On Mon, 2014-07-07 at 10:09 -0400, Tom Callaway wrote:
On 07/07/2014 08:15 AM, Martyn Plummer wrote:
Dear Tom,
The change in the Fedora RPM from using R's internal BLAS to external
BLAS means the Fedora R binary now fails one of R's regression tests,
specifically: tests/reg-BLAS.R. You can run this code by hand to verify
the issue.
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.
The version of BLAS that comes with R contains patched versions of
DGBMV, DGEMM, and DGEMV. The patch has been in place since 2010.
Presumably R blas and reference BLAS have been divergent ever since.
I guess this should be reported upstream as a BLAS bug. Recalling the
previous thread on openblas, I note that openblas does pass the
regression test.
Seems like it. In the interim, is there a patch handy, or do I need to
try to untangle it from the R code?
I have reconstructed a patch (attached) that you can apply directly to
the BLAS source code from Netlib.
Martyn
~tom
==
¸.·´¯`·.´¯`·.¸¸.·´¯`·.¸(((º OSAS @ Red Hat
University Outreach || Fedora Special Projects || Fedora Legal
---
This message and its attachments are strictly confidential. If you are
not the intended recipient of this message, please immediately notify
the sender and delete it. Since its integrity cannot be guaranteed,
its content cannot involve the sender's responsibility. Any misuse,
any disclosure or publication of its content, either whole or partial,
is prohibited, exception made of formally approved use
---
diff -uNr BLAS/dgbmv.f BLAS-patched/dgbmv.f
--- BLAS/dgbmv.f 2011-04-19 21:07:23.0 +0200
+++ BLAS-patched/dgbmv.f 2014-07-07 16:39:26.509772771 +0200
@@ -240,18 +240,18 @@
JX = KX
IF (INCY.EQ.1) THEN
DO 60 J = 1,N
- IF (X(JX).NE.ZERO) THEN
+c 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
+c END IF
JX = JX + INCX
60 CONTINUE
ELSE
DO 80 J = 1,N
- IF (X(JX).NE.ZERO) THEN
+c IF (X(JX).NE.ZERO) THEN
TEMP = ALPHA*X(JX)
IY = KY
K = KUP1 - J
@@ -259,7 +259,7 @@
Y(IY) = Y(IY) + TEMP*A(K+I,J)
IY = IY + INCY
70 CONTINUE
- END IF
+c END IF
JX = JX + INCX
IF (J.GT.KU) KY = KY + INCY
80 CONTINUE
diff -uNr BLAS/dgemm.f BLAS-patched/dgemm.f
--- BLAS/dgemm.f 2011-04-19 21:07:23.0 +0200
+++ BLAS-patched/dgemm.f 2014-07-07 16:41:46.510379952 +0200
@@ -239,12 +239,12 @@
60 CONTINUE
END IF
DO 80 L = 1,K
- IF (B(L,J).NE.ZERO) THEN
+c 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
+c END IF
80 CONTINUE
90 CONTINUE
ELSE
@@ -281,12 +281,12 @@
140 CONTINUE
END IF
DO 160 L = 1,K
- IF (B(J,L).NE.ZERO) THEN
+c 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
+c END IF
160 CONTINUE
170 CONTINUE
ELSE
diff -uNr BLAS/dgemv.f BLAS-patched/dgemv.f
--- BLAS/dgemv.f 2011-04-19 21:07:23.0 +0200
+++ BLAS-patched/dgemv.f 2014-07-07 16:40:29.334045215 +0200
@@ -209,24 +209,24 @@
JX = KX
IF (INCY.EQ.1) THEN
DO 60 J = 1,N
- IF (X(JX).NE.ZERO) THEN
+c 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
+c END IF
JX = JX + INCX
60 CONTINUE
