Merge branch 'master' of ssh://scm.sourcemage.org/smgl/grimoire into smglMaster

10 files changed, 203 insertions, 18 deletions

diff --git a/cluster/atlas/BUILD b/cluster/atlas/BUILD
index e16378d5e7..69350786b9 100755
--- a/cluster/atlas/BUILD
+++ b/cluster/atlas/BUILD
@@ -2,18 +2,11 @@ cd  $SOURCE_DIRECTORY/bld                            &&
 if is_depends_enabled $SPELL lapack; then
   OPTS="--with-netlib-lapack=$INSTALL_ROOT/usr/lib/liblapack.a $OPTS"
 fi                                                   &&
-if [ $WALL_TIMER == y ]; then
-  if [[ ${SMGL_COMPAT_ARCHS[1]} == "ia32" || ${SMGL_COMPAT_ARCHS[1]} == "x86_64" ]]; then
-    OPTS="-D c -DPentiumCPS=$CPU_FREQ $OPTS"
-  else
-    OPTS="-D c -DWALL $OPTS"
-  fi
-fi                                                   &&
 
 ../configure -Si cputhrchk 0 \
              -Fa alg -fPIC \
              -b ${SMGL_COMPAT_ARCHS[0]} \
-             --prefix=$INSTALL_ROOT/usr              &&
+             --prefix=$INSTALL_ROOT/usr  ${OPTS}     &&
 sedit '/RANLIB/s/echo/ranlib/' Make.inc              &&
 
 make_single &&
diff --git a/cluster/atlas/CONFIGURE b/cluster/atlas/CONFIGURE
index 72d9da5cb6..13ae5e6b7b 100755
--- a/cluster/atlas/CONFIGURE
+++ b/cluster/atlas/CONFIGURE
@@ -2,12 +2,3 @@ config_query SHARED_LIB "Do you want shared libraries to be built?" y
 if [ $SHARED_LIB == y ]; then
   config_query PTSHARED_LIB "Do you want parallelized shared libraries to be built?" y
 fi
-
-config_query WALL_TIMER "Do you want to enable wall timer? (if your comupter load is not high, this will provide a higher resolution timer)" y
-
-# Haven't tried with other archs than ia32 yet
-if [ $WALL_TIMER == y ]; then
-  if [[ ${SMGL_COMPAT_ARCHS[1]} == "ia32" || ${SMGL_COMPAT_ARCHS[1]} == "x86_64" ]]; then
-    config_query_string CPU_FREQ "What is your CPU frequency in MHz?" 1000
-  fi
-fi
diff --git a/cluster/atlas/DETAILS b/cluster/atlas/DETAILS
index b6122a4654..ba91f4604d 100755
--- a/cluster/atlas/DETAILS
+++ b/cluster/atlas/DETAILS
@@ -1,5 +1,6 @@
            SPELL=atlas
          VERSION=3.8.3
+      PATCHLEVEL=1
           SOURCE=${SPELL}$VERSION.tar.bz2
 SOURCE_DIRECTORY=$BUILD_DIRECTORY/ATLAS
    SOURCE_URL[0]=$SOURCEFORGE_URL/math-atlas/$SOURCE
diff --git a/cluster/atlas/HISTORY b/cluster/atlas/HISTORY
index 2c2d89f4f5..4c8c9d854b 100644
--- a/cluster/atlas/HISTORY
+++ b/cluster/atlas/HISTORY
@@ -1,3 +1,12 @@
+2011-05-13 Peng Chang (Charles) <chp@sourcemage.org>
+	* DETAILS: PATCHLEVEL++
+	* BUILD, CONFIGURE: clean up ineffective options
+	* BUILD: fixed a bug unnoticed for 2 years, appending ${OPTS} to the end
+	  of configure
+	* PRE_BUILD: applying upstream patch to fix code generation problems
+	  during build
+	* emit_mm.patch: the above patch generated from upstream update
+
 2009-05-17 Peng Chang (Charles) <chp516@gmail.com>
 	* BUILD: changed accordingly
 	* CONFIGURE: added this file to query various options
diff --git a/cluster/atlas/PRE_BUILD b/cluster/atlas/PRE_BUILD
index cc0a8ec1da..ce52e773e0 100755
--- a/cluster/atlas/PRE_BUILD
+++ b/cluster/atlas/PRE_BUILD
@@ -1,2 +1,5 @@
 default_pre_build             &&
-mkdir  $SOURCE_DIRECTORY/bld
+mkdir  $SOURCE_DIRECTORY/bld  &&
+
+cd $SOURCE_DIRECTORY          &&
+patch tune/blas/gemm/emit_mm.c $SPELL_DIRECTORY/emit_mm.patch
diff --git a/cluster/atlas/emit_mm.patch b/cluster/atlas/emit_mm.patch
new file mode 100644
index 0000000000..0ce40f249b
--- /dev/null
+++ b/cluster/atlas/emit_mm.patch
@@ -0,0 +1,154 @@
+Generated by Charles Peng <chp@sourcemage.org>
+--- emit_mm.c	2009-02-19 02:48:25.000000000 +0800
++++ emit_mm.c	2011-05-13 16:21:41.491001028 +0800
+@@ -1,5 +1,5 @@
+ /*
+- *             Automatically Tuned Linear Algebra Software v3.8.3
++ *             Automatically Tuned Linear Algebra Software v3.8.4
+  *                    (C) Copyright 1997 R. Clint Whaley
+  *
+  * Redistribution and use in source and binary forms, with or without
+@@ -1638,7 +1638,7 @@ void MMDeclare(FILE *fpout, char *spc, c
+            cTA, cTB, M, N, K);
+    fprintf(fpout, " * lda=%d, ldb=%d, ldc=%d, mu=%d, nu=%d, ku=%d, pf=%d\n",
+            lda, ldb, ldc, mu, nu, ku, pfA);
+-   fprintf(fpout, " * Generated by ATLAS/tune/blas/gemm/emit_mm.c (3.8.3)\n");
++   fprintf(fpout, " * Generated by ATLAS/tune/blas/gemm/emit_mm.c (3.8.4)\n");
+    fprintf(fpout, " */\n");
+ }
+ 
+@@ -3082,7 +3082,17 @@ int CompMultHandled(CLEANNODE *cp, int n
+  * Returns 1 if nb is handled by succeeding case, 0 otherwise
+  */
+ {
+-   for (; cp; cp = cp->next) if (nb % cp->imult == 0) return(1);
++
++   for (; cp; cp = cp->next)
++   {
++      if (cp->fixed == 2)
++      {
++         if (cp->imult == nb)
++            return(1);
++      }
++      else if (nb % cp->imult == 0)
++         return(1);
++   }
+    return(0);
+ }
+ 
+@@ -3110,14 +3120,6 @@ int *GetCompNBs(enum CW which, CLEANNODE
+       istop = cp0->nb;
+       while (istop % cp0->imult) istop--;
+       if (istop == cp0->nb) istop -= cp0->imult;
+-      for (cp=cp0->next; cp; cp = cp->next)
+-      {
+-         if (cp->imult % cp0->imult == 0 && cp->fixed != 2)
+-         {
+-            istop = cp->imult;
+-            break;
+-         }
+-      }
+ 
+       for (i=2*cp0->imult; i <= istop; i += cp0->imult)
+       {
+@@ -3582,7 +3584,7 @@ void GenUpNB_if(char pre, enum CW which,
+    CLEANNODE *wp, *cp0;
+    FILE *fp;
+    int i;
+-   const char *ifs = "else if", *ifp;
++   const char *ifs = "else if", *ifp, *sp;
+    const char cwh[3] = {'M', 'N', 'K'};
+    char ln[128], st[2], *typ;
+ 
+@@ -3613,7 +3615,11 @@ void GenUpNB_if(char pre, enum CW which,
+ 
+    if (pre == 'c') pre = 'C';
+    else if (pre == 'z') pre = 'Z';
+-
++/*
++ * fixed=2 means a kernel specialized for that exact N.  They will have not
++ * survived pruning if they weren't better than all the general algorithms,
++ * so we can test for them all up front
++ */
+    for (cp=cp0; cp; cp = cp->next)  /* handle fixed = 2 cases */
+    {
+       if (cp->fixed == 2)
+@@ -3625,36 +3631,49 @@ void GenUpNB_if(char pre, enum CW which,
+          ifp = ifs;
+       }
+    }
+-
+-   for (cp=cp0; cp; cp = cp->next)  /* fixed = 1 cases */
+-   {
+-      if (cp->fixed == 1)
+-      {
+-         for (i=cp->ncomps-1; i >= 0; i--)
+-         {
+-            if (cp->imult > 1)
+-               fprintf(fp, "   %s (%c == %d)\n", ifp, cwh[which], cp->NBs[i]);
+-            else fprintf(fp, "   else\n");
+-            fprintf(fp, "   {\n      ATL_%cup%cBmm%d_%d_%d_b%c%s;\n   }\n",
+-                    pre, cwh[which], cp->NBs[i], cp->imult, cp->fixed,
+-                    cbeta, MMARGS);
+-            ifp = ifs;
+-         }
+-      }
+-   }
+-   for (cp=cp0; cp; cp = cp->next)  /* fixed = 0 cases */
+-   {
++/*
++ * All remaining kernels are selected by being a multiple of imult;
++ * fixed=0 will be called directly, while fixed=1 will have a nested
++ * if to find the right compiled version to call
++ */
++   for (cp=cp0; cp; cp = cp->next)  /* fixed = 0/1 cases */
++   {
++      if (cp->fixed != 1 && cp->fixed != 0)
++         continue;
++      if (cp->imult > 1)
++         fprintf(fp, "   %s (%c == %s)\n", ifp, cwh[which],
++                 GetInc(cp->imult, GetDiv(cp->imult, st)));
++      else if (ifp == ifs) fprintf(fp, "   else\n");
+       if (cp->fixed == 0)
+       {
+-         if (cp->imult > 1)
+-            fprintf(fp, "   %s (%c == %s)\n", ifp, cwh[which],
+-                    GetInc(cp->imult, GetDiv(cp->imult, st)));
+-         else if (ifp == ifs) fprintf(fp, "   else\n");
+          fprintf(fp, "   {\n      ATL_%cup%cBmm0_%d_%d_b%c%s;\n   }\n",
+                  pre, cwh[which], cp->imult, cp->fixed, cbeta, MMARGS);
+          ifp = ifs;
+       }
++      else if (cp->fixed == 1)
++      {
++         fprintf(fp, "   {\n");
++         if (cp->ncomps == 1)
++            fprintf(fp, "      ATL_%cup%cBmm%d_%d_%d_b%c%s;\n",
++                    pre, cwh[which], cp->NBs[0], cp->imult, cp->fixed,
++                    cbeta, MMARGS);
++         else  /* must select kernel by NB[i] */
++         {
++            sp = "if";
++            for (i=cp->ncomps-1; i >= 0; i--)
++            {
++               fprintf(fp, "      %s (%c == %d)\n", sp, cwh[which], cp->NBs[i]);
++               fprintf(fp,
++               "      {\n         ATL_%cup%cBmm%d_%d_%d_b%c%s;\n      }\n",
++                       pre, cwh[which], cp->NBs[i], cp->imult, cp->fixed,
++                       cbeta, MMARGS);
++               sp = "else if";
++            }
++         }
++         fprintf(fp, "   }\n");
++      }
+    }
++
+    for (cp=cp0; cp && cp->imult != 1; cp = cp->next);
+    if (!cp)
+    {
+@@ -4330,3 +4349,5 @@ main(int nargs, char **args)
+    }
+    exit(0);
+ }
++
++ 	  	 
diff --git a/utils/hddtemp/DETAILS b/utils/hddtemp/DETAILS
index ec5ea28a5b..d747e13e0f 100755
--- a/utils/hddtemp/DETAILS
+++ b/utils/hddtemp/DETAILS
@@ -1,14 +1,18 @@
             SPELL=hddtemp
           VERSION=0.3-beta15
+       PATCHLEVEL=1
            SOURCE=${SPELL}-${VERSION}.tar.bz2
           SOURCE2=${SPELL}.db
+          SOURCE3=hddtemp_0.3-beta15-46.diff.gz
  SOURCE_DIRECTORY=${BUILD_DIRECTORY}/${SPELL}-${VERSION}
     SOURCE_URL[0]=http://download.savannah.nongnu.org/releases/hddtemp/$SOURCE
    SOURCE2_URL[0]=http://download.savannah.nongnu.org/releases/hddtemp/$SOURCE2
+   SOURCE3_URL[0]=http://ftp.debian.org/debian/pool/main/h/hddtemp/$SOURCE3
          WEB_SITE=http://www.guzu.net/linux/hddtemp.php
           ENTERED=20020721
       SOURCE_HASH=sha512:7db5a3dff60c59ce147b996ea4f8b6de1abcd34301bb863507b4d4b44e72fdc031078867a7f37161e67e74f6b426a1d856d3081179c678d2a442815bb0faa94d
    SOURCE2_IGNORE=volatile
+     SOURCE3_HASH=sha512:2a8dda152de012280a6fcb2ac5c90724c39a06f183208c46d90efc95e06d6f72421e8667448767ea981828c861ba17deaf89681cfae2796588df29553c643009
        LICENSE[0]=GPL
        LICENSE[1]=GPL
 FORCE_DOWNLOAD[2]="yes"
diff --git a/utils/hddtemp/HISTORY b/utils/hddtemp/HISTORY
index 6da18068ea..668ab246d0 100644
--- a/utils/hddtemp/HISTORY
+++ b/utils/hddtemp/HISTORY
@@ -1,3 +1,8 @@
+2011-05-13 Ladislav Hagara <hgr@vabo.cz>
+	* DETAILS: PATCHLEVEL=1, SOURCE3 added, Debian patch
+	* hddtemp-0.3-beta15-reg-eip.patch: added, Arch patch
+	* PRE_BUILD: updated
+
 2008-08-22 Julien "_kaze_" ROZO <julien@rozo.org>
 	* DETAILS: changed SOURCE2_URL to match SOURCE_URL
 	* init.d/hddtemp, init.d/hddtemp.conf: added an init script to start
diff --git a/utils/hddtemp/PRE_BUILD b/utils/hddtemp/PRE_BUILD
index 965bba3898..d7dc04e34f 100755
--- a/utils/hddtemp/PRE_BUILD
+++ b/utils/hddtemp/PRE_BUILD
@@ -1,4 +1,7 @@
 default_pre_build                  &&
 cd  ${SOURCE_DIRECTORY}            &&
 unpack_file 2        &&
+unpack_file 3        &&
+zcat ${SOURCE_CACHE}/$SOURCE3 | patch -p1 &&
+patch -p1 < $SPELL_DIRECTORY/hddtemp-0.3-beta15-reg-eip.patch &&
 cp  ${SOURCE_CACHE}/${SOURCE2}  .
diff --git a/utils/hddtemp/hddtemp-0.3-beta15-reg-eip.patch b/utils/hddtemp/hddtemp-0.3-beta15-reg-eip.patch
new file mode 100644
index 0000000000..504a0366e3
--- /dev/null
+++ b/utils/hddtemp/hddtemp-0.3-beta15-reg-eip.patch
@@ -0,0 +1,22 @@
+__USE_GNU needs to be in effect when including sys/ucontext.h,
+and signal.h pulls it in in some setups.
+
+diff -up hddtemp-0.3-beta15/src/backtrace.c~ hddtemp-0.3-beta15/src/backtrace.c
+--- hddtemp-0.3-beta15/src/backtrace.c~	2006-04-19 05:38:14.000000000 +0300
++++ hddtemp-0.3-beta15/src/backtrace.c	2010-02-14 21:59:47.000000000 +0200
+@@ -27,13 +27,12 @@
+ #include <stdlib.h>
+ #include <unistd.h>
+ #include <linux/ptrace.h>
++#define __USE_GNU
++#include <ucontext.h>
+ #include <signal.h>
+ #include <bits/sigcontext.h>
+ #include <sys/param.h>
+ 
+-#define __USE_GNU
+-#include <ucontext.h>
+-
+ #define MAX_BTSIZE 64
+ 
+ void backtrace_handler(int n, siginfo_t *ist, void *extra) {