ifndef WITH_INTERNAL_METRICS then lets not

dib-lab · Mar 10, 2014 · 85ca06a · 85ca06a
1 parent 7e8a2c1
commit 85ca06a
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Showing 10 changed files with 54 additions and 31 deletions.
diff --git a/.ycm_extra_conf.py b/.ycm_extra_conf.py
@@ -35,6 +35,12 @@
     '/usr/include',
     '-isystem',
     '/usr/local/include',
+    '-system',
+    '/usr/include/c++/4.8',
+    '-I',
+    '/usr/include/python2.7',
+    '-I',
+    'lib'
 ]
 
 

diff --git a/ChangeLog b/ChangeLog
@@ -4,9 +4,11 @@
     scalar field (UNINIT_CTOR) 
     * lib/node.cc: fix for Coverity CID 1173035:  Uninitialized scalar field
     (UNINIT_CTOR)
-
     * lib/hashbits.hh: fix for Coverity CID 1153101:  Resource leak in object
     (CTOR_DTOR_LEAK)
+    * lib/{perf_metrics.{cc,hh},hashtable.{cc,hh}
+    ,read_parsers.{cc,hh},trace_logger.{cc,hh}}: ifndef WITH_INTERNAL_METRICS
+    then lets not + astyle -A10
 
 2014-02-27  Michael R. Crusoe <mcrusoe@msu.edu>
 

diff --git a/lib/hashtable.cc b/lib/hashtable.cc
@@ -15,7 +15,7 @@ using namespace std;
 using namespace khmer;
 using namespace khmer:: read_parsers;
 
-
+#ifdef WITH_INTERNAL_METRICS
 HashTablePerformanceMetrics::
 HashTablePerformanceMetrics( )
 : IPerformanceMetrics( ),
@@ -62,7 +62,7 @@ accumulate_timer_deltas( uint32_t metrics_key )
   }
 
 }
-
+#endif
 
 Hashtable:: Hasher::
 Hasher(
@@ -72,7 +72,9 @@ Hasher(
 )
 : pool_id( pool_id ),
   thread_id( thread_id ),
+#ifdef WITH_INTERNAL_METRICS
   pmetrics( HashTablePerformanceMetrics( ) ),
+#endif
   trace_logger(
     TraceLogger(
       trace_level, "hashtable-%lu-%lu.log",

diff --git a/lib/hashtable.hh b/lib/hashtable.hh
@@ -36,7 +36,7 @@
 #define CALLBACK_PERIOD 100000
 
 namespace khmer {
-
+#ifdef WITH_INTERNAL_METRICS
   struct HashTablePerformanceMetrics : public IPerformanceMetrics
   {
 
@@ -60,7 +60,7 @@ namespace khmer {
 	virtual void	accumulate_timer_deltas( uint32_t metrics_key );
 
   };
-
+#endif
   //
   // Sequence iterator class, test.  Not really a C++ iterator yet.
   //
@@ -152,7 +152,9 @@ namespace khmer {
 
 	uint32_t			pool_id;
 	uint32_t			thread_id;
+#ifdef WITH_INTERNAL_METRICS
 	HashTablePerformanceMetrics	pmetrics;
+#endif
 	TraceLogger			trace_logger;
 
 	Hasher(

diff --git a/lib/perf_metrics.cc b/lib/perf_metrics.cc
@@ -9,7 +9,7 @@
 namespace khmer
 {
 
-
+#ifdef WITH_INTERNAL_METRICS
 IPerformanceMetrics::
 IPerformanceMetrics( )
 { }
@@ -28,7 +28,7 @@ _timespec_diff_in_nsecs( timespec const &start, timespec const &stop )
 	    ((stop.tv_sec * 1000000000U) + (uint64_t)stop.tv_nsec)
 	-   ((start.tv_sec * 1000000000U) + (uint64_t)start.tv_nsec);
 }
-
+#endif
 } // namespace khmer
 
 // vim: set ft=cpp sts=4 sw=4 tw=79:
diff --git a/lib/perf_metrics.hh b/lib/perf_metrics.hh
@@ -19,23 +19,23 @@
 namespace khmer
 {
 
-
+#ifdef WITH_INTERNAL_METRICS
 struct InvalidPerformanceMetricsKey : public std:: exception
 { };
 
 
 struct IPerformanceMetrics
 {
 
-	    IPerformanceMetrics( );
+	     IPerformanceMetrics( );
     virtual ~IPerformanceMetrics( );
 
     inline void	    start_timers( )
     {
 #if defined (__linux__)
 	clock_gettime( CLOCK_REALTIME, &_temp_clock_start );
 	clock_gettime( CLOCK_THREAD_CPUTIME_ID, &_temp_cpu_start );
-// TODO: Create proper stopwatches for MacOS X and Windows.
+// TODO: Create proper stopwatches for MacOS X.
 #else
 	memset( &_temp_clock_start, 0, sizeof( timespec ) );
 	memset( &_temp_cpu_start, 0, sizeof( timespec ) );
@@ -46,7 +46,7 @@ struct IPerformanceMetrics
 #if defined (__linux__)
 	clock_gettime( CLOCK_THREAD_CPUTIME_ID, &_temp_cpu_stop );
 	clock_gettime( CLOCK_REALTIME, &_temp_clock_stop );
-// TODO: Create proper stopwatches for MacOS X and Windows.
+// TODO: Create proper stopwatches for MacOS X.
 #else
 	memset( &_temp_cpu_stop, 0, sizeof( timespec ) );
 	memset( &_temp_clock_stop, 0, sizeof( timespec ) );
@@ -69,8 +69,9 @@ protected:
 
 };
 
-} // namespace khmer
+#endif // WITH_INTERNAL_METRICS
 
+} // namespace khmer
 #endif // PERF_METRICS_HH
 
 // vim: set ft=cpp sts=4 sw=4 tw=79:
diff --git a/lib/read_parsers.cc b/lib/read_parsers.cc
@@ -63,7 +63,7 @@ InvalidFASTQFileFormat( char const * reason, char const * evidence )
 : InvalidReadFileFormat( "InvalidFASTQFileFormat", reason, evidence )
 { }
 
-
+#ifdef WITH_INTERNAL_METRICS
 StreamReaderPerformanceMetrics::
 StreamReaderPerformanceMetrics( )
 :   IPerformanceMetrics( ),
@@ -95,11 +95,14 @@ accumulate_timer_deltas( uint32_t metrics_key )
     }
 
 }
-
+#endif
 
 IStreamReader::
 IStreamReader( )
-:   pmetrics( StreamReaderPerformanceMetrics( ) ),
+:
+#ifdef WITH_INTERNAL_METRICS
+    pmetrics( StreamReaderPerformanceMetrics( ) ),
+#endif
     _alignment( 0 ),
     _max_aligned( SSIZE_MAX ),
     _at_eos( false )
@@ -374,7 +377,7 @@ read_into_cache( uint8_t * const cache, uint64_t const cache_size )
     return nbread_total;
 }
 
-
+#ifdef WITH_INTERNAL_METRICS
 CacheSegmentPerformanceMetrics::
 CacheSegmentPerformanceMetrics( )
 :   IPerformanceMetrics( ),
@@ -481,7 +484,7 @@ accumulate_metrics( CacheSegmentPerformanceMetrics &source )
     source._accumulated_count;
 
 }
-
+#endif
 
 CacheManager::
 CacheManager(
@@ -548,7 +551,9 @@ CacheSegment(
     cursor_in_ca_buffer( false ),
     fill_id( 0 ),
     found_EOS( false ),
+#ifdef WITH_INTERNAL_METRICS
     pmetrics( CacheSegmentPerformanceMetrics( ) ),
+#endif
     trace_logger(
 	TraceLogger(
 	    trace_level, "cmgr-%lu.log", (unsigned long int)thread_id
@@ -1176,7 +1181,7 @@ _get_segment_ref_count_ATOMIC( )
     return __sync_and_and_fetch( &_segment_ref_count, (uint32_t)0xffffffff );
 }
 
-
+#ifdef WITH_INTERNAL_METRICS
 ParserPerformanceMetrics::
 ParserPerformanceMetrics( )
 :   numlines_copied( 0 ),
@@ -1194,7 +1199,7 @@ void
 ParserPerformanceMetrics::
 accumulate_timer_deltas( uint32_t metrics_key )
 { }
-
+#endif
 
 IParser * const
 IParser::
@@ -1374,7 +1379,9 @@ ParserState( uint32_t const thread_id, uint8_t const trace_level )
     need_new_line( true ),
     buffer_pos( 0 ),
     buffer_rem( 0 ), 
+#ifdef WITH_INTERNAL_METRICS
     pmetrics( ParserPerformanceMetrics( ) ),
+#endif
     trace_logger(
 	TraceLogger(
 	    trace_level, "parser-%lu.log", (unsigned long int)thread_id

diff --git a/lib/read_parsers.hh b/lib/read_parsers.hh
@@ -98,7 +98,7 @@ struct UnknownPairReadingMode : public std:: exception
 struct InvalidReadPair : public std:: exception
 { };
 
-
+#ifdef WITH_INTERNAL_METRICS
 struct StreamReaderPerformanceMetrics : public IPerformanceMetrics
 {
 
@@ -117,13 +117,13 @@ struct StreamReaderPerformanceMetrics : public IPerformanceMetrics
     virtual void    accumulate_timer_deltas( uint32_t metrics_key );
 
 };
-
+#endif
 
 struct IStreamReader
 {
-
+#ifdef WITH_INTERNAL_METRICS
     StreamReaderPerformanceMetrics  pmetrics;
-    
+#endif
 	    IStreamReader( );
     virtual ~IStreamReader( );
 
@@ -198,7 +198,7 @@ private:
 
 };
 
-
+#ifdef WITH_INTERNAL_METRICS
 struct CacheSegmentPerformanceMetrics : public IPerformanceMetrics
 {
 
@@ -240,7 +240,7 @@ protected:
     uint32_t	    _accumulated_count;
 
 };
-
+#endif
 
 struct CacheManager
 {
@@ -285,7 +285,9 @@ private:
 	std:: string			ca_buffer;
 	uint64_t			fill_id;
 	bool				found_EOS;
+#ifdef WITH_INTERNAL_METRICS
 	CacheSegmentPerformanceMetrics	pmetrics;
+#endif
 	TraceLogger			trace_logger;
 
 	CacheSegment(
@@ -360,7 +362,7 @@ struct Read
 
 typedef std:: pair< Read, Read >	ReadPair;
 
-
+#ifdef WITH_INTERNAL_METRICS
 struct ParserPerformanceMetrics: public IPerformanceMetrics
 {
 
@@ -374,6 +376,7 @@ struct ParserPerformanceMetrics: public IPerformanceMetrics
     virtual void    accumulate_timer_deltas( uint32_t metrics_key );
 
 };
+#endif
 
 
 struct IParser
@@ -446,8 +449,9 @@ protected:
 	uint8_t			    buffer[ BUFFER_SIZE + 1 ];
 	uint64_t		    buffer_pos;
 	uint64_t		    buffer_rem;
-
+#ifdef WITH_INTERNAL_METRICS
 	ParserPerformanceMetrics    pmetrics;
+#endif
 	TraceLogger		    trace_logger;
 
 	ParserState( uint32_t const thread_id, uint8_t const trace_level );

diff --git a/lib/trace_logger.cc b/lib/trace_logger.cc
@@ -27,8 +27,8 @@ TraceLogger( uint8_t const level, FILE * stream_handle )
 
 TraceLogger::
 TraceLogger( uint8_t const level, char const * const file_name_format, ... )
-    : _level( level ), _shared_stream( false )
 #ifdef WITH_INTERNAL_TRACING
+    : _level( level ), _shared_stream( false )
 {
     char	tfile_name[ FILENAME_MAX + 1 ];
     va_list	varargs;

diff --git a/lib/trace_logger.hh b/lib/trace_logger.hh
@@ -58,10 +58,9 @@ struct TraceLogger {
 #endif	// !WITH_INTERNAL_TRACING
 
 private:
-
-    uint8_t	    _level;
-    bool	    _shared_stream;
 #ifdef WITH_INTERNAL_TRACING
+    bool	    _shared_stream;
+    uint8_t	    _level;
     FILE *	    _stream_handle;
 #endif
 };