[med-svn] r6953 - in trunk/packages/ncbi-blast+/trunk/debian: . patches

[Aaron M. Ucko]

Author: ucko
Date: 2011-06-09 00:35:24 +0000 (Thu, 09 Jun 2011)
New Revision: 6953

Added:
   trunk/packages/ncbi-blast+/trunk/debian/patches/support_other_cpus
Modified:
   trunk/packages/ncbi-blast+/trunk/debian/changelog
   trunk/packages/ncbi-blast+/trunk/debian/patches/series
Log:
debian/patches/support_other_cpus (new; committed upstream too):
build correctly on architectures that wound up defining
NCBI_SLOW_ATOMIC_SWAP (spuriously in the case of powerpc,
whose detection the patch fixes as well).  [Also for #629656.]


Modified: trunk/packages/ncbi-blast+/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog	2011-06-09 00:20:18 UTC (rev 6952)
+++ trunk/packages/ncbi-blast+/trunk/debian/changelog	2011-06-09 00:35:24 UTC (rev 6953)
@@ -5,8 +5,12 @@
   * Fix several sources of build failures (per #629656):
     - debian/rules (override_dh_install): Correctly support building only
       architecture-dependent packages.
+    - debian/patches/support_other_cpus (new; committed upstream too):
+      build correctly on architectures that wound up defining
+      NCBI_SLOW_ATOMIC_SWAP (spuriously in the case of powerpc,
+      whose detection the patch fixes as well).
 
- -- Aaron M. Ucko <ucko at debian.org>  Wed, 08 Jun 2011 20:20:13 -0400
+ -- Aaron M. Ucko <ucko at debian.org>  Wed, 08 Jun 2011 20:35:16 -0400
 
 ncbi-blast+ (2.2.25-1) unstable; urgency=low
 

Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/series	2011-06-09 00:20:18 UTC (rev 6952)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/series	2011-06-09 00:35:24 UTC (rev 6953)
@@ -1,3 +1,4 @@
 legacy_rename_rpsblast
 fix_checks
 fix_gcc46_errors
+support_other_cpus

Added: trunk/packages/ncbi-blast+/trunk/debian/patches/support_other_cpus
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/support_other_cpus	                        (rev 0)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/support_other_cpus	2011-06-09 00:35:24 UTC (rev 6953)
@@ -0,0 +1,66 @@
+Index: b/c++/include/corelib/impl/ncbi_atomic_defs.h
+===================================================================
+--- a/c++/include/corelib/impl/ncbi_atomic_defs.h	2011-06-08 20:26:07.000000000 -0400
++++ b/c++/include/corelib/impl/ncbi_atomic_defs.h	2011-06-08 20:29:25.000000000 -0400
+@@ -259,7 +259,7 @@
+ #  endif
+ #endif
+ 
+-#if !defined(NCBI_SWAP_POINTERS)  &&  !defined(NCBI_SWAP_POINTERS_CONDITIONALLY)  &&  !defined(NCBI_NO_THREADS)  &&  (!defined(NCBI_COUNTER_ASM_OK)  ||  (!defined(__i386) && !defined(__ppc__) && !defined(__ppc64__) && !defined(__sparc) && !defined(__x86_64)))
++#if !defined(NCBI_SWAP_POINTERS)  &&  !defined(NCBI_SWAP_POINTERS_CONDITIONALLY)  &&  !defined(NCBI_NO_THREADS)  &&  (!defined(NCBI_COUNTER_ASM_OK)  ||  (!defined(__i386) && !defined(__powerpc__) && !defined(__powerpc64__) && !defined(__ppc__) && !defined(__ppc64__) && !defined(__sparc) && !defined(__x86_64)))
+ #  define NCBI_SWAP_POINTERS_EXTERN 1
+ #  define NCBI_SLOW_ATOMIC_SWAP 1
+ #endif
+Index: b/c++/include/corelib/ncbiatomic.h
+===================================================================
+--- a/c++/include/corelib/ncbiatomic.h	2011-06-08 20:26:00.000000000 -0400
++++ b/c++/include/corelib/ncbiatomic.h	2011-06-08 20:30:34.000000000 -0400
+@@ -121,14 +121,14 @@
+     asm volatile("swap [%2], %1" : "=m" (*nv_loc), "=r" (old_value)
+                  : "r" (nv_loc), "1" (new_value), "m" (*nv_loc));
+     return old_value;
+-#    elif defined(__ppc__) ||  defined(__ppc64__)
++#    elif defined(__powerpc__) || defined(__powerpc64__) || defined(__ppc__) ||  defined(__ppc64__)
+     void* old_value;
+     int   swapped = 0;
+     NCBI_SCHED_SPIN_INIT();
+     while ( !swapped ) {
+         swapped = 0;
+         asm volatile(
+-#ifdef __ppc64__
++#if defined(__powerpc64__)  ||  defined(__ppc64__)
+                      "ldarx %1,0,%4\n\tstdcx. %3,0,%4"
+ #else
+                      "lwarx %1,0,%4\n\tstwcx. %3,0,%4"
+Index: b/c++/src/objects/seq/seq_id_handle.cpp
+===================================================================
+--- a/c++/src/objects/seq/seq_id_handle.cpp	2011-06-08 20:26:34.000000000 -0400
++++ b/c++/src/objects/seq/seq_id_handle.cpp	2011-06-08 20:28:43.000000000 -0400
+@@ -47,11 +47,6 @@
+ // CSeq_id_Info
+ //
+ 
+-//#define NCBI_SLOW_ATOMIC_SWAP
+-#ifdef NCBI_SLOW_ATOMIC_SWAP
+-DEFINE_STATIC_FAST_MUTEX(sx_GetSeqIdMutex);
+-#endif
+-
+ 
+ CSeq_id_Info::CSeq_id_Info(CSeq_id::E_Choice type,
+                            CSeq_id_Mapper* mapper)
+Index: b/c++/src/objects/seq/seq_id_tree.cpp
+===================================================================
+--- a/c++/src/objects/seq/seq_id_tree.cpp	2011-06-08 20:26:34.000000000 -0400
++++ b/c++/src/objects/seq/seq_id_tree.cpp	2011-06-08 20:28:53.000000000 -0400
+@@ -42,6 +42,11 @@
+ BEGIN_NCBI_SCOPE
+ BEGIN_SCOPE(objects)
+ 
++//#define NCBI_SLOW_ATOMIC_SWAP
++#ifdef NCBI_SLOW_ATOMIC_SWAP
++DEFINE_STATIC_FAST_MUTEX(sx_GetSeqIdMutex);
++#endif
++
+ ////////////////////////////////////////////////////////////////////
+ //
+ //  CSeq_id_***_Tree::