Update to 3.8.4 before the 3.10 release; clean up (substantially

reduce build times, introduce options, drop unneeded dependencies,
and make linking with ATLAS shared libraries easier)

Thanks to maho and A. Shterenlikht for review and testing, and to
mm, T.  Ludwig, skreuzer, and E. Lemos de Sa for reminders or related
submissions

PR:		117923, 139169, 155650, 159876

9 files changed, 200 insertions, 213 deletions

diff --git a/math/atlas/files/Makefile.test b/math/atlas/files/Makefile.test
deleted file mode 100644
index 1eaae571f323..000000000000
--- a/math/atlas/files/Makefile.test
+++ /dev/null
@@ -1,35 +0,0 @@
-ALLTESTS =	xsl3blastst xdl3blastst xcl3blastst xzl3blastst \
-		xsl2blastst xdl2blastst xcl2blastst xzl2blastst \
-		xsl1blastst xdl1blastst xcl1blastst xzl1blastst \
-		xslutst xslutstF xdlutst xdlutstF xclutst xclutstF \
-		xzlutst xzlutstF xsllttst xsllttstF xdllttst xdllttstF \
-		xcllttst xcllttstF xzllttst xzllttstF
-
-ALLTESTS_PT =	xsl3blastst_pt xdl3blastst_pt xcl3blastst_pt xzl3blastst_pt \
-		xslutst_pt xslutstF_pt xdlutst_pt xdlutstF_pt xclutst_pt xclutstF_pt \
-		xzlutst_pt xzlutstF_pt xsllttst_pt xsllttstF_pt xdllttst_pt \
-		xdllttstF_pt xcllttst_pt xcllttstF_pt xzllttst_pt xzllttstF_pt
-#build errors?
-#		xsl2blastst_pt xdl2blastst_pt xcl2blastst_pt xzl2blastst_pt \
-#		xsl1blastst_pt xdl1blastst_pt xcl1blastst_pt xzl1blastst_pt \
-#Failed tests
-do-test:
-	@for i in ${ALLTESTS} ; do \
-		${ECHO_CMD} "Making $${i}" ; \
-		cd ${WRKDIR}/ATLAS/NON_THREADED_PIC/bin ; ${MAKE} $${i} ; \
-	done
-	@for i in ${ALLTESTS_PT} ; do \
-		${ECHO_CMD} "Making $${i}" ; \
-		cd ${WRKDIR}/ATLAS/THREADED_PIC/bin ; ${MAKE} $${i} ; \
-	done
-	@for i in ${ALLTESTS} ; do \
-		${ECHO_CMD} "Benchmarking $${i}" ; \
-		cd ${WRKDIR}/ATLAS/NON_THREADED_PIC/bin ; ./$${i} ; \
-	done
-	@for i in ${ALLTESTS_PT} ; do \
-		${ECHO_CMD} "Benchmarking $${i}" ; \
-		cd ${WRKDIR}/ATLAS/THREADED_PIC/bin ; ./$${i} ; \
-	done
-		
-
-
diff --git a/math/atlas/files/alpha-patch b/math/atlas/files/alpha-patch
deleted file mode 100644
index 564198d5be91..000000000000
--- a/math/atlas/files/alpha-patch
+++ /dev/null
@@ -1,9 +0,0 @@
---- src/blas/gemm/GOTO/ATLU_usergemm.c~ Mon Jun 17 10:38:22 2002
-+++ src/blas/gemm/GOTO/ATLU_usergemm.c  Sun Aug 18 10:41:19 2002
-@@ -1,5 +1,5 @@
- #include "atlas_misc.h"
--#include <sys/mman.h>
-+/*#include <sys/mman.h>*/
- 
- #ifdef EV6
-    #ifdef ATL_OS_OSF1
diff --git a/math/atlas/files/patch-CONFIG+src+SpewMakeInc.c b/math/atlas/files/patch-CONFIG+src+SpewMakeInc.c
index 975591f13f3b..6f41c19512da 100644
--- a/math/atlas/files/patch-CONFIG+src+SpewMakeInc.c
+++ b/math/atlas/files/patch-CONFIG+src+SpewMakeInc.c
@@ -1,15 +1,60 @@
---- CONFIG/src/SpewMakeInc.c.orig	2007-10-11 05:40:21.000000000 +0900
-+++ CONFIG/src/SpewMakeInc.c	2007-10-29 11:03:11.000000000 +0900
-@@ -693,14 +693,14 @@
+--- CONFIG/src/SpewMakeInc.c.orig	2011-05-14 13:33:24.000000000 -0400
++++ CONFIG/src/SpewMakeInc.c	2011-09-06 06:06:00.000000000 -0400
+@@ -399,7 +399,8 @@
+             &mhz, &ptrbits, &ncpu, comps, &gccflags, &outfile, &srcdir,
+             &blddir, &USEDEFL1, &USEARCHDEF, &nof77, &f2cdefs, &cdefs, &pmake,
+             &flapack, &smaflags, &dmaflags, &f77lib, &l2size, &targ);
+-   if (ncpu > 1) THREADS = 1;
++ /*   if (ncpu > 1) THREADS = 1; */
++    THREADS = 1;
+    if (!outfile)
+       fpout = stdout;
+    else
+@@ -482,7 +483,7 @@
+    fprintf(fpout, "#  -------------------------------------------------\n");
+    fprintf(fpout, "#  Name indicating the platform to configure BLAS to\n");
+    fprintf(fpout, "#  -------------------------------------------------\n");
+-   fprintf(fpout, "   ARCH = %s", machnam[mach]);
++   fprintf(fpout, "   ATLAS_ARCH = %s", machnam[mach]);
+    fprintf(fpout, "%d", ptrbits);
+    if (ISAX)
+       fprintf(fpout, "%s", ISAXNAM[ISAX]);
+@@ -649,7 +650,7 @@
+           comps[i][j-2] == 'c' && comps[i][j-1] == 'c')
+          break;
+    }
+-   goodgcc = (j < NCOMP) ? comps[j] : "gcc";
++   goodgcc = (j < NCOMP) ? comps[j] : "%%CC%%";
+    fprintf(fpout, "   GOODGCC = %s", goodgcc);
+    if (gccflags)
+       fprintf(fpout, " %s", gccflags);
+@@ -661,7 +662,7 @@
+        fprintf(fpout, " %s", sp);
+    fprintf(fpout, "\n");
+ 
+-   fprintf(fpout, "   LDFLAGS =");
++   fprintf(fpout, "   LDFLAGS = %%LDFLAGS%% ");
+    if (MachIsX86(mach))
+    {
+       if (ptrbits == 32)
+@@ -679,7 +680,7 @@
+    fprintf(fpout, "   FCLINKFLAGS = $(FLINKFLAGS)");
+    if (strstr(comps[F77_], "ifort") && !OSIsWin(OS))
+       fprintf(fpout, " -nofor_main");
+-   fprintf(fpout, "\n   ARCHIVER = ar\n");
++   fprintf(fpout, "\n   ARCHIVER = $(AR)\n");
+    fprintf(fpout, "   ARFLAGS  = r\n");
+ /*
+  * JF Mertens says that even x86 OS X still need ranlib for safety
+@@ -702,14 +703,14 @@
     fprintf(fpout, "#  ------------------------------------\n");
     fprintf(fpout, "#  Reference and system libraries\n");
     fprintf(fpout, "#  ------------------------------------\n");
 -   fprintf(fpout, "   BLASlib = \n");
 -   fprintf(fpout, "   FBLASlib = \n");
--   fprintf(fpout, "   FLAPACKlib = ");
-+   fprintf(fpout, "   BLASlib = -L%%LOCALBASE%%/lib -lblas\n");
-+   fprintf(fpout, "   FBLASlib = -L%%LOCALBASE%%/lib -lblas\n");
-+   fprintf(fpout, "   FLAPACKlib = -L%%LOCALBASE%%/lib -llapack");
++   fprintf(fpout, "   BLASlib = $(BLAS)\n");
++   fprintf(fpout, "   FBLASlib = $(BLAS)\n");
+    fprintf(fpout, "   FLAPACKlib = ");
     if (flapack) fprintf(fpout, "%s", flapack);
     fprintf(fpout, "\n");
     fprintf(fpout, "   SLAPACKlib = \n");
diff --git a/math/atlas/files/patch-CONFIG+src+atlcomp.txt b/math/atlas/files/patch-CONFIG+src+atlcomp.txt
deleted file mode 100644
index eba33bc10892..000000000000
--- a/math/atlas/files/patch-CONFIG+src+atlcomp.txt
+++ /dev/null
@@ -1,124 +0,0 @@
---- CONFIG/src/atlcomp.txt.orig	2009-02-19 03:47:37.000000000 +0900
-+++ CONFIG/src/atlcomp.txt	2009-04-13 16:46:44.000000000 +0900
-@@ -40,34 +40,34 @@
- #
- # Core2Solo and Core2Duo
- MACH=Core2Solo OS=ALL LVL=1000 COMPS=smc,dmc,skc,dkc,icc
--   'gcc' '-fomit-frame-pointer -mfpmath=sse -msse3 -O2'
-+   '%%CC%%' '-fomit-frame-pointer -mfpmath=sse -msse3 -O2'
- # Core2 & Corei7
- MACH=Corei7 OS=ALL LVL=1000 COMPS=smc,dmc,skc,dkc,icc
--   'gcc' '-fomit-frame-pointer -mfpmath=sse -msse3 -O2 -fno-schedule-insns2'
-+   '%%CC%%' '-fomit-frame-pointer -mfpmath=sse -msse3 -O2 -fno-schedule-insns2'
- MACH=Core2 OS=ALL LVL=1000 COMPS=smc,dmc,skc,dkc,icc
--   'gcc' '-fomit-frame-pointer -mfpmath=sse -msse3 -O2'
-+   '%%CC%%' '-fomit-frame-pointer -mfpmath=sse -msse3 -O2'
- # PPRO,PII,PIII,P4,P4E,K7,HAMMER
- MACH=PPRO,PII,PIII,P4,P4E,K7,HAMMER OS=ALL LVL=1000 COMPS=f77
--   'gfortran' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
-+   '%%FC%%' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
- MACH=PPRO,PII,PIII,P4,P4E,K7,HAMMER OS=ALL LVL=1000 COMPS=smc,dmc,skc,dkc,icc
--   'gcc' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
-+   '%%CC%%' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
- # CoreSolo,CoreDuo
- MACH=CoreSolo,CoreDuo OS=ALL LVL=1000 COMPS=smc,dmc,skc,dkc,icc
--   'gcc' '-fomit-frame-pointer -O3 -mfpmath=387'
-+   '%%CC%%' '-fomit-frame-pointer -O3 -mfpmath=387'
- # 3rd generation opteron (Barcelona and descendents)
- MACH=AMD64K10h OS=ALL LVL=1000 COMPS=f77
--   'gfortran' '-fomit-frame-pointer -mfpmath=sse -msse3 -O2 -falign-loops=32'
-+   '%%FC%%' '-fomit-frame-pointer -mfpmath=sse -msse3 -O2 -falign-loops=32'
- MACH=AMD64K10h OS=ALL LVL=1000 COMPS=smc,dmc,skc,dkc,icc
--   'gcc' '-fomit-frame-pointer -mfpmath=sse -msse3 -O2 -falign-loops=32'
-+   '%%CC%%' '-fomit-frame-pointer -mfpmath=sse -msse3 -O2 -falign-loops=32'
- # UltraSPARC III & IV
- MACH=USIII,USIV OS=ALL LVL=1000 COMPS=smc,dmc,skc,dkc
--   'gcc' '-mcpu=ultrasparc3 -mtune=ultrasparc3 -O3 -funroll-all-loops'
-+   '%%CC%%' '-mcpu=ultrasparc3 -mtune=ultrasparc3 -O3 -funroll-all-loops'
- MACH=USIII,USIV OS=ALL LVL=1000 COMPS=icc,xcc
--   'gcc' '-mcpu=ultrasparc3 -mtune=ultrasparc3 -O'
-+   '%%CC%%' '-mcpu=ultrasparc3 -mtune=ultrasparc3 -O'
- MACH=USIII,USIV OS=ALL LVL=1000 COMPS=f77
-    'f77' '-dalign -native -xO5'
- MACH=USIII,USIV OS=ALL LVL=100 COMPS=f77
--   'gfortran' '-O -mcpu=ultrasparc3 -mtune=ultrasparc3'
-+   '%%FC%%' '-O -mcpu=ultrasparc3 -mtune=ultrasparc3'
- MACH=USIII,USIV OS=ALL LVL=10 COMPS=f77
-    'g77' '-O -mcpu=ultrasparc3 -mtune=ultrasparc3'
- #
-@@ -75,11 +75,11 @@
- #
- # These gcc 4 default flags will die on gcc3, allowing gcc3's flags to be used
- MACH=IA64Itan,IA64Itan2 OS=ALL LVL=1010 COMPS=smc,dmc,skc,dkc
--   'gcc' '-fomit-frame-pointer -O2 -fno-tree-loop-optimize'
-+   '%%CC%%' '-fomit-frame-pointer -O2 -fno-tree-loop-optimize'
- MACH=IA64Itan,IA64Itan2 OS=ALL LVL=1000 COMPS=smc,dmc,skc,dkc
--   'gcc' '-fomit-frame-pointer -O2'
-+   '%%CC%%' '-fomit-frame-pointer -O2'
- MACH=IA64Itan,IA64Itan2 OS=ALL LVL=1010 COMPS=f77
--   'gfortran' '-fomit-frame-pointer -O2 -fno-tree-loop-optimize'
-+   '%%FC%%' '-fomit-frame-pointer -O2 -fno-tree-loop-optimize'
- #
- # IRIX/MIPS
- #
-@@ -93,16 +93,16 @@
- # Linux/MIPSICE9
- #
- MACH=MIPSICE9 OS=ALL LVL=1000 COMPS=icc,smc,dmc,skc,dkc,xcc
--   'gcc' '-O2 -mips64 -march=5kf -mtune=5kf -fno-schedule-insns -fschedule-insns2 -fno-peephole -fno-peephole2'
-+   '%%CC%%' '-O2 -mips64 -march=5kf -mtune=5kf -fno-schedule-insns -fschedule-insns2 -fno-peephole -fno-peephole2'
- MACH=MIPSICE9 OS=ALL LVL=100 COMPS=f77
-    'pathf95' '-march=auto -O2'
- #
- # G4 flags
- #
- MACH=PPCG4 OS=ALL LVL=1000 COMPS=icc,smc,dmc,skc,dkc,xcc
--   'gcc' '-O3 -maltivec -mabi=altivec -mcpu=7400 -mtune=7400'
-+   '%%CC%%' '-O3 -maltivec -mabi=altivec -mcpu=7400 -mtune=7400'
- MACH=PPCG4 OS=OSX LVL=1001 COMPS=icc,smc,dmc,skc,dkc,xcc
--   'gcc' '-O3 -maltivec -mabi=altivec -mcpu=7400 -mtune=7400 -no-cpp-precomp -faltivec'
-+   '%%CC%%' '-O3 -maltivec -mabi=altivec -mcpu=7400 -mtune=7400 -no-cpp-precomp -faltivec'
- 
- #
- # OS X / PowerPC970; the
-@@ -111,19 +111,19 @@
- # performance by removing them (for all PowerPC platforms)
- #
- MACH=PPCG5 OS=OSX LVL=1001 COMPS=icc,smc,dmc,skc,dkc,xcc
--   'gcc' '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -faltivec -O3'
-+   '%%CC%%' '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -faltivec -O3'
- MACH=PPCG5 OS=OSX LVL=1010 COMPS=icc,smc,dmc,skc,dkc,xcc
--   'gcc' '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -faltivec -force_cpusubtype_ALL -O3 -fno-schedule-insns -fno-rerun-loop-opt'
-+   '%%CC%%' '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -faltivec -force_cpusubtype_ALL -O3 -fno-schedule-insns -fno-rerun-loop-opt'
- MACH=PPCG5 OS=ALL LVL=1000 COMPS=icc,smc,dmc,skc,dkc,xcc
--   'gcc' '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -O3'
-+   '%%CC%%' '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -O3'
- MACH=POWER5 OS=ALL LVL=1010 COMPS=icc,smc,dmc,skc,dkc,xcc
--   'gcc' '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns -fno-rerun-loop-opt'
-+   '%%CC%%' '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns -fno-rerun-loop-opt'
- MACH=POWER5 OS=ALL LVL=1010 COMPS=f77
--   'gfortran' '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns -fno-rerun-loop-opt'
-+   '%%FC%%' '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns -fno-rerun-loop-opt'
- MACH=POWER5 OS=ALL LVL=1010 COMPS=f77
-    'xlf' '-qtune=pwr5 -qarch=pwr5 -O3 -qmaxmem=-1 -qfloat=hsflt'
- MACH=POWER4 OS=ALL LVL=1010 COMPS=icc,dmc,smc,dkc,skc,xcc
--   'gcc' '-mcpu=power4 -mtune=power4 -O3 -fno-schedule-insns -fno-rerun-loop-opt'
-+   '%%CC%%' '-mcpu=power4 -mtune=power4 -O3 -fno-schedule-insns -fno-rerun-loop-opt'
- MACH=POWER4 OS=ALL LVL=1010 COMPS=f77
-    'xlf' '-qtune=pwr4 -qarch=pwr4 -O3 -qmaxmem=-1 -qfloat=hsflt'
- #
-@@ -143,10 +143,10 @@
- # Generic defaults
- #
- MACH=ALL OS=ALL LVL=5 COMPS=icc,smc,dmc,skc,dkc,xcc
--   'gcc' '-O -fomit-frame-pointer'
-+   '%%CC%%' '-O -fomit-frame-pointer'
- MACH=ALL OS=ALL LVL=5 COMPS=f77
--   'gfortran' '-O'
-+   '%%FC%%' '-O'
- MACH=ALL OS=ALL LVL=4 COMPS=f77
--   'g77' '-O'
-+   '%%FC%%' '-O'
- MACH=ALL OS=ALL LVL=0 COMPS=f77
--   'f77' '-O'
-+   '%%FC%%' '-O'
diff --git a/math/atlas/files/patch-CONFIG+src+backend+archinfo_freebsd.c b/math/atlas/files/patch-CONFIG+src+backend+archinfo_freebsd.c
index a8f1e062dab5..b390c3540a3e 100644
--- a/math/atlas/files/patch-CONFIG+src+backend+archinfo_freebsd.c
+++ b/math/atlas/files/patch-CONFIG+src+backend+archinfo_freebsd.c
@@ -1,32 +1,50 @@
---- CONFIG/src/backend/archinfo_freebsd.c.orig	Wed Jan 31 06:30:00 2007
-+++ CONFIG/src/backend/archinfo_freebsd.c	Thu Feb  8 16:37:05 2007
-@@ -73,13 +73,24 @@
+--- CONFIG/src/backend/archinfo_freebsd.c.orig	2011-05-14 13:33:24.000000000 -0400
++++ CONFIG/src/backend/archinfo_freebsd.c	2011-09-20 07:05:52.000000000 -0400
+@@ -62,7 +62,7 @@
+    switch(fam)
+    {
+    case AFPPC: /* don't know */
+-      if (!CmndOneLine(NULL, "sysctl hw.model", res))
++      if (!CmndOneLine(NULL, "sysctl -n hw.model", res))
+       {
+          if (strstr(res, "PowerMac"))
+          {
+@@ -97,32 +97,57 @@
+          }
        }
        break;
-    case AFSPARC: /* don't know */
-+      if (!CmndOneLine(NULL, "sysctl hw.model", res))
-+      {
+-   case AFSPARC: /* don't know */
+-      break;
+-   case AFALPHA:
+-      #if 0
+-      if (!CmndOneLine(NULL, "sysctl hw.model", res))
++   case AFSPARC: /* from src/sys/sparc64/sparc64/identcpu.c */
++      if (!CmndOneLine(NULL, "sysctl -n hw.model", res))
+       {
+-         if (strstr(res, "433au")) mach = Dec21164;
+-         else if (strstr(res, "XP1000")) mach = Dec21264;
 +          if (strstr(res, "UltraSparc-IV"))  mach = SunUSIV;
-+          if (strstr(res, "UltraSparc-II")) mach = SunUSII;
-+          if (strstr(res, "UltraSparc-I")) mach = SunUSI;
-+          if (strstr(res, "UltraSparc")) mach = SunUSI;
++          else if (strstr(res, "UltraSparc-III"))  mach = SunUSIII;
++          else if (strstr(res, "UltraSparc-II")) mach = SunUSII;
 +          else mach = SunUSI;
-+      }
-       break;
-    case AFALPHA:
-       #if 0
-       if (!CmndOneLine(NULL, "sysctl hw.model", res))
-       {
-          if (strstr(res, "433au")) mach = Dec21164;
-+         else if (strstr(res, "500au")) mach = Dec21164;
-+         else if (strstr(res, "AlphaPC 164")) mach = Dec21164;
-          else if (strstr(res, "XP1000")) mach = Dec21264;
-+         else mach = Dec21264;
        }
-       #endif
+-      #endif
+       break;
+-   case AFIA64: /* don't know */
++   case AFIA64: /* from src/sys/ia64/ia64/machdep.c */
++	if (!CmndOneLine(NULL, "sysctl -n hw.model", res))
++      {
++	 if (strstr(res, "Deerfield")) mach = IA64Itan2;
++	 else if (strstr(res, "McKinley")) mach = IA64Itan2;
++	 else if (strstr(res, "Madison")) mach = IA64Itan2;
++	 else if (strstr(res, "Montecito")) mach = IA64Itan2;
++	 else if (strstr(res, "Montvale")) mach = IA64Itan2;
++         else if (strstr(res, "Merced")) mach = IA64Itan;
++      }	   
        break;
-@@ -89,15 +100,33 @@
-       if (!CmndOneLine(NULL, "sysctl hw.model", res))
+    case AFX86:
+-      if (!CmndOneLine(NULL, "sysctl hw.model", res))
++      if (!CmndOneLine(NULL, "sysctl -n hw.model", res))
        {
           if (strstr(res, "Pentium Pro")) mach = IntPPRO;
 +         else if (strstr(res, "Pentium(R) D")) mach = IntP4E;
@@ -63,13 +81,57 @@
        }
        break;
     default:;
-@@ -156,8 +185,8 @@
+@@ -135,7 +160,7 @@
+    int ncpu = 0;
+    char *reslns, res[1024];
+ 
+-   if (!CmndOneLine(NULL, "sysctl hw.ncpu", res)) ncpu = GetLastInt(res);
++   if (!CmndOneLine(NULL, "sysctl -n hw.ncpu", res)) ncpu = GetFirstInt(res);
+    return(ncpu);
+ }
+ 
+@@ -169,7 +194,8 @@
+  *    If uname is a known 64-bit platform, we're sure we've got OS support
+  *    for 64bits (may not have compiler support, but that's not our fault)
+  */
+-      if (strstr(res, "x86_64") || strstr(res, "ppc64") || strstr(res, "ia64"))
++      if (strstr(res, "amd64") || strstr(res, "ia64") || 
++	strstr(res, "powerpc64") || strstr(res, "sparc64"))
+       {
+          iret = 64;
+          *sure = 1;
+@@ -182,8 +208,10 @@
  {
     int mhz=0;
     char res[1024];
 -   if (!CmndOneLine(NULL, "sysctl hw.cpufrequency", res) )
-+   if (!CmndOneLine(NULL, "sysctl machdep.tsc_freq", res) )
-       mhz = GetFirstDouble(res) / 1000000;
+-      mhz = GetFirstDouble(res) / 1000000;
++   if (!CmndOneLine(NULL, "sysctl -n dev.cpu.0.freq", res) )
++      mhz = GetFirstInt(res);
++   else if (!CmndOneLine(NULL, "sysctl -n hw.freq.cpu", res) )
++      mhz = GetFirstInt(res);
     return(mhz);
  }
  
+@@ -192,20 +220,7 @@
+  * RETURNS: 1 if cpu throttling is detected, 0 otherwise
+  */
+ {
+-   int iret=0;
+-   int imax=0, imin=0, icur=0;
+-   char res[1024];
+-
+-   if (!CmndOneLine(NULL, "sysctl hw.cpufrequency_max", res) )
+-      imax = GetFirstInt(res);
+-   if (!CmndOneLine(NULL, "sysctl hw.cpufrequency_min", res) )
+-      imin = GetFirstInt(res);
+-   if (imax)
+-   {
+-      if (imax != imin)
+-         iret = 1;
+-   }
+-   return(iret);
++   return(0);
+ }
+ 
+ main(int nargs, char **args)
diff --git a/math/atlas/files/patch-CONFIG+src+backend+archinfo_x86.c b/math/atlas/files/patch-CONFIG+src+backend+archinfo_x86.c
new file mode 100644
index 000000000000..23f5948eceea
--- /dev/null
+++ b/math/atlas/files/patch-CONFIG+src+backend+archinfo_x86.c
@@ -0,0 +1,14 @@
+--- CONFIG/src/backend/archinfo_x86.c.orig	2011-05-14 13:33:24.000000000 -0400
++++ CONFIG/src/backend/archinfo_x86.c	2011-09-06 05:59:18.000000000 -0400
+@@ -309,9 +309,10 @@
+       case 0x1A:
+       case 0x1E:
+       case 0x1F:
++      case 0x25:
++      case 0x2C:
+          iret = IntCorei1;
+          break;
+-      case 0x25:
+       case 0x2A:
+          iret = IntCorei2;
+ 	 break;
diff --git a/math/atlas/files/patch-makes+Make.sysinfo b/math/atlas/files/patch-makes+Make.sysinfo
new file mode 100644
index 000000000000..51f755c68e4f
--- /dev/null
+++ b/math/atlas/files/patch-makes+Make.sysinfo
@@ -0,0 +1,11 @@
+--- makes/Make.sysinfo.orig	2011-05-14 13:33:24.000000000 -0400
++++ makes/Make.sysinfo	2011-09-03 12:30:23.000000000 -0400
+@@ -13,7 +13,7 @@
+ res/L1CacheSize:
+ 	$(MAKE) RunL1 MaxL1=$(MaxL1)
+ RunL1 : xL1
+-	$(ATLRUN) $(SYSdir) xL1 $(MaxL1)
++	$(ATLRUN) $(SYSdir) xL1
+ 
+ $(INCAdir)/atlas_type.h:
+ 	$(MAKE) RunTyp
diff --git a/math/atlas/files/thread-patch b/math/atlas/files/thread-patch
deleted file mode 100644
index ea23f566a144..000000000000
--- a/math/atlas/files/thread-patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- CONFIG/src/SpewMakeInc.c~	Fri Feb 16 11:40:19 2007
-+++ CONFIG/src/SpewMakeInc.c	Fri Feb 16 11:41:06 2007
-@@ -332,7 +332,8 @@
-             &mhz, &ptrbits, &ncpu, comps, &gccflags, &outfile, &srcdir,
-             &blddir, &USEDEFL1, &USEARCHDEF, &nof77, &f2cdefs, &cdefs, &pmake,
-             &flapack, &smaflags, &dmaflags, &f77lib, &l2size, &targ);
--   if (ncpu > 1) THREADS = 1;
-+ /*   if (ncpu > 1) THREADS = 1; */
-+    THREADS = 1;
-    if (!outfile)
-       fpout = stdout;
-    else
diff --git a/math/atlas/files/tuning-message b/math/atlas/files/tuning-message
new file mode 100644
index 000000000000..a78973ba4bdc
--- /dev/null
+++ b/math/atlas/files/tuning-message
@@ -0,0 +1,35 @@
+
+	This port engages in a long, computationally-demanding tuning process.
+	Builds can take a day or more on older hardware, and can temporarily
+	occupy several hundred megabytes of disk space.  You are advised to
+	disable all forms of power management or CPU throttling during the
+	build, and to set operating parameters to static values at which you
+	ultimately intend to use the software.  You should also avoid placing
+	heavy loads on the system during the build, and temporarily disable
+	any automatons that may do so.  If you fail to follow these guidelines,
+	you may prolong the build and obtain libraries with sub-optimal
+	performance.
+
+	Occasionally the auto-configuration may fail for certain platforms,
+	and you may have to override the architecture, compiler flags, assembly
+	language dialect, or pointer bit-width by issuing additional configure
+	arguments.  Consult the FAQ, installation guide, and errata page at
+	the project website for help if this is necessary, and notify the
+	port maintainer.  Note that in most cases the port intentionally
+	overrides user-selected compiler flags.
+
+	If your machine will be solely dedicated to building atlas during the
+	lengthy optimization process, and not subjected to other loads, you
+	may enable the more accurate wall timer (instead of the default
+	CPU-time timer) with the WALL_TIMER option.
+
+	If you want to override the architecture auto-detection, and use a
+	specific architectural default, then set WITH_ARCHDEF and define
+	ARCHDEF to be either the full path to a gzipped architectural default
+	tarball with suffix .tgz, or the basename of such a tarball in the
+	distribution CONFIG/ARCHS sub-directory.  If you want to ignore all
+	architectural defaults, set WITH_ARCHDEF and define ARCHDEF=NONE.
+	Note that the use of versioned compiler names in Ports may prevent
+	the use of architectural default tarballs constructed on other systems
+	without some changes to their directory structure.
+