Date: Sat, 10 Feb 2007 07:17:54 +0900 (JST) From: Maho NAKATA <chat95@mac.com> To: rpvoland@facstaff.wisc.edu Cc: eric+fbports@vangyzen.net, vdemart1@tin.it, freebsd-ports@freebsd.org Subject: A workaround for math/R (was Re: math/R eats up all.) Message-ID: <20070210.071754.71112797.chat95@mac.com> In-Reply-To: <20070209.180418.85375367.chat95@mac.com> References: <20070126.113458.35660495.chat95@mac.com> <20070209.154656.63087958.chat95@mac.com> <20070209.180418.85375367.chat95@mac.com>
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Dear all,
First, Eric, I'd like to ask your opinion about the patch I proposed.
If you approve I'll commit to math/R for atlas users.
Several tries I found that for my Pentium M, status of buildablity of R
is following:
ATLAS + internal LAPACK o
ATLAS + external LAPACK x
ATLAS + ATLAS's LAPACK x
---
BLAS + external LAPACK o
BLAS + internal LAPACK o
---
GOTOBLAS + internal LAPACK o
GOTOBLAS + external LAPACK o
o means build successfully
x means build hangs up at:
cc -std=gnu99 -shared -L/usr/local/lib -o grDevices.so chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o -L../../../../lib -lR
mkdir ../../../../library/grDevices/libs
.
internal LAPACK means using LAPACK comes with R.
external LAPACK means using math/lapack
ATLAS's LAPACK means using libalapack from math/atlas.
I briefly read the source code what routines are used in internal LAPACK of R,
it contains, Cholesky factorization etc, which are accelerated by ATLAS.
Anyway, vanilla Lapack+atlas blas combination
is 10%~20% faster than atlas's LAPACK. This is unfortunate perfomance loss.
Here I propose a patch; just workarounding hang up during the build.
there may be performance loss by not using ATLAS's LAPACK.
Index: Makefile
===================================================================
RCS file: /home/pcvs/ports/math/R/Makefile,v
retrieving revision 1.57
diff -u -r1.57 Makefile
--- Makefile 25 Jan 2007 17:56:40 -0000 1.57
+++ Makefile 9 Feb 2007 22:08:12 -0000
@@ -72,9 +72,15 @@
.if defined(WITH_ATLAS)
LIB_DEPENDS+= atlas.2:${PORTSDIR}/math/atlas
-CONFIGURE_ARGS+=--with-lapack="-lalapack -lcblas" --with-blas="-lf77blas"
+CONFIGURE_ARGS+=--with-blas="-lf77blas -latlas"
+# A workaround to prevent hangs up during the build.
+.if ${ARCH} != "i386"
+CONFIGURE_ARGS+=--with-lapack="-lalapack -lcblas"
PLIST_SUB+= BLAS="@comment "
.else
+PLIST_SUB+= BLAS=""
+.endif
+.else
LIB_DEPENDS+= blas.2:${PORTSDIR}/math/blas
CONFIGURE_ARGS+=--with-blas="-lblas"
PLIST_SUB+= BLAS=""
Thanks for your patience, and sorry for inconvenience.
Sincerely yours,
-- NAKATA, Maho (maho@FreeBSD.org)
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