Hi all, Okey doc. I just changed this. See log below. This is for the better.
Cheers, Julien.
Author: langou
Date: Sat Jul 12 15:58:39 2014
New Revision: 1488
URL: https://icl.cs.utk.edu/trac/lapackdev/changeset/1488
Log:
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 NaNpropagation in a pretty adhoc 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@Domain.Removed.
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
Modified:
lapack/trunk/BLAS/SRC/cgbmv.f
lapack/trunk/BLAS/SRC/cgemm.f
lapack/trunk/BLAS/SRC/cgemv.f
lapack/trunk/BLAS/SRC/dgbmv.f
lapack/trunk/BLAS/SRC/dgemm.f
lapack/trunk/BLAS/SRC/dgemv.f
lapack/trunk/BLAS/SRC/sgbmv.f
lapack/trunk/BLAS/SRC/sgemm.f
lapack/trunk/BLAS/SRC/sgemv.f
lapack/trunk/BLAS/SRC/zgbmv.f
lapack/trunk/BLAS/SRC/zgemm.f
lapack/trunk/BLAS/SRC/zgemv.f
Modified: lapack/trunk/BLAS/SRC/cgbmv.f
URL:
https://icl.cs.utk.edu/trac/lapackdev/file/lapack/trunk/BLAS/SRC/cgbmv.f?rev=1488
==============================================================================
 lapack/trunk/BLAS/SRC/cgbmv.f (original)
+++ lapack/trunk/BLAS/SRC/cgbmv.f Sat Jul 12 15:58:39 2014
@@ 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,JKU),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,JKU),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,JKU),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,JKU),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
Modified: lapack/trunk/BLAS/SRC/cgemm.f
URL:
https://icl.cs.utk.edu/trac/lapackdev/file/lapack/trunk/BLAS/SRC/cgemm.f?rev=1488
==============================================================================
 lapack/trunk/BLAS/SRC/cgemm.f (original)
+++ lapack/trunk/BLAS/SRC/cgemm.f Sat Jul 12 15:58:39 2014
@@ 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
Modified: lapack/trunk/BLAS/SRC/cgemv.f
URL:
https://icl.cs.utk.edu/trac/lapackdev/file/lapack/trunk/BLAS/SRC/cgemv.f?rev=1488
==============================================================================
 lapack/trunk/BLAS/SRC/cgemv.f (original)
+++ lapack/trunk/BLAS/SRC/cgemv.f Sat Jul 12 15:58:39 2014
@@ 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
Modified: lapack/trunk/BLAS/SRC/dgbmv.f
URL:
https://icl.cs.utk.edu/trac/lapackdev/file/lapack/trunk/BLAS/SRC/dgbmv.f?rev=1488
==============================================================================
 lapack/trunk/BLAS/SRC/dgbmv.f (original)
+++ lapack/trunk/BLAS/SRC/dgbmv.f Sat Jul 12 15:58:39 2014
@@ 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,JKU),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,JKU),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,JKU),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,JKU),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
Modified: lapack/trunk/BLAS/SRC/dgemm.f
URL:
https://icl.cs.utk.edu/trac/lapackdev/file/lapack/trunk/BLAS/SRC/dgemm.f?rev=1488
==============================================================================
 lapack/trunk/BLAS/SRC/dgemm.f (original)
+++ lapack/trunk/BLAS/SRC/dgemm.f Sat Jul 12 15:58:39 2014
@@ 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
Modified: lapack/trunk/BLAS/SRC/dgemv.f
URL:
https://icl.cs.utk.edu/trac/lapackdev/file/lapack/trunk/BLAS/SRC/dgemv.f?rev=1488
==============================================================================
 lapack/trunk/BLAS/SRC/dgemv.f (original)
+++ lapack/trunk/BLAS/SRC/dgemv.f Sat Jul 12 15:58:39 2014
@@ 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
Modified: lapack/trunk/BLAS/SRC/sgbmv.f
URL:
https://icl.cs.utk.edu/trac/lapackdev/file/lapack/trunk/BLAS/SRC/sgbmv.f?rev=1488
==============================================================================
 lapack/trunk/BLAS/SRC/sgbmv.f (original)
+++ lapack/trunk/BLAS/SRC/sgbmv.f Sat Jul 12 15:58:39 2014
@@ 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,JKU),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,JKU),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,JKU),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,JKU),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
Modified: lapack/trunk/BLAS/SRC/sgemm.f
URL:
https://icl.cs.utk.edu/trac/lapackdev/file/lapack/trunk/BLAS/SRC/sgemm.f?rev=1488
==============================================================================
 lapack/trunk/BLAS/SRC/sgemm.f (original)
+++ lapack/trunk/BLAS/SRC/sgemm.f Sat Jul 12 15:58:39 2014
@@ 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
Modified: lapack/trunk/BLAS/SRC/sgemv.f
URL:
https://icl.cs.utk.edu/trac/lapackdev/file/lapack/trunk/BLAS/SRC/sgemv.f?rev=1488
==============================================================================
 lapack/trunk/BLAS/SRC/sgemv.f (original)
+++ lapack/trunk/BLAS/SRC/sgemv.f Sat Jul 12 15:58:39 2014
@@ 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
Modified: lapack/trunk/BLAS/SRC/zgbmv.f
URL:
https://icl.cs.utk.edu/trac/lapackdev/file/lapack/trunk/BLAS/SRC/zgbmv.f?rev=1488
==============================================================================
 lapack/trunk/BLAS/SRC/zgbmv.f (original)
+++ lapack/trunk/BLAS/SRC/zgbmv.f Sat Jul 12 15:58:39 2014
@@ 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,JKU),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,JKU),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,JKU),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,JKU),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
Modified: lapack/trunk/BLAS/SRC/zgemm.f
URL:
https://icl.cs.utk.edu/trac/lapackdev/file/lapack/trunk/BLAS/SRC/zgemm.f?rev=1488
==============================================================================
 lapack/trunk/BLAS/SRC/zgemm.f (original)
+++ lapack/trunk/BLAS/SRC/zgemm.f Sat Jul 12 15:58:39 2014
@@ 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
Modified: lapack/trunk/BLAS/SRC/zgemv.f
URL:
https://icl.cs.utk.edu/trac/lapackdev/file/lapack/trunk/BLAS/SRC/zgemv.f?rev=1488
==============================================================================
 lapack/trunk/BLAS/SRC/zgemv.f (original)
+++ lapack/trunk/BLAS/SRC/zgemv.f Sat Jul 12 15:58:39 2014
@@ 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
On Jul 10, 2014, at 10:32 AM, James Demmel <demmel@Domain.Removed> wrote:
How about this for a careful (nonreckless) matmul (or other BLAS):
Spend O(n^2) to check the inputs for NaNs (and perhaps infinities) ...
cheap
If (a NaN appears) ... very unlikely
use a version of matmul that we know will propagate them correctly
... could be slower matmul, or we could just fill in selected
rows and
... columns of product with NaNs depending on where NaNs appeared
in the input
else
use your favorite performance tuned (reckless) version, including
Strassen etc.
end if
How to do this of course depends on how we decide to treat the cases alpha=0,
beta=0.
A less portable version might use some kind of exceptions flags at the end
(of course
the usual ones will not be set by quiet NaNs) to see if a NaN appeared, and
recomputation
is necessary (so slow with low probability). This would of course not fix the
problem identified
in Julien's email, where the NaN may not be touched at all.
Jim
On 7/10/14, 8:34 AM, Julien Langou wrote:
Hi all,
1) Below is an email that we just received from some R & redhat folks about
NaN propagation in the BLAS. Please read the email discussion between them
and I.
I summarized their request in my reply to them. (So you can just read my
answer.)
2) Please see as well my question to them. Starting with: "A related
question. How do you feel about the other of IF statements if DGEMM?? (I do
not have an answer yet from them.)
3) Please see as well:
http://icl.cs.utk.edu/lapackforum/viewtopic.php?f=5&t=4499
4) Please see as well email from Jim (Demmel) to Penny Andrerson (MathWorks)
"[LAPACKDEV] NaNs and consistent exception handling" from DEC142012.
So basically this is the recurring of issue of NaN propagation.
1) I think we will apply the patch of these guys. Reason: I am OK with
keeping the nonpropagation of NaNs when ALPHA and BETA have special values
(for now), but this nonpropagation here is really weird. It is specific to
the JLI variant of DGEMM, it applies when an entry of B is ZERO, pfff . . .
Oh my. I just have a headache to think what the output would look like.
There would be NaN at some places in C, no NaN at other places. A mess. I am
OK with keeping the nonpropagation of NaNs when ALPHA and BETA have special
values (for now), but not based on values of the entries of the matrices A
and B.
(Does this make sense?)
2) We can rethink the NaN propagation in DGEMM (and BLAS in general) for
values of ALPHA and BETA. (???) So bottom line: do we want the reference
DGEMM to just be three loops and propagate everything? I think this is more
a question for users, superusers, etc. Jim might have some answers with his
related projects.
3) Note: Strassen version of DGEMM will not propagate NaN correctly. Too
many NaNs will be created. (Just a random comment, I was just thinking about
this.)
Cheers,
Julien.
Begin forwarded message:
From: Julien Langou <julien.langou@Domain.Removed>
Subject: Re: [Lapack] Issue with BLAS causing regression test failure in R
Date: July 10, 2014 at 9:12:10 AM MDT
To: Tom Callaway <tcallawa@Domain.Removed>
Cc: Martyn Plummer <plummerm@Domain.Removed>, "peljasz@Domain.Removed"
<peljasz@Domain.Removed>, julie langou <julie@Domain.Removed>
Hi Tom, Hi Martyn, Hi Lejeczek,
Thanks for pointing this, just to let you know that we (LAPACK folks) are
discussing this.
So just 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 each L (from 1 to K), whether
B(L,J) is zero (or not) to save (or not) the 2M following operations.
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
You suggest to remove the IF statement so that NaNs are correctly
propagated.
So as I said, we (LAPACK folks) are discussing this.
A related question. How do you feel about the other of IF statements if
DGEMM?
For example: (always on DGEMM)
(1) if BETA = 0, we set C to ZERO, then we follow with
computation, etc. So if BETA = 0 and NaN in C, the NaN in C are removed.
Are you OK with this?
(2) if ALPHA = 0 and BETA = 1, we return directly. So if
ALPHA = 0 and BETA = 1, and NaNs in A or in B, these NaNs are not
propagated to output C. Are you OK with this?
What I am trying to say is that there are plenty of other places where NaN
are not necessarily propagated within DGEMM.
(Pretty much each time there is an IF statement in the DGEMM subroutine is
a case of this.)
So my question is how do you feel about the other places where NaN in input
(A, B, C, or alpha, or beta) do not propagate?
Cheers,
Julien.
On Jul 7, 2014, at 9:58 AM, Tom Callaway <tcallawa@Domain.Removed> wrote:
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
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