[Genabel-commits] r1263 - pkg/OmicABEL/src

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Mon Jul 1 10:50:00 CEST 2013 

Author: dfabregat
Date: 2013-07-01 10:50:00 +0200 (Mon, 01 Jul 2013)
New Revision: 1263

Modified:
   pkg/OmicABEL/src/GWAS.c
   pkg/OmicABEL/src/REML.c
   pkg/OmicABEL/src/fgls_chol.c
   pkg/OmicABEL/src/fgls_eigen.c
   pkg/OmicABEL/src/ooc_BLAS.c
   pkg/OmicABEL/src/ooc_BLAS.h
   pkg/OmicABEL/src/utils.c
   pkg/OmicABEL/src/utils.h
Log:
Parallelizing the impute of data.


Modified: pkg/OmicABEL/src/GWAS.c
===================================================================
--- pkg/OmicABEL/src/GWAS.c	2013-06-30 18:53:54 UTC (rev 1262)
+++ pkg/OmicABEL/src/GWAS.c	2013-07-01 08:50:00 UTC (rev 1263)
@@ -121,7 +121,7 @@
 	load_file ( cf->XL_data_path,   "rb", cf->XL,   cf->n * cf->wXL );
 	// Sanity check (XL)
 	average( cf->XL, cf->n, cf->wXL, cf->threshold, "Covariate", 
-			&cf->XL_fvi->fvi_data[cf->n*NAMELENGTH], NAMELENGTH, 1 );
+			&cf->XL_fvi->fvi_data[cf->n*NAMELENGTH], NAMELENGTH, 1, cf->num_threads );
 	cf->ZtXL = NULL;
 	cf->Z    = NULL;
 	cf->W    = NULL;

Modified: pkg/OmicABEL/src/REML.c
===================================================================
--- pkg/OmicABEL/src/REML.c	2013-06-30 18:53:54 UTC (rev 1262)
+++ pkg/OmicABEL/src/REML.c	2013-07-01 08:50:00 UTC (rev 1263)
@@ -84,7 +84,7 @@
 	premultiplyXL( data.n, data.wXL, data.Z, data.X, data.ZtX );
 	// Premultiply ZtY
 	ooc_gemm( data.n, cf->t, cf->ooc_b, data.Z, cf->Y_data_path, cf->ZtY_path,
-			cf->threshold, "TRAIT", &cf->Y_fvi->fvi_data[cf->n*NAMELENGTH], NAMELENGTH);
+			cf->threshold, "TRAIT", &cf->Y_fvi->fvi_data[cf->n*NAMELENGTH], NAMELENGTH, cf->num_threads);
 
 	// Iterate over phenotypes (Y)
 	data.Y = fgls_malloc( data.n * sizeof(double) );
@@ -95,7 +95,7 @@
 	{
 		sync_read( data.Y, cf->Y, cf->n, cf->n * j );
 		// Sanity
-		average( data.Y, cf->n, 1, cf->threshold, "TRAIT", &cf->Y_fvi->fvi_data[(cf->n+j)*NAMELENGTH], NAMELENGTH, 0 );
+		average( data.Y, cf->n, 1, cf->threshold, "TRAIT", &cf->Y_fvi->fvi_data[(cf->n+j)*NAMELENGTH], NAMELENGTH, 0, cf->num_threads );
 
 		sync_read( data.ZtY, cf->ZtY, cf->n, cf->n * j );
 		data.sigma = variance(data.Y, data.n);

Modified: pkg/OmicABEL/src/fgls_chol.c
===================================================================
--- pkg/OmicABEL/src/fgls_chol.c	2013-06-30 18:53:54 UTC (rev 1262)
+++ pkg/OmicABEL/src/fgls_chol.c	2013-07-01 08:50:00 UTC (rev 1263)
@@ -216,7 +216,7 @@
 		Y_comp = double_buffering_get_comp_buffer( &db_Y );
 		// Sanity check
 		average( Y_comp, n, 1, cf.threshold, "TRAIT", 
-				&cf.Y_fvi->fvi_data[n*NAMELENGTH], NAMELENGTH, 0 );
+				&cf.Y_fvi->fvi_data[n*NAMELENGTH], NAMELENGTH, 0, cf.num_threads );
         dtrsv_(LOWER, NO_TRANS, NON_UNIT, &n, M, &n, Y_comp, &iONE);
 
         /* B_t := XL' * y */
@@ -264,7 +264,7 @@
             int rhss  = wXR * x_inc;
 			// Sanity check
 			average( XR_comp, n, x_inc, cf.threshold, "SNP", 
-					&cf.XR_fvi->fvi_data[(n+ib)*NAMELENGTH], NAMELENGTH, 1 );
+					&cf.XR_fvi->fvi_data[(n+ib)*NAMELENGTH], NAMELENGTH, 1, cf.num_threads );
 			// Computation
             dtrsm_(LEFT, LOWER, NO_TRANS, NON_UNIT, &n, &rhss, &ONE, M, &n, XR_comp, &n);
 

Modified: pkg/OmicABEL/src/fgls_eigen.c
===================================================================
--- pkg/OmicABEL/src/fgls_eigen.c	2013-06-30 18:53:54 UTC (rev 1262)
+++ pkg/OmicABEL/src/fgls_eigen.c	2013-07-01 08:50:00 UTC (rev 1263)
@@ -73,7 +73,7 @@
 
     // Premultiply Z' XR
     ooc_gemm( cf->n, cf->m * cf->wXR, cf->ooc_b, cf->Z, cf->XR_data_path, cf->ZtXR_path,
-			cf->threshold, "SNP", &cf->XR_fvi->fvi_data[cf->n*NAMELENGTH], NAMELENGTH );
+			cf->threshold, "SNP", &cf->XR_fvi->fvi_data[cf->n*NAMELENGTH], NAMELENGTH, cf->num_threads );
     
 #if VAMPIR
     VT_USER_END("PRELOOP");

Modified: pkg/OmicABEL/src/ooc_BLAS.c
===================================================================
--- pkg/OmicABEL/src/ooc_BLAS.c	2013-06-30 18:53:54 UTC (rev 1262)
+++ pkg/OmicABEL/src/ooc_BLAS.c	2013-07-01 08:50:00 UTC (rev 1263)
@@ -52,7 +52,8 @@
  * The other matrix is m x n
  */
 void ooc_gemm( int m, int n, int ooc_b, double *Z, char *in, char *out, 
-		int threshold, const char *obj_type, char *obj_name, int namelength )
+		int threshold, const char *obj_type, char *obj_name, int namelength,
+		int nths )
 {
 	/* Files */
 	FILE *fp_in  = fgls_fopen( in, "rb" );
@@ -105,7 +106,7 @@
 		/*printf("Compute\n");*/
 
 		// Sanity check
-		average( in_comp, m, cur_n, threshold, obj_type, &obj_name[i*namelength], namelength, 1 );
+		average( in_comp, m, cur_n, threshold, obj_type, &obj_name[i*namelength], namelength, 1, nths );
 #if VAMPIR
     VT_USER_START("OOC_GEMM");
 #endif

Modified: pkg/OmicABEL/src/ooc_BLAS.h
===================================================================
--- pkg/OmicABEL/src/ooc_BLAS.h	2013-06-30 18:53:54 UTC (rev 1262)
+++ pkg/OmicABEL/src/ooc_BLAS.h	2013-07-01 08:50:00 UTC (rev 1263)
@@ -26,6 +26,7 @@
 #define OOC_BLAS_H
 
 void ooc_gemm( int m, int n, int ooc_b, double *Z, char *in, char *out,
-		int threshold, const char *obj_type, char *obj_name, int namelength );
+		int threshold, const char *obj_type, char *obj_name, int namelength,
+		int nths );
 
 #endif // OOC_BLAS_H

Modified: pkg/OmicABEL/src/utils.c
===================================================================
--- pkg/OmicABEL/src/utils.c	2013-06-30 18:53:54 UTC (rev 1262)
+++ pkg/OmicABEL/src/utils.c	2013-07-01 08:50:00 UTC (rev 1263)
@@ -321,12 +321,13 @@
 	printf( "%lld:%lld seconds\n", (long long)t.tv_sec, (long long)t.tv_usec );
 }
 
-void average( double *data, int n, int ncols, int threshold, const char *obj_type, char *obj_name, int namelength, int verbose )
+void average( double *data, int n, int ncols, int threshold, const char *obj_type, char *obj_name, int namelength, int verbose, int nths )
 {
 	int i, j;
 	double sum, avg;
 	int nans, infs;
 
+	#pragma omp parallel for private(j, sum, nans, infs, i, avg) schedule(static, 4) num_threads(nths)
 	for ( j = 0; j < ncols; j++ )
 	{
 		sum = 0.0;

Modified: pkg/OmicABEL/src/utils.h
===================================================================
--- pkg/OmicABEL/src/utils.h	2013-06-30 18:53:54 UTC (rev 1262)
+++ pkg/OmicABEL/src/utils.h	2013-07-01 08:50:00 UTC (rev 1263)
@@ -45,7 +45,7 @@
 void print_timestamp( void );
 
 // Sanity
-void average( double *data, int n, int ncols, int threshold, const char *obj_type, char *obj_name, int namelength, int verbose );
+void average( double *data, int n, int ncols, int threshold, const char *obj_type, char *obj_name, int namelength, int verbose, int nths );
 void checkNoNans( size_t n, double *buff, const char* err_msg);
 
 #endif // UTILS_H

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