From 2b911746d5d7173ccee0067a4ad09159cdfce1a2 Mon Sep 17 00:00:00 2001 From: langou Date: Sat, 12 Jul 2014 19:58:39 +0000 Subject: [PATCH] Edited the code of xGBMV, xGEMV and xGEMM by removing the test for an entry of B (or X) being zero to skip a loop so as to enable better NaN (or Inf) propagation. Taking DGEMM as an example, if you use notation: C(I,J) = C(I,J) + alpha * A(I,L) * B(L,J), the reference BLAS DGEMM is using the JLI version of matrix matrix multiply and is checking, for each J (from 1 to N) and for each L (from 1 to K), whether B(L,J) is zero (or not) to save (or not) the 2M following operations. (See the "IF (B(L,J).NE.ZERO) THEN" in the code below.) The snippets of code is as follows DO 90 J = 1,N DO 80 L = 1,K IF (B(L,J).NE.ZERO) THEN TEMP = ALPHA*B(L,J) DO 70 I = 1,M C(I,J) = C(I,J) + TEMP*A(I,L) 70 CONTINUE END IF 80 CONTINUE 90 CONTINUE This induces some non NaN-propagation in a pretty ad-hoc way. For better NaN propagation, this patch removes the above IF statement. The snippet of code now becomes DO 90 J = 1,N DO 80 L = 1,K TEMP = ALPHA*B(L,J) DO 70 I = 1,M C(I,J) = C(I,J) + TEMP*A(I,L) 70 CONTINUE 80 CONTINUE 90 CONTINUE This enables correct NaN propagation for this piece of code. Rationale: BLAS does not correctly propagate all NaNs (and Infs). We still have no NaN propagation where for example ALPHA=0, etc. The goal of this commit is to have correct NaN propagation no matter what the entries of the input matrices/vectors (A, B, C, X, etc.) are. BLAS do not correctly propagate NaNs and Infs based on some values of the scalars (ALPHA, BETA, etc.). See below the email from Tom Callaway from RedHat, sent on July 9th to lapack@cs.utk.edu. Hello LAPACK people, Martyn & Lejeczek (on CC) reported an issue to Fedora relating to R using our system copy of BLAS (from LAPACK). As noted in the R administration and Installation Manual, "R relies on ISO/IEC 60559 compliance of an external BLAS. This can be broken if for example the code assumes that terms with a zero factor are always zero and do not need to be computed - whereas x*0 can be NaN. This is checked in the test suite." In the stock BLAS, DGBMV, DGEMM, and DGEMV fail this. R has been patching their bundled BLAS to resolve this issue since 2010, but Fedora now uses the system BLAS. Attached is a patch (from upstream R) to fix this issue in the LAPACK BLAS. Please consider applying it. Thanks, ~tom --- BLAS/SRC/cgbmv.f | 28 ++++++++++++---------------- BLAS/SRC/cgemm.f | 32 +++++++++++++------------------- BLAS/SRC/cgemv.f | 24 ++++++++++-------------- BLAS/SRC/dgbmv.f | 28 ++++++++++++---------------- BLAS/SRC/dgemm.f | 20 ++++++++------------ BLAS/SRC/dgemv.f | 24 ++++++++++-------------- BLAS/SRC/sgbmv.f | 28 ++++++++++++---------------- BLAS/SRC/sgemm.f | 20 ++++++++------------ BLAS/SRC/sgemv.f | 24 ++++++++++-------------- BLAS/SRC/zgbmv.f | 28 ++++++++++++---------------- BLAS/SRC/zgemm.f | 32 +++++++++++++------------------- BLAS/SRC/zgemv.f | 24 ++++++++++-------------- 12 files changed, 130 insertions(+), 182 deletions(-) diff --git a/BLAS/SRC/cgbmv.f b/BLAS/SRC/cgbmv.f index cd597f9..62001f2 100644 --- a/BLAS/SRC/cgbmv.f +++ b/BLAS/SRC/cgbmv.f @@ -319,26 +319,22 @@ JX = KX IF (INCY.EQ.1) THEN DO 60 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - K = KUP1 - J - DO 50 I = MAX(1,J-KU),MIN(M,J+KL) - Y(I) = Y(I) + TEMP*A(K+I,J) - 50 CONTINUE - END IF + TEMP = ALPHA*X(JX) + K = KUP1 - J + DO 50 I = MAX(1,J-KU),MIN(M,J+KL) + Y(I) = Y(I) + TEMP*A(K+I,J) + 50 CONTINUE JX = JX + INCX 60 CONTINUE ELSE DO 80 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - IY = KY - K = KUP1 - J - DO 70 I = MAX(1,J-KU),MIN(M,J+KL) - Y(IY) = Y(IY) + TEMP*A(K+I,J) - IY = IY + INCY - 70 CONTINUE - END IF + TEMP = ALPHA*X(JX) + IY = KY + K = KUP1 - J + DO 70 I = MAX(1,J-KU),MIN(M,J+KL) + Y(IY) = Y(IY) + TEMP*A(K+I,J) + IY = IY + INCY + 70 CONTINUE JX = JX + INCX IF (J.GT.KU) KY = KY + INCY 80 CONTINUE diff --git a/BLAS/SRC/cgemm.f b/BLAS/SRC/cgemm.f index ecfe12e..8d92e24 100644 --- a/BLAS/SRC/cgemm.f +++ b/BLAS/SRC/cgemm.f @@ -317,12 +317,10 @@ 60 CONTINUE END IF DO 80 L = 1,K - IF (B(L,J).NE.ZERO) THEN - TEMP = ALPHA*B(L,J) - DO 70 I = 1,M - C(I,J) = C(I,J) + TEMP*A(I,L) - 70 CONTINUE - END IF + TEMP = ALPHA*B(L,J) + DO 70 I = 1,M + C(I,J) = C(I,J) + TEMP*A(I,L) + 70 CONTINUE 80 CONTINUE 90 CONTINUE ELSE IF (CONJA) THEN @@ -376,17 +374,15 @@ 170 CONTINUE END IF DO 190 L = 1,K - IF (B(J,L).NE.ZERO) THEN - TEMP = ALPHA*CONJG(B(J,L)) - DO 180 I = 1,M - C(I,J) = C(I,J) + TEMP*A(I,L) - 180 CONTINUE - END IF + TEMP = ALPHA*CONJG(B(J,L)) + DO 180 I = 1,M + C(I,J) = C(I,J) + TEMP*A(I,L) + 180 CONTINUE 190 CONTINUE 200 CONTINUE ELSE * -* Form C := alpha*A*B**T + beta*C +* Form C := alpha*A*B**T + beta*C * DO 250 J = 1,N IF (BETA.EQ.ZERO) THEN @@ -399,12 +395,10 @@ 220 CONTINUE END IF DO 240 L = 1,K - IF (B(J,L).NE.ZERO) THEN - TEMP = ALPHA*B(J,L) - DO 230 I = 1,M - C(I,J) = C(I,J) + TEMP*A(I,L) - 230 CONTINUE - END IF + TEMP = ALPHA*B(J,L) + DO 230 I = 1,M + C(I,J) = C(I,J) + TEMP*A(I,L) + 230 CONTINUE 240 CONTINUE 250 CONTINUE END IF diff --git a/BLAS/SRC/cgemv.f b/BLAS/SRC/cgemv.f index 507d19e..5447086 100644 --- a/BLAS/SRC/cgemv.f +++ b/BLAS/SRC/cgemv.f @@ -285,24 +285,20 @@ JX = KX IF (INCY.EQ.1) THEN DO 60 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - DO 50 I = 1,M - Y(I) = Y(I) + TEMP*A(I,J) - 50 CONTINUE - END IF + TEMP = ALPHA*X(JX) + DO 50 I = 1,M + Y(I) = Y(I) + TEMP*A(I,J) + 50 CONTINUE JX = JX + INCX 60 CONTINUE ELSE DO 80 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - IY = KY - DO 70 I = 1,M - Y(IY) = Y(IY) + TEMP*A(I,J) - IY = IY + INCY - 70 CONTINUE - END IF + TEMP = ALPHA*X(JX) + IY = KY + DO 70 I = 1,M + Y(IY) = Y(IY) + TEMP*A(I,J) + IY = IY + INCY + 70 CONTINUE JX = JX + INCX 80 CONTINUE END IF diff --git a/BLAS/SRC/dgbmv.f b/BLAS/SRC/dgbmv.f index 4a608bd..b20516f 100644 --- a/BLAS/SRC/dgbmv.f +++ b/BLAS/SRC/dgbmv.f @@ -312,26 +312,22 @@ JX = KX IF (INCY.EQ.1) THEN DO 60 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - K = KUP1 - J - DO 50 I = MAX(1,J-KU),MIN(M,J+KL) - Y(I) = Y(I) + TEMP*A(K+I,J) - 50 CONTINUE - END IF + TEMP = ALPHA*X(JX) + K = KUP1 - J + DO 50 I = MAX(1,J-KU),MIN(M,J+KL) + Y(I) = Y(I) + TEMP*A(K+I,J) + 50 CONTINUE JX = JX + INCX 60 CONTINUE ELSE DO 80 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - IY = KY - K = KUP1 - J - DO 70 I = MAX(1,J-KU),MIN(M,J+KL) - Y(IY) = Y(IY) + TEMP*A(K+I,J) - IY = IY + INCY - 70 CONTINUE - END IF + TEMP = ALPHA*X(JX) + IY = KY + K = KUP1 - J + DO 70 I = MAX(1,J-KU),MIN(M,J+KL) + Y(IY) = Y(IY) + TEMP*A(K+I,J) + IY = IY + INCY + 70 CONTINUE JX = JX + INCX IF (J.GT.KU) KY = KY + INCY 80 CONTINUE diff --git a/BLAS/SRC/dgemm.f b/BLAS/SRC/dgemm.f index 45d001b..2136740 100644 --- a/BLAS/SRC/dgemm.f +++ b/BLAS/SRC/dgemm.f @@ -311,12 +311,10 @@ 60 CONTINUE END IF DO 80 L = 1,K - IF (B(L,J).NE.ZERO) THEN - TEMP = ALPHA*B(L,J) - DO 70 I = 1,M - C(I,J) = C(I,J) + TEMP*A(I,L) - 70 CONTINUE - END IF + TEMP = ALPHA*B(L,J) + DO 70 I = 1,M + C(I,J) = C(I,J) + TEMP*A(I,L) + 70 CONTINUE 80 CONTINUE 90 CONTINUE ELSE @@ -353,12 +351,10 @@ 140 CONTINUE END IF DO 160 L = 1,K - IF (B(J,L).NE.ZERO) THEN - TEMP = ALPHA*B(J,L) - DO 150 I = 1,M - C(I,J) = C(I,J) + TEMP*A(I,L) - 150 CONTINUE - END IF + TEMP = ALPHA*B(J,L) + DO 150 I = 1,M + C(I,J) = C(I,J) + TEMP*A(I,L) + 150 CONTINUE 160 CONTINUE 170 CONTINUE ELSE diff --git a/BLAS/SRC/dgemv.f b/BLAS/SRC/dgemv.f index 675257f..6c29338 100644 --- a/BLAS/SRC/dgemv.f +++ b/BLAS/SRC/dgemv.f @@ -278,24 +278,20 @@ JX = KX IF (INCY.EQ.1) THEN DO 60 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - DO 50 I = 1,M - Y(I) = Y(I) + TEMP*A(I,J) - 50 CONTINUE - END IF + TEMP = ALPHA*X(JX) + DO 50 I = 1,M + Y(I) = Y(I) + TEMP*A(I,J) + 50 CONTINUE JX = JX + INCX 60 CONTINUE ELSE DO 80 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - IY = KY - DO 70 I = 1,M - Y(IY) = Y(IY) + TEMP*A(I,J) - IY = IY + INCY - 70 CONTINUE - END IF + TEMP = ALPHA*X(JX) + IY = KY + DO 70 I = 1,M + Y(IY) = Y(IY) + TEMP*A(I,J) + IY = IY + INCY + 70 CONTINUE JX = JX + INCX 80 CONTINUE END IF diff --git a/BLAS/SRC/sgbmv.f b/BLAS/SRC/sgbmv.f index 797ac7f..26e5116 100644 --- a/BLAS/SRC/sgbmv.f +++ b/BLAS/SRC/sgbmv.f @@ -312,26 +312,22 @@ JX = KX IF (INCY.EQ.1) THEN DO 60 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - K = KUP1 - J - DO 50 I = MAX(1,J-KU),MIN(M,J+KL) - Y(I) = Y(I) + TEMP*A(K+I,J) - 50 CONTINUE - END IF + TEMP = ALPHA*X(JX) + K = KUP1 - J + DO 50 I = MAX(1,J-KU),MIN(M,J+KL) + Y(I) = Y(I) + TEMP*A(K+I,J) + 50 CONTINUE JX = JX + INCX 60 CONTINUE ELSE DO 80 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - IY = KY - K = KUP1 - J - DO 70 I = MAX(1,J-KU),MIN(M,J+KL) - Y(IY) = Y(IY) + TEMP*A(K+I,J) - IY = IY + INCY - 70 CONTINUE - END IF + TEMP = ALPHA*X(JX) + IY = KY + K = KUP1 - J + DO 70 I = MAX(1,J-KU),MIN(M,J+KL) + Y(IY) = Y(IY) + TEMP*A(K+I,J) + IY = IY + INCY + 70 CONTINUE JX = JX + INCX IF (J.GT.KU) KY = KY + INCY 80 CONTINUE diff --git a/BLAS/SRC/sgemm.f b/BLAS/SRC/sgemm.f index 9a3d9e1..ce264ab 100644 --- a/BLAS/SRC/sgemm.f +++ b/BLAS/SRC/sgemm.f @@ -311,12 +311,10 @@ 60 CONTINUE END IF DO 80 L = 1,K - IF (B(L,J).NE.ZERO) THEN - TEMP = ALPHA*B(L,J) - DO 70 I = 1,M - C(I,J) = C(I,J) + TEMP*A(I,L) - 70 CONTINUE - END IF + TEMP = ALPHA*B(L,J) + DO 70 I = 1,M + C(I,J) = C(I,J) + TEMP*A(I,L) + 70 CONTINUE 80 CONTINUE 90 CONTINUE ELSE @@ -353,12 +351,10 @@ 140 CONTINUE END IF DO 160 L = 1,K - IF (B(J,L).NE.ZERO) THEN - TEMP = ALPHA*B(J,L) - DO 150 I = 1,M - C(I,J) = C(I,J) + TEMP*A(I,L) - 150 CONTINUE - END IF + TEMP = ALPHA*B(J,L) + DO 150 I = 1,M + C(I,J) = C(I,J) + TEMP*A(I,L) + 150 CONTINUE 160 CONTINUE 170 CONTINUE ELSE diff --git a/BLAS/SRC/sgemv.f b/BLAS/SRC/sgemv.f index eef133f..4ec3f06 100644 --- a/BLAS/SRC/sgemv.f +++ b/BLAS/SRC/sgemv.f @@ -278,24 +278,20 @@ JX = KX IF (INCY.EQ.1) THEN DO 60 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - DO 50 I = 1,M - Y(I) = Y(I) + TEMP*A(I,J) - 50 CONTINUE - END IF + TEMP = ALPHA*X(JX) + DO 50 I = 1,M + Y(I) = Y(I) + TEMP*A(I,J) + 50 CONTINUE JX = JX + INCX 60 CONTINUE ELSE DO 80 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - IY = KY - DO 70 I = 1,M - Y(IY) = Y(IY) + TEMP*A(I,J) - IY = IY + INCY - 70 CONTINUE - END IF + TEMP = ALPHA*X(JX) + IY = KY + DO 70 I = 1,M + Y(IY) = Y(IY) + TEMP*A(I,J) + IY = IY + INCY + 70 CONTINUE JX = JX + INCX 80 CONTINUE END IF diff --git a/BLAS/SRC/zgbmv.f b/BLAS/SRC/zgbmv.f index 0e7311a..1a7fb4b 100644 --- a/BLAS/SRC/zgbmv.f +++ b/BLAS/SRC/zgbmv.f @@ -319,26 +319,22 @@ JX = KX IF (INCY.EQ.1) THEN DO 60 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - K = KUP1 - J - DO 50 I = MAX(1,J-KU),MIN(M,J+KL) - Y(I) = Y(I) + TEMP*A(K+I,J) - 50 CONTINUE - END IF + TEMP = ALPHA*X(JX) + K = KUP1 - J + DO 50 I = MAX(1,J-KU),MIN(M,J+KL) + Y(I) = Y(I) + TEMP*A(K+I,J) + 50 CONTINUE JX = JX + INCX 60 CONTINUE ELSE DO 80 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - IY = KY - K = KUP1 - J - DO 70 I = MAX(1,J-KU),MIN(M,J+KL) - Y(IY) = Y(IY) + TEMP*A(K+I,J) - IY = IY + INCY - 70 CONTINUE - END IF + TEMP = ALPHA*X(JX) + IY = KY + K = KUP1 - J + DO 70 I = MAX(1,J-KU),MIN(M,J+KL) + Y(IY) = Y(IY) + TEMP*A(K+I,J) + IY = IY + INCY + 70 CONTINUE JX = JX + INCX IF (J.GT.KU) KY = KY + INCY 80 CONTINUE diff --git a/BLAS/SRC/zgemm.f b/BLAS/SRC/zgemm.f index f423315..9d422f4 100644 --- a/BLAS/SRC/zgemm.f +++ b/BLAS/SRC/zgemm.f @@ -317,12 +317,10 @@ 60 CONTINUE END IF DO 80 L = 1,K - IF (B(L,J).NE.ZERO) THEN - TEMP = ALPHA*B(L,J) - DO 70 I = 1,M - C(I,J) = C(I,J) + TEMP*A(I,L) - 70 CONTINUE - END IF + TEMP = ALPHA*B(L,J) + DO 70 I = 1,M + C(I,J) = C(I,J) + TEMP*A(I,L) + 70 CONTINUE 80 CONTINUE 90 CONTINUE ELSE IF (CONJA) THEN @@ -376,17 +374,15 @@ 170 CONTINUE END IF DO 190 L = 1,K - IF (B(J,L).NE.ZERO) THEN - TEMP = ALPHA*DCONJG(B(J,L)) - DO 180 I = 1,M - C(I,J) = C(I,J) + TEMP*A(I,L) - 180 CONTINUE - END IF + TEMP = ALPHA*DCONJG(B(J,L)) + DO 180 I = 1,M + C(I,J) = C(I,J) + TEMP*A(I,L) + 180 CONTINUE 190 CONTINUE 200 CONTINUE ELSE * -* Form C := alpha*A*B**T + beta*C +* Form C := alpha*A*B**T + beta*C * DO 250 J = 1,N IF (BETA.EQ.ZERO) THEN @@ -399,12 +395,10 @@ 220 CONTINUE END IF DO 240 L = 1,K - IF (B(J,L).NE.ZERO) THEN - TEMP = ALPHA*B(J,L) - DO 230 I = 1,M - C(I,J) = C(I,J) + TEMP*A(I,L) - 230 CONTINUE - END IF + TEMP = ALPHA*B(J,L) + DO 230 I = 1,M + C(I,J) = C(I,J) + TEMP*A(I,L) + 230 CONTINUE 240 CONTINUE 250 CONTINUE END IF diff --git a/BLAS/SRC/zgemv.f b/BLAS/SRC/zgemv.f index 4e174c9..6242cbb 100644 --- a/BLAS/SRC/zgemv.f +++ b/BLAS/SRC/zgemv.f @@ -285,24 +285,20 @@ JX = KX IF (INCY.EQ.1) THEN DO 60 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - DO 50 I = 1,M - Y(I) = Y(I) + TEMP*A(I,J) - 50 CONTINUE - END IF + TEMP = ALPHA*X(JX) + DO 50 I = 1,M + Y(I) = Y(I) + TEMP*A(I,J) + 50 CONTINUE JX = JX + INCX 60 CONTINUE ELSE DO 80 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - IY = KY - DO 70 I = 1,M - Y(IY) = Y(IY) + TEMP*A(I,J) - IY = IY + INCY - 70 CONTINUE - END IF + TEMP = ALPHA*X(JX) + IY = KY + DO 70 I = 1,M + Y(IY) = Y(IY) + TEMP*A(I,J) + IY = IY + INCY + 70 CONTINUE JX = JX + INCX 80 CONTINUE END IF -- 2.7.4