Collect all system/hardware related functions into system.H.

addCopyrights.dat

@@ -13900,3 +13900,6 @@ D src/utility/strings.H src/utility/findKeyAndValue.H
 D src/utility/strings.C src/utility/findKeyAndValue.H
 D src/utility/strings.H src/utility/AS_UTL_decodeRange.H
 D src/utility/strings.C src/utility/splitToWords.H
+D src/utility/arrays.H src/utility/AS_UTL_alloc.H
+D src/utility/system.C src/utility/timeAndSize.C
+D src/utility/system.H src/utility/timeAndSize.H

src/AS_global.C

@@ -40,8 +40,7 @@
 
 #include "AS_UTL_stackTrace.H"
 #include "files.H"
-
-#include "timeAndSize.H"
+#include "system.H"
 
 #ifdef X86_GCC_LINUX
 #include <fpu_control.h>

src/AS_global.H

@@ -110,7 +110,7 @@ int AS_configure(int argc, char **argv);
 #endif
 
 
-#include "AS_UTL_alloc.H"
+#include "arrays.H"
 
 
 

src/bogart/AS_BAT_OverlapCache.C

@@ -49,6 +49,8 @@
 #include "AS_BAT_Unitig.H"            //  sizeof(ufNode)
 #include "AS_BAT_Logging.H"
 
+#include "system.H"
+
 #include <sys/types.h>
 
 uint64  ovlCacheMagic = 0x65686361436c766fLLU;  //0102030405060708LLU;

src/correction/readConsensus.C

@@ -28,6 +28,7 @@
  */
 
 #include "AS_global.H"
+#include "system.H"
 
 #include "sweatShop.H"
 //#include <pthread.h>
@@ -43,8 +44,6 @@
 
 #include "AS_UTL_reverseComplement.H"
 
-#include "timeAndSize.H" //  getTime();
-
 
 //  This uses the RED/OEA framework to generate corrected reads.  It probably isn't worth keeping.
 

src/main.mk

@@ -32,19 +32,17 @@ SOURCES      := AS_global.C \
                 utility/files-memoryMapped.C \
                 \
                 utility/strings.C \
+                utility/system.C \
                 \
                 utility/AS_UTL_reverseComplement.C \
                 utility/AS_UTL_stackTrace.C \
                 \
-                utility/AS_UTL_alloc.C \
-                \
                 utility/hexDump.C \
                 utility/md5.C \
                 utility/mt19937ar.C \
                 utility/objectStore.C \
                 utility/speedCounter.C \
                 utility/sweatShop.C \
-                utility/timeAndSize.C \
                 \
                 correction/computeGlobalScore.C \
                 correction/falconConsensus.C \

src/meryl-san/meryl-san.H

@@ -24,13 +24,13 @@
 
 #include "AS_global.H"
 #include "files.H"
+#include "system.H"
 
 #include "kMer.H"
 #include "bitPackedFile.H"
 #include "libmeryl-san.H"
 
 #include "speedCounter.H"
-#include "timeAndSize.H"
 
 #define PERSONALITY_MERGE         0xff
 

src/meryl-san/simple.C

@@ -21,6 +21,7 @@
 
 #include "AS_global.H"
 #include "files.H"
+#include "system.H"
 
 #include "kMer.H"
 #include "bitPackedFile.H"
@@ -31,7 +32,6 @@
 #include "speedCounter.H"
 
 #include "speedCounter.H"
-#include "timeAndSize.H"
 
 #include <algorithm>
 

src/overlapInCore/overlapPair.C

@@ -32,6 +32,7 @@
  */
 
 #include "AS_global.H"
+#include "system.H"
 
 #include <pthread.h>
 
@@ -44,8 +45,6 @@
 
 #include "AS_UTL_reverseComplement.H"
 
-#include "timeAndSize.H" //  getTime();
-
 //  The process will load BATCH_SIZE overlaps into memory, then load all the reads referenced by
 //  those overlaps.  Once all data is loaded, compute threads are spawned.  Each thread will reserve
 //  THREAD_SIZE overlaps to compute.  A small THREAD_SIZE relative to BATCH_SIZE will result in

src/utility/AS_UTL_alloc.H → src/utility/arrays.H

@@ -19,14 +19,8 @@
  *  full conditions and disclaimers for each license.
  */
 
-#ifndef AS_UTL_ALLOC_H
-#define AS_UTL_ALLOC_H
-
-#include "AS_global.H"
-
-
-uint64    getPhysicalMemorySize(void);
-
+#ifndef ARRAYS_H
+#define ARRAYS_H
 
 
 const uint32  resizeArray_doNothing = 0x00;
@@ -143,4 +137,4 @@ resizeArrayPair(T1*& array1, T2*& array2, uint64 arrayLen, LL &arrayMax, LL newM
 }
 
 
-#endif // AS_UTL_ALLOC_H
+#endif  //  ARRAYS_H

src/utility/speedCounter.H

@@ -39,7 +39,7 @@
 #define SPEEDCOUNTER_H
 
 #include "AS_global.H"
-#include "timeAndSize.H"
+#include "system.H"
 
 class speedCounter {
 public:

src/utility/sweatShop.C

@@ -20,7 +20,7 @@
  */
 
 #include "sweatShop.H"
-#include "timeAndSize.H"
+#include "system.H"
 
 #include <sched.h>  //  pthread scheduling stuff
 

src/utility/timeAndSize.C → src/utility/system.C

@@ -25,6 +25,10 @@
 #include <sys/time.h>
 #include <sys/resource.h>
 
+#if !defined(__CYGWIN__) && !defined(_WIN32)
+#include <sys/sysctl.h>
+#endif
+
 
 
 double
@@ -127,3 +131,43 @@ getProcessSizeLimit(void) {
   return(sz);
 }
 
+
+
+#ifdef HW_PHYSMEM
+
+uint64
+getPhysicalMemorySize(void) {
+  uint64  physMemory = 0;
+
+  int     mib[2] = { CTL_HW, HW_PHYSMEM };
+  size_t  len    = sizeof(uint64);
+
+  errno = 0;
+
+  if (sysctl(mib, 2, &physMemory, &len, NULL, 0) != 0)
+    fprintf(stderr, "getPhysicalMemorySize()-- sysctl() failed to return CTL_HW, HW_PHYSMEM: %s\n", strerror(errno)), exit(1);
+
+  if (len != sizeof(uint64)) {
+#ifdef HW_MEMSIZE
+    mib[1] = HW_MEMSIZE;
+    len = sizeof(uint64);
+    if (sysctl(mib, 2, &physMemory, &len, NULL, 0) != 0 || len != sizeof(uint64))
+#endif
+      fprintf(stderr, "getPhysicalMemorySize()-- sysctl() failed to return CTL_HW, HW_PHYSMEM: %s\n", strerror(errno)), exit(1);
+  }
+
+  return(physMemory);
+}
+
+#else
+
+uint64
+getPhysicalMemorySize(void) {
+  uint64  physPages  = sysconf(_SC_PHYS_PAGES);
+  uint64  pageSize   = sysconf(_SC_PAGESIZE);
+  uint64  physMemory = physPages * pageSize;
+
+  return(physMemory);
+}
+
+#endif

src/utility/timeAndSize.H → src/utility/system.H

@@ -36,3 +36,5 @@ double   getProcessTime(void);
 
 uint64   getProcessSize(void);
 uint64   getProcessSizeLimit(void);
+
+uint64   getPhysicalMemorySize(void);