[Genabel-commits] r1507 - pkg/OmicABELnoMM/src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Dec 27 22:00:05 CET 2013
Author: lckarssen
Date: 2013-12-27 22:00:05 +0100 (Fri, 27 Dec 2013)
New Revision: 1507
Modified:
pkg/OmicABELnoMM/src/Algorithm.cpp
Log:
Fixed a couple of simple-to-fix cpplint warnings in OmicABELnoMM's Algorithm.cpp. Thanks to Jenkins for reporting these.
Modified: pkg/OmicABELnoMM/src/Algorithm.cpp
===================================================================
--- pkg/OmicABELnoMM/src/Algorithm.cpp 2013-12-27 12:04:16 UTC (rev 1506)
+++ pkg/OmicABELnoMM/src/Algorithm.cpp 2013-12-27 21:00:05 UTC (rev 1507)
@@ -49,7 +49,6 @@
int dim1_ini, int dim1_end, int dim2_ini,
int dim2_end)
{
-
int i, j, idx = 0;
int size, source_ini;
for (i = dim2_ini; i < dim2_end; i++)
@@ -112,7 +111,6 @@
type_precision* bot, int dim1_QY,
int dim2_QY, int dim1_qy_bot, int bot_blocks )
{
-
int i, k, w, top_idx, bot_idx, max = dim1_QY*dim2_QY;
top_idx = 0;
bot_idx = 0;
@@ -276,7 +274,7 @@
int index_new = 0;
for (i = 0; i < rhs; i++)
{
- copy_vec( &ynew[index], &new_sol[index_new], colsA);
+ copy_vec(&ynew[index], &new_sol[index_new], colsA);
index += rowsA;
index_new += colsA;
}
@@ -323,7 +321,7 @@
int max_threads = params.threads;
- srand (time(NULL));
+ srand(time(NULL));
blas_set_num_threads(max_threads);
@@ -356,7 +354,7 @@
for (int j = 0; j < y_iters; j++)
{
- if (y_iters >= 40 && (i%(y_iters/40))==0)
+ if (y_iters >= 40 && (i%(y_iters/40)) == 0)
{
cout << "*" << flush;
}
@@ -404,8 +402,7 @@
for (int j = 0; j < y_iters; j++)
{
-
- if (y_iters >= 40 && (i%(y_iters/40))==0)
+ if (y_iters >= 40 && (i%(y_iters/40)) == 0)
{
cout << AIOfile.io_overhead << flush;
AIOfile.io_overhead = "*";
@@ -454,18 +451,18 @@
if (y_iters < 40 &&
(y_block_size < 3 ||
- (jj%(y_block_size/3))==0))
+ (jj%(y_block_size/3)) == 0))
{
cout << AIOfile.io_overhead << flush;
AIOfile.io_overhead = "*";
}
- copy_vec(backupAL,&AL[aL_idx], n * l);
+ copy_vec(backupAL, &AL[aL_idx], n * l);
replace_with_zeros(&y_nan_idxs[jj], &AL[aL_idx], n, l, 1);
//! Generate Stl
cblas_ssyrk(CblasColMajor, CblasUpper, CblasTrans,
- l, n, 1.0,&AL[aL_idx], lda, 0.0, Stl, l);
+ l, n, 1.0, &AL[aL_idx], lda, 0.0, Stl, l);
copy_vec(backupAR,&AR[aR_idx], n*r*a_block_size);
replace_with_zeros(&y_nan_idxs[jj], &AR[aR_idx],
@@ -475,7 +472,7 @@
//! Generate Str
cblas_sgemm(CblasColMajor, CblasTrans, CblasNoTrans,
l, r * a_block_size, n, 1.0, &AL[aL_idx],
- n,&AR[aR_idx], n, 0.0, Str, l);
+ n, &AR[aR_idx], n, 0.0, Str, l);
get_ticks(end_tick);
out.acc_RTL_QLY += ticks2sec(end_tick - start_tick2,
cpu_freq);
@@ -518,13 +515,13 @@
get_ticks(start_tick2);
//! b = S\Ay
- info = LAPACKE_sposv(STORAGE_TYPE,'U', p, 1, S, p,
+ info = LAPACKE_sposv(STORAGE_TYPE, 'U', p, 1, S, p,
&Ay[ii*p], p);
get_ticks(end_tick);
out.acc_loadxr += ticks2sec(end_tick - start_tick2,
cpu_freq);
- assert(info == 0,"POSV");
+ assert(info == 0, "POSV");
if (ForceCheck)
{
@@ -562,7 +559,6 @@
delete []AL;
// delete []backupAL;
// delete []backupAR;
-
}
@@ -574,7 +570,7 @@
{
int max_threads = params.threads;
- srand (time(NULL));
+ srand(time(NULL));
blas_set_num_threads(max_threads);
@@ -650,7 +646,7 @@
for (i = 0; i < a_iters; i++)
{
- if (a_iters > 10 && (i%(a_iters/10))==0)
+ if (a_iters > 10 && (i%(a_iters/10)) == 0)
{
cout << "%" << flush;
}
@@ -682,7 +678,7 @@
for (j = 0; j < y_iters; j++)
{
- if (a_iters < 10 && (y_iters < 10 || (j%(y_iters/10))==0))
+ if (a_iters < 10 && (y_iters < 10 || (j%(y_iters/10)) == 0))
{
cout << "%" << flush;
}
@@ -704,8 +700,8 @@
for (int jj = 0; jj < y_block_size; jj++)
{
- copy_vec(&Ay_top[j*l*y_block_size+jj*l],&Ay[jj*p], l);
- copy_vec(&Ay_bot[ii*r + jj*r*a_block_size],&Ay[l+jj*p], r);
+ copy_vec(&Ay_top[j*l*y_block_size+jj*l], &Ay[jj*p], l);
+ copy_vec(&Ay_bot[ii*r + jj*r*a_block_size], &Ay[l+jj*p], r);
}
type_precision* B = Ay;
@@ -758,7 +754,7 @@
int max_threads = params.threads;
- srand (time(NULL));
+ srand(time(NULL));
blas_set_num_threads(max_threads);
@@ -890,7 +886,7 @@
int max_threads = params.threads;
- srand (time(NULL));
+ srand(time(NULL));
blas_set_num_threads(max_threads);
@@ -1010,7 +1006,7 @@
int max_threads = params.threads;
- srand (time(NULL));
+ srand(time(NULL));
blas_set_num_threads(max_threads);
@@ -1073,7 +1069,7 @@
get_ticks(start_tick);
for (i = 0; i < a_iters; i++)
{
- if (a_iters < 10 || (i%(a_iters/10))==0)
+ if (a_iters < 10 || (i%(a_iters/10)) == 0)
{
cout << "%" << flush;
}
@@ -1086,12 +1082,12 @@
//! Generate R
info = LAPACKE_sgeqrf(STORAGE_TYPE, n, p, A, lda, tau);
- assert(info == 0,"QR decomp");
+ assert(info == 0, "QR decomp");
type_precision* R = extract_R(A, n, p);
//! generate Q
info = LAPACKE_sorgqr(STORAGE_TYPE, n, p, k, Q, lda, tau);
- assert(info == 0,"Q form");
+ assert(info == 0, "Q form");
@@ -1100,7 +1096,6 @@
for (j = 0; j < y_iters; j++)
{
-
// matlab_print_matrix("RR", p, p, R);
// matlab_print_matrix("QQ", n, p, Q);
@@ -1147,7 +1142,7 @@
int max_threads = params.threads;
- srand (time(NULL));
+ srand(time(NULL));
blas_set_num_threads(max_threads);
@@ -1199,7 +1194,7 @@
type_precision* QL;
type_precision* QR = &Q[n*l];
- int y_iters = y_amount/y_block_size;
+ int y_iters = y_amount / y_block_size;
type_precision* Y;
@@ -1211,7 +1206,7 @@
get_ticks(start_tick);
//! Generate RTL
info = LAPACKE_sgeqrf(STORAGE_TYPE, n, l, AL, lda, tau);
- assert(info == 0,"QR decomp");
+ assert(info == 0, "QR decomp");
type_precision* R =prepare_R(AL, n, l, r);
type_precision* Rtl = R;
@@ -1221,14 +1216,14 @@
//! generate QL
info = LAPACKE_sorgqr(STORAGE_TYPE, n, l, k, QL, lda, tau);
- assert(info == 0,"Q form");
+ assert(info == 0, "Q form");
// printf("\n\n%%Computations\n%%");
for (i = 0; i < a_iters; i++)
{
- if (a_iters < 10 || (i%(a_iters/10))==0)
+ if (a_iters < 10 || (i%(a_iters/10)) == 0)
{
cout << "%" << flush;
}
@@ -1249,14 +1244,14 @@
type_precision* QrRbr = QR;
copy_vec(Atemp, QrRbr, n*r);
info = LAPACKE_sgeqrf(STORAGE_TYPE, n, r, QrRbr, lda, tau);
- assert(info == 0,"QR decomp of QrRbr");
+ assert(info == 0, "QR decomp of QrRbr");
// reuse of old function
type_precision* Rbrtemp = prepare_R(QrRbr, n, r, 0);
copy_vec(Rbrtemp, Rbr, r*r);
info = LAPACKE_sorgqr(STORAGE_TYPE, n, r, r, QrRbr, lda, tau);
- assert(info == 0,"QR form");
+ assert(info == 0, "QR form");
free(Rbrtemp);
update_R(R, Rtr, Rbr, p, p, r);
@@ -1427,14 +1422,14 @@
// printf("\n\n%%Computations\n%%");
for (i = 0; i < a_iters; i++)
{
- if (a_iters >= 10 && (i%(a_iters/10))==0)
+ if (a_iters >= 10 && (i%(a_iters/10)) == 0)
{
// cout << "*" << flush;
}
for (j = 0; j < y_iters; j++)
{
- if (a_iters < 10 && (y_iters < 10 || (j%(y_iters/10))==0))
+ if (a_iters < 10 && (y_iters < 10 || (j%(y_iters/10)) == 0))
{
// cout << "*" << flush;
}
@@ -1449,7 +1444,7 @@
info = LAPACKE_sgeqrf(STORAGE_TYPE, n, l, AL, lda, tau);
- assert(info == 0,"QR decomp");
+ assert(info == 0, "QR decomp");
type_precision* Rtl = prepare_R(AL, n, l, 0);
@@ -1458,7 +1453,7 @@
info = LAPACKE_sorgqr(STORAGE_TYPE, n, l, k, QL, lda, tau);
- assert(info == 0,"Q form");
+ assert(info == 0, "Q form");
matlab_print_matrix("QL", n, l, QL);
@@ -1502,8 +1497,8 @@
for (int i = 0; i < a_iters; i++)
{
- cout << i<<":i\n" << flush;
- if (a_iters >= 10 && (i%(a_iters/10))==0)
+ cout << i << ":i\n" << flush;
+ if (a_iters >= 10 && (i%(a_iters/10)) == 0)
{
cout << AIOfile.io_overhead << flush;
AIOfile.io_overhead = "*";
@@ -1536,7 +1531,6 @@
l, r * a_block_size, n, 1.0, QL, n,
Ar, n, 0.0, Rtr, l);
// matlab_print_matrix("QL'*Ar", l, r*a_block_size, Rtr);
-
}
#pragma omp section
{
@@ -1555,7 +1549,7 @@
//! Atemp = AR-Q1*Rtr
cblas_sgemm(CblasColMajor, CblasNoTrans, CblasNoTrans,
- n, r*a_block_size, l,-1.0, QL, n, Rtr, l, 1.0, Atemp, n);
+ n, r*a_block_size, l, -1.0, QL, n, Rtr, l, 1.0, Atemp, n);
//! H = RTL\Rtr
cblas_strsm(CblasColMajor, CblasLeft, CblasUpper,
@@ -1565,7 +1559,7 @@
#pragma omp parallel default(shared)
{
#pragma omp for private(tau) nowait schedule(static, sch_block_size)
- for (int ii = 0; ii<a_block_size; ii++)
+ for (int ii = 0; ii < a_block_size; ii++)
{
type_precision* QrRbr = &Qr[n*r*ii];
copy_vec(&Atemp[n*r*ii], QrRbr, n*r);
@@ -1576,7 +1570,7 @@
// reuse of old function
type_precision* Rbrtemp = prepare_R(QrRbr, n, r, 0);
- copy_vec(Rbrtemp,&Rbr[r*r*ii], r*r);
+ copy_vec(Rbrtemp, &Rbr[r*r*ii], r*r);
info = LAPACKE_sorgqr(STORAGE_TYPE, n, r, r, QrRbr, lda, tau);
@@ -1601,7 +1595,7 @@
int qy_bot_idx = 0;
for (int j = 0; j < y_iters; j++)
{
- if (a_iters < 10 && (y_iters < 10 || (j%(y_iters/10))==0))
+ if (a_iters < 10 && (y_iters < 10 || (j%(y_iters/10)) == 0))
{
cout << AIOfile.io_overhead << flush;
AIOfile.io_overhead = "*";
@@ -1668,7 +1662,7 @@
#pragma omp parallel default(shared)
{
#pragma omp for nowait schedule(static, sch_block_size)
- for (int ii = 0; ii<a_block_size; ii++)
+ for (int ii = 0; ii < a_block_size; ii++)
{
int thread_id = omp_get_thread_num();
int b_bot_idx = thread_id*y_block_size*r;
@@ -1677,14 +1671,14 @@
extract_subMatrix(Qy_bot, &B_bot[b_bot_idx],
r*a_block_size, y_block_size,
- ii*r,(ii+1)*r, 0, y_block_size);
+ ii*r, (ii+1)*r, 0, y_block_size);
copy_vec(&RQy_top[top_idx], &B_top[b_top_idx],
l*y_block_size);
//! bBot = Rbr\qy_bot
cblas_strsm(CblasColMajor, CblasLeft,
CblasUpper, CblasNoTrans, CblasNonUnit,
- r, y_block_size, 1.0,&Rbr[ii*r*r], r,
+ r, y_block_size, 1.0, &Rbr[ii*r*r], r,
&B_bot[b_bot_idx], r);
//! Btop = K-H*bBot Btop=(Rtl\(Ql'*Y))-(Rtl\Rtr)*(Rbr\(Qr'*Y));
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