
tasks[tid].bypass_tips = bypass_tips;
Expand Down Expand Up @@ -1463,7 +1466,7 @@ MergeStatus validate_partial(const partial_dyn_mat_t* const * partial_mats, int
}


MergeStatus merge_partial(partial_mat_t** partial_mats, int n_partials, unsigned int nthreads, mat_t** result) {
MergeStatus merge_partial(partial_mat_t** partial_mats, int n_partials, unsigned int dummy, mat_t** result) {
MergeStatus err = check_partial(partial_mats, n_partials, false);
if (err!=merge_okay) return err;

Expand Down
32 changes: 16 additions & 16 deletions src/api.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -171,7 +171,7 @@ EXTERN void destroy_results_vec(r_vec** result);
* variance_adjust <bool> whether to apply variance adjustment.
* alpha <double> GUniFrac alpha, only relevant if method == generalized.
* bypass_tips <bool> disregard tips, reduces compute by about 50%
* threads <uint> the number of threads to use.
* n_substeps <uint> the number of substeps to use.
* result <mat_t**> the resulting distance matrix in condensed form, this is initialized within the method so using **
*
* one_off returns the following error codes:
Expand All @@ -184,7 +184,7 @@ EXTERN void destroy_results_vec(r_vec** result);
*/
EXTERN ComputeStatus one_off(const char* biom_filename, const char* tree_filename,
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, unsigned int threads, mat_t** result);
bool bypass_tips, unsigned int n_substeps, mat_t** result);


/* Compute UniFrac - against in-memory objects returning full form matrix
Expand All @@ -195,7 +195,7 @@ EXTERN ComputeStatus one_off(const char* biom_filename, const char* tree_filenam
* variance_adjust <bool> whether to apply variance adjustment.
* alpha <double> GUniFrac alpha, only relevant if method == generalized.
* bypass_tips <bool> disregard tips, reduces compute by about 50%
* threads <uint> the number of threads to use.
* n_substeps <uint> the number of substeps to use.
* result <mat_full_fp64_t**> the resulting distance matrix in full form, this is initialized within the method so using **
*
* one_off_inmem returns the following error codes:
Expand All @@ -206,7 +206,7 @@ EXTERN ComputeStatus one_off(const char* biom_filename, const char* tree_filenam
*/
EXTERN ComputeStatus one_off_inmem(const support_biom_t *table_data, const support_bptree_t *tree_data,
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, unsigned int threads, mat_full_fp64_t** result);
bool bypass_tips, unsigned int n_substeps, mat_full_fp64_t** result);

/* Compute UniFrac - against in-memory objects returning full form matrix, fp32
*
Expand All @@ -216,7 +216,7 @@ EXTERN ComputeStatus one_off_inmem(const support_biom_t *table_data, const suppo
* variance_adjust <bool> whether to apply variance adjustment.
* alpha <double> GUniFrac alpha, only relevant if method == generalized.
* bypass_tips <bool> disregard tips, reduces compute by about 50%
* threads <uint> the number of threads to use.
* n_substeps <uint> the number of substeps to use.
* result <mat_full_fp32_t**> the resulting distance matrix in full form, this is initialized within the method so using **
*
* one_off_inmem returns the following error codes:
Expand All @@ -227,7 +227,7 @@ EXTERN ComputeStatus one_off_inmem(const support_biom_t *table_data, const suppo
*/
EXTERN ComputeStatus one_off_inmem_fp32(const support_biom_t *table_data, const support_bptree_t *tree_data,
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, unsigned int threads, mat_full_fp32_t** result);
bool bypass_tips, unsigned int n_substeps, mat_full_fp32_t** result);

/* Compute UniFrac - matrix form
*
Expand All @@ -237,7 +237,7 @@ EXTERN ComputeStatus one_off_inmem_fp32(const support_biom_t *table_data, const
* variance_adjust <bool> whether to apply variance adjustment.
* alpha <double> GUniFrac alpha, only relevant if method == generalized.
* bypass_tips <bool> disregard tips, reduces compute by about 50%
* threads <uint> the number of threads/blocks to use.
* n_substeps <uint> the number of substeps/blocks to use.
* mmap_dir <const char*> If not NULL, area to use for temp memory storage
* result <mat_full_fp64_t**> the resulting distance matrix in matrix form, this is initialized within the method so using **
*
Expand All @@ -251,7 +251,7 @@ EXTERN ComputeStatus one_off_inmem_fp32(const support_biom_t *table_data, const
*/
EXTERN ComputeStatus one_off_matrix(const char* biom_filename, const char* tree_filename,
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, unsigned int nthreads,
bool bypass_tips, unsigned int n_substeps,
const char *mmap_dir,
mat_full_fp64_t** result);

Expand All @@ -263,7 +263,7 @@ EXTERN ComputeStatus one_off_matrix(const char* biom_filename, const char* tree_
* variance_adjust <bool> whether to apply variance adjustment.
* alpha <double> GUniFrac alpha, only relevant if method == generalized.
* bypass_tips <bool> disregard tips, reduces compute by about 50%
* threads <uint> the number of threads/blocks to use.
* n_substeps <uint> the number of substeps/blocks to use.
* mmap_dir <const char*> If not NULL, area to use for temp memory storage
* result <mat_full_fp32_t**> the resulting distance matrix in matrix form, this is initialized within the method so using **
*
Expand All @@ -277,7 +277,7 @@ EXTERN ComputeStatus one_off_matrix(const char* biom_filename, const char* tree_
*/
EXTERN ComputeStatus one_off_matrix_fp32(const char* biom_filename, const char* tree_filename,
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, unsigned int nthreads,
bool bypass_tips, unsigned int n_substeps,
const char *mmap_dir,
mat_full_fp32_t** result);

Expand Down Expand Up @@ -306,7 +306,7 @@ EXTERN ComputeStatus faith_pd_one_off(const char* biom_filename, const char* tre
* variance_adjust <bool> whether to apply variance adjustment.
* alpha <double> GUniFrac alpha, only relevant if method == generalized.
* bypass_tips <bool> disregard tips, reduces compute by about 50%
* threads <uint> the number of threads to use.
* n_substeps <uint> the number of substeps to use.
* format <const char*> output format to use.
* pcoa_dims <uint> if not 0, number of dimensions to use or PCoA
* mmap_dir <const char*> if not empty, temp dir to use for disk-based memory
Expand All @@ -322,7 +322,7 @@ EXTERN ComputeStatus faith_pd_one_off(const char* biom_filename, const char* tre
*/
EXTERN ComputeStatus unifrac_to_file(const char* biom_filename, const char* tree_filename, const char* out_filename,
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, unsigned int threads, const char* format,
bool bypass_tips, unsigned int n_substeps, const char* format,
unsigned int pcoa_dims, const char *mmap_dir);

/* Write a matrix object
Expand Down Expand Up @@ -429,7 +429,7 @@ EXTERN IOStatus write_vec(const char* filename, r_vec* result);
* variance_adjust <bool> whether to apply variance adjustment.
* alpha <double> GUniFrac alpha, only relevant if method == generalized.
* bypass_tips <bool> disregard tips, reduces compute by about 50%
* threads <uint> the number of threads to use.
* n_substeps <uint> the number of substeps to use.
* stripe_start <uint> the starting stripe to compute
* stripe_stop <uint> the last stripe to compute
* dm_stripes <vector of double*> the unique branch length stripes. This is expected to be
Expand All @@ -448,7 +448,7 @@ EXTERN IOStatus write_vec(const char* filename, r_vec* result);

EXTERN ComputeStatus partial(const char* biom_filename, const char* tree_filename,
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, unsigned int threads, unsigned int stripe_start,
bool bypass_tips, unsigned int n_substeps, unsigned int stripe_start,
unsigned int stripe_stop, partial_mat_t** result);

/* Write a partial matrix object
Expand Down Expand Up @@ -558,7 +558,7 @@ EXTERN MergeStatus validate_partial(const partial_dyn_mat_t* const * partial_mat
* sample_id_consistency : samples described by stripes are inconsistent
* square_mismatch : inconsistency on denotation of square matrix
*/
EXTERN MergeStatus merge_partial(partial_mat_t** partial_mats, int n_partials, unsigned int nthreads, mat_t** result);
EXTERN MergeStatus merge_partial(partial_mat_t** partial_mats, int n_partials, unsigned int dummy, mat_t** result);

/* Merge partial results
*
Expand Down Expand Up @@ -651,6 +651,6 @@ void set_tasks(std::vector<su::task_parameters> &tasks,
unsigned int stripe_start,
unsigned int stripe_stop,
bool bypass_tips,
unsigned int nthreads);
unsigned int n_tasks);

#endif

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