1. Matthew Turk
  2. enzo-timing-woc

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Matthew Turk  committed a534ffe Merge

Automated merge with file:///Users/matthewturk/enzo/svn-wok

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  • Parent commits 84b93ce, 40abc55
  • Branches trunk

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Files changed (303)

File doc/examples/CoolingTest.enzo

View file
 DensityUnits = 1.673e-24
 LengthUnits  = 3.086e24
 TimeUnits    = 3.1557e+13
+
+OutputTemperature = 1
+OutputCoolingTime = 1

File src/enzo/CosmologyComputeExpansionFactor.C

View file
  
 #define OMEGA_TOLERANCE 1.0e-5
  
-#ifdef p4
+#ifdef CONFIG_PFLOAT_4
 #define ETA_TOLERANCE 1.0e-5
 #endif
-#ifdef p8
+#ifdef CONFIG_PFLOAT_8
 #define ETA_TOLERANCE 1.0e-10
 #endif
-#ifdef p16
+#ifdef CONFIG_PFLOAT_16
 #define ETA_TOLERANCE 1.0e-20
 #endif
  

File src/enzo/FastFourierTransformSGIMATH.C

View file
  
 /* Call correct routine for single/double precision. */
  
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
 #define RTOC(X)          scfft##X
 #define RTOC_INVERSE(X)  csfft##X
 #define RTOC_SCALE(X)    sscal##X
 #define CMPLX_CAST    (complex *)
 #endif /* r4 */
  
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
 #define RTOC(X)          dzfft##X
 #define RTOC_INVERSE(X)  zdfft##X
 #define RTOC_SCALE(X)    dscal##X

File src/enzo/FindRootGrid.C

View file
 #include "TopGridData.h"
 #include "LevelHierarchy.h"
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
 #define ROUNDOFF 1e-5
 #endif
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
 #define ROUNDOFF 1e-10
 #endif
-#ifdef r16
+#ifdef CONFIG_BFLOAT_16
 #define ROUNDOFF 1e-14
 #endif
 

File src/enzo/Grid.h

View file
   // Flag cells that overlap a subgrid (used for analysis).
   int FlagRefinedCells(grid *Subgrid);
   
+#if defined(CONFIG_PFLOAT_8) || defined(CONFIG_PFLOAT_16)
+  // FLOAT version of above
+  inline int IsInVolume( FLOAT *LeftEdge, FLOAT *RightEdge ){
+    for( int i = 0; i < GridRank; i++ ){
+      if( (GridLeftEdge[i] >= RightEdge[i]) ||
+	  (GridRightEdge[i] <= LeftEdge[i]) ){
+	return FALSE;
+      }
+    }
+     return TRUE;
+  }
+#else
   // Check to see if the grid overlaps a volume.
   // Doesn't care about periodicity. */
   inline int IsInVolume( float *LeftEdge, float *RightEdge ){
      return TRUE;
   }
 
-#if defined(r4) || defined(p16)
-  // FLOAT version of above
-  inline int IsInVolume( FLOAT *LeftEdge, FLOAT *RightEdge ){
-    for( int i = 0; i < GridRank; i++ ){
-      if( (GridLeftEdge[i] >= RightEdge[i]) ||
-	  (GridRightEdge[i] <= LeftEdge[i]) ){
-	return FALSE;
-      }
-    }
-     return TRUE;
-  }
 #endif
 
 
-  // Check to see if a point is in the grid.
-  inline int PointInGrid( float *point ){
+#if defined(CONFIG_PFLOAT_8) || defined(CONFIG_PFLOAT_16)
+  // Check to see if a FLOAT point is in the grid.
+  inline int PointInGrid( FLOAT *point ){
     for( int i = 0; i < GridRank; i++ ){
       if( ((point[i] >= GridLeftEdge[i]) &&
 	  (point[i] <= GridRightEdge[i])) == FALSE )
     }
     return TRUE;
   }
-
-#if defined(r4) || defined(p16)
-  // Check to see if a FLOAT point is in the grid.
-  inline int PointInGrid( FLOAT *point ){
+#else
+  // Check to see if a point is in the grid.
+  inline int PointInGrid( float *point ){
     for( int i = 0; i < GridRank; i++ ){
       if( ((point[i] >= GridLeftEdge[i]) &&
 	  (point[i] <= GridRightEdge[i])) == FALSE )

File src/enzo/Grid_AddFeedbackSphere.C

View file
 #include "Hierarchy.h"
 #include "CosmologyParameters.h"
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
 #define TOLERANCE 1e-06
 #endif
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
 #define TOLERANCE 1e-12
 #endif
-#ifdef r16
+#ifdef CONFIG_BFLOAT_16
 #define TOLERANCE 1e-15
 #endif
 

File src/enzo/Grid_Group_WriteGrid.C

View file
 #include <string.h>
 #include <stdio.h>
 #include <stdlib.h>
- 
+#include <math.h>
 
 
  
 void WriteListOfInts(FILE *fptr, int N, int nums[]);
 int WriteStringAttr(hid_t dset_id, char *Alabel, char *String, FILE *log_fptr);
 int FindField(int field, int farray[], int numfields);
- 
- 
+
+int GetUnits(float *DensityUnits, float *LengthUnits,
+	     float *TemperatureUnits, float *TimeUnits,
+	     float *VelocityUnits, float *MassUnits, FLOAT Time);
+
 int grid::Group_WriteGrid(FILE *fptr, char *base_name, int grid_id, HDF5_hid_t file_id)
 {
  
     /* If this is cosmology, compute the temperature field as well since
        its such a pain to compute after the fact. */
  
-    if (ComovingCoordinates || ProblemType == 62) {
+    if (OutputTemperature) {
  
       /* Allocate field and compute temperature. */
  
  
       delete temperature;
  
-    } // end: if (ComovingCoordinates)
+    } // end: if (OutputTemperature)
+
+    if (OutputCoolingTime) {
+ 
+      /* Allocate field and compute cooling time. */
+
+      float *cooling_time = new float[size];
+ 
+      float TemperatureUnits = 1, DensityUnits = 1, LengthUnits = 1,
+	VelocityUnits = 1, TimeUnits = 1, MassUnits = 1, aUnits = 1;
+      GetUnits(&DensityUnits, &LengthUnits, &TemperatureUnits,
+	       &TimeUnits, &VelocityUnits, &MassUnits, Time);
+
+      if (this->ComputeCoolingTime(cooling_time) == FAIL) {
+	fprintf(stderr, "Error in grid->ComputeCoolingTime.\n");
+	return FAIL;
+      }
+
+      // Make all cooling time values positive and convert to seconds.
+      for (i = 0;i < size;i++) {
+	cooling_time[i] = fabs(cooling_time[i]) * TimeUnits;
+      }
+ 
+      /* Copy active part of field into grid */
+ 
+      for (k = GridStartIndex[2]; k <= GridEndIndex[2]; k++)
+	for (j = GridStartIndex[1]; j <= GridEndIndex[1]; j++)
+	  for (i = GridStartIndex[0]; i <= GridEndIndex[0]; i++)
+	    temp[(i-GridStartIndex[0])                           +
+	         (j-GridStartIndex[1])*ActiveDim[0]              +
+	         (k-GridStartIndex[2])*ActiveDim[0]*ActiveDim[1] ] =
+		     io_type(
+		   cooling_time[(k*GridDimension[1] + j)*GridDimension[0] + i]
+			     );
+ 
+       file_dsp_id = H5Screate_simple((Eint32) GridRank, OutDims, NULL);
+        if (io_log) fprintf(log_fptr, "H5Screate file_dsp_id: %"ISYM"\n", file_dsp_id);
+        if( file_dsp_id == h5_error ){my_exit(EXIT_FAILURE);}
+ 
+      if (io_log) fprintf(log_fptr,"H5Dcreate with Name = Cooling_Time\n");
+ 
+      dset_id = H5Dcreate(group_id, "Cooling_Time", file_type_id, file_dsp_id, H5P_DEFAULT);
+        if (io_log) fprintf(log_fptr, "H5Dcreate id: %"ISYM"\n", dset_id);
+        if( dset_id == h5_error ){my_exit(EXIT_FAILURE);}
+ 
+      if ( DataUnits[field] == NULL )
+      {
+        DataUnits[field] = "none";
+      }
+ 
+      WriteStringAttr(dset_id, "Label", "Temperature", log_fptr);
+      WriteStringAttr(dset_id, "Units", "K", log_fptr);
+      WriteStringAttr(dset_id, "Format", "e10.4", log_fptr);
+      WriteStringAttr(dset_id, "Geometry", "Cartesian", log_fptr);
+ 
+      h5_status = H5Dwrite(dset_id, float_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, (VOIDP) temp);
+        if (io_log) fprintf(log_fptr, "H5Dwrite: %"ISYM"\n", h5_status);
+        if( h5_status == h5_error ){my_exit(EXIT_FAILURE);}
+ 
+      h5_status = H5Sclose(file_dsp_id);
+        if (io_log) fprintf(log_fptr, "H5Sclose: %"ISYM"\n", h5_status);
+        if( h5_status == h5_error ){my_exit(EXIT_FAILURE);}
+ 
+      h5_status = H5Dclose(dset_id);
+        if (io_log) fprintf(log_fptr, "H5Dclose: %"ISYM"\n", h5_status);
+        if( h5_status == h5_error ){my_exit(EXIT_FAILURE);}
+ 
+      delete cooling_time;
+ 
+    } // if (OutputCoolingTime)
  
     /* Make sure that there is a copy of dark matter field to save
        (and at the right resolution). */

File src/enzo/Grid_TransportPhotonPackages.C

View file
 #include "GridList.h"
 #include "Grid.h"
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
 #define ROUNDOFF 1e-6
 #endif
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
 #define ROUNDOFF 1e-12
 #endif
-#ifdef r16
+#ifdef CONFIG_BFLOAT_16
 #define ROUNDOFF 1e-16
 #endif
 

File src/enzo/Grid_WalkPhotonPackage.C

View file
 #include "Grid.h"
 #include "CosmologyParameters.h"
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
 #define ROUNDOFF 1e-6
 #endif
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
 #define ROUNDOFF 1e-12
 #endif
-#ifdef r16
+#ifdef CONFIG_BFLOAT_16
 #define ROUNDOFF 1e-16
 #endif
 

File src/enzo/Grid_WriteGrid.C

View file
 #include <string.h>
 #include <stdio.h>
 #include <stdlib.h>
- 
+#include <math.h>
 
 
  
 int WriteStringAttr(hid_t dset_id, char *Alabel, char *String, FILE *log_fptr);
  
 int FindField(int field, int farray[], int numfields);
- 
+
+int GetUnits(float *DensityUnits, float *LengthUnits,
+	     float *TemperatureUnits, float *TimeUnits,
+	     float *VelocityUnits, float *MassUnits, FLOAT Time);
  
 int grid::WriteGrid(FILE *fptr, char *base_name, int grid_id)
 {
     /* If this is cosmology, compute the temperature field as well since
        its such a pain to compute after the fact. */
  
-    if (ComovingCoordinates || ProblemType == 62) {
+    if (OutputTemperature) {
  
       /* Allocate field and compute temperature. */
  
  
       delete temperature;
  
-    } // end: if (ComovingCoordinates)
+    } // end: if (OutputTemperature)
+
+    if (OutputCoolingTime) {
+ 
+      /* Allocate field and compute cooling time. */
+
+      float *cooling_time = new float[size];
+ 
+      float TemperatureUnits = 1, DensityUnits = 1, LengthUnits = 1,
+	VelocityUnits = 1, TimeUnits = 1, MassUnits = 1, aUnits = 1;
+      GetUnits(&DensityUnits, &LengthUnits, &TemperatureUnits,
+	       &TimeUnits, &VelocityUnits, &MassUnits, Time);
+
+      if (this->ComputeCoolingTime(cooling_time) == FAIL) {
+	fprintf(stderr, "Error in grid->ComputeCoolingTime.\n");
+	return FAIL;
+      }
+
+      // Make all cooling time values positive and convert to seconds.
+      for (i = 0;i < size;i++) {
+	cooling_time[i] = fabs(cooling_time[i]) * TimeUnits;
+      }
+ 
+      /* Copy active part of field into grid */
+ 
+      for (k = GridStartIndex[2]; k <= GridEndIndex[2]; k++)
+	for (j = GridStartIndex[1]; j <= GridEndIndex[1]; j++)
+	  for (i = GridStartIndex[0]; i <= GridEndIndex[0]; i++)
+	    temp[(i-GridStartIndex[0])                           +
+	         (j-GridStartIndex[1])*ActiveDim[0]              +
+	         (k-GridStartIndex[2])*ActiveDim[0]*ActiveDim[1] ] =
+		     io_type(
+		   cooling_time[(k*GridDimension[1] + j)*GridDimension[0] + i]
+			     );
+ 
+ 
+      file_dsp_id = H5Screate_simple((Eint32) GridRank, OutDims, NULL);
+        if (io_log) fprintf(log_fptr, "H5Screate file_dsp_id: %"ISYM"\n", file_dsp_id);
+        if( file_dsp_id == h5_error ){my_exit(EXIT_FAILURE);}
+ 
+      if (io_log) fprintf(log_fptr,"H5Dcreate with Name = Cooling_Time\n");
+ 
+      dset_id = H5Dcreate(file_id, "Cooling_Time", file_type_id, file_dsp_id, H5P_DEFAULT);
+        if (io_log) fprintf(log_fptr, "H5Dcreate id: %"ISYM"\n", dset_id);
+        if( dset_id == h5_error ){my_exit(EXIT_FAILURE);}
+ 
+      if ( DataUnits[field] == NULL )
+      {
+        DataUnits[field] = "none";
+      }
+ 
+      WriteStringAttr(dset_id, "Label", "Cooling_Time", log_fptr);
+      WriteStringAttr(dset_id, "Units", "s", log_fptr);
+      WriteStringAttr(dset_id, "Format", "e10.4", log_fptr);
+      WriteStringAttr(dset_id, "Geometry", "Cartesian", log_fptr);
+ 
+      h5_status = H5Dwrite(dset_id, float_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, (VOIDP) temp);
+        if (io_log) fprintf(log_fptr, "H5Dwrite: %"ISYM"\n", h5_status);
+        if( h5_status == h5_error ){my_exit(EXIT_FAILURE);}
+ 
+      h5_status = H5Sclose(file_dsp_id);
+        if (io_log) fprintf(log_fptr, "H5Sclose: %"ISYM"\n", h5_status);
+        if( h5_status == h5_error ){my_exit(EXIT_FAILURE);}
+ 
+      h5_status = H5Dclose(dset_id);
+        if (io_log) fprintf(log_fptr, "H5Dclose: %"ISYM"\n", h5_status);
+        if( h5_status == h5_error ){my_exit(EXIT_FAILURE);}
+ 
+      delete cooling_time;
+ 
+    } // if (OutputCoolingTime)
  
     /* Make sure that there is a copy of dark matter field to save
        (and at the right resolution). */

File src/enzo/Grid_WriteGridX.C

View file
     /* If this is cosmology, compute the temperature field as well since
        its such a pain to compute after the fact. */
  
-    if (ComovingCoordinates) {
+    if (OutputTemperature) {
  
       /* Allocate field and compute temperature. */
  

File src/enzo/Make.config.assemble

View file
 
     ifeq ($(CONFIG_PRECISION),32)
         ERROR_PRECISION = 0
-        ASSEMBLE_PRECISION_DEFINES = -Dr4
+        ASSEMBLE_PRECISION_DEFINES = -DCONFIG_BFLOAT_4
         ASSEMBLE_PRECISION_FFLAGS = $(MACH_FFLAGS_REAL_32)
     endif
 
 
     ifeq ($(CONFIG_PRECISION),64)
         ERROR_PRECISION = 0
-        ASSEMBLE_PRECISION_DEFINES = -Dr8
+        ASSEMBLE_PRECISION_DEFINES = -DCONFIG_BFLOAT_8
         ASSEMBLE_PRECISION_FFLAGS = $(MACH_FFLAGS_REAL_64)
     endif
 
 
     ifeq ($(CONFIG_PARTICLES),32)
         ERROR_PARTICLES = 0
-        ASSEMBLE_PARTICLES_DEFINES = -Dp4
+        ASSEMBLE_PARTICLES_DEFINES = -DCONFIG_PFLOAT_4
     endif
 
     # Settings for 64-bit particle position precision
 
     ifeq ($(CONFIG_PARTICLES),64)
         ERROR_PARTICLES = 0
-        ASSEMBLE_PARTICLES_DEFINES = -Dp8
+        ASSEMBLE_PARTICLES_DEFINES = -DCONFIG_PFLOAT_8
     endif
 
     # Settings for 128-bit particle position precision
 
     ifeq ($(CONFIG_PARTICLES),128)
         ERROR_PARTICLES = 0
-        ASSEMBLE_PARTICLES_DEFINES = -Dp16
+        ASSEMBLE_PARTICLES_DEFINES = -DCONFIG_PFLOAT_16
     endif
 
     # error if CONFIG_PARTICLES is incorrect

File src/enzo/Make.mach.nics-kraken

View file
 #-----------------------------------------------------------------------
 
 LOCAL_MPI_INSTALL    = 
-LOCAL_HDF5_INSTALL   = /sw/xt/pkgs/hdf5/1.6.7/cnl2.0_pgi7.0.7
+LOCAL_HDF5_INSTALL   = /sw/xt5/hdf5/1.6.7/cnl2.1_pgi7.2.3
 
 LOCAL_HDF4_INSTALL   = $(HDF4_HOME)
-LOCAL_SPRNG_INSTALL  = /sw/xt/pkgs/sprng/2.0b/cnl2.0_pgi7.0.7
+LOCAL_SPRNG_INSTALL  = /sw/xt5/sprng/2.0b/cnl2.1_pgi7.2.3
 LOCAL_PNG_INSTALL    = 
 LOCAL_HYPRE_INSTALL  = 
 LOCAL_JBPERF_INSTALL = 
 LOCAL_LIBS_PNG    = 
 
 LOCAL_LIBS_MACH   =  $(LOCAL_LIBS_SPRNG) \
-                    -L/sw/xt/pkgs/szip/2.1/sles9.2_pgi7.0.7/lib -lsz \
+                    -L/sw/xt5/szip/2.1/sles10.1_pgi7.2.3/lib -lsz \
                     -L/usr/local/lib -lz \
                     -L/opt/acml/4.0.1a/pgi64/lib -lacml -lm \
                     -L/opt/pgi/$(PGI_VERS_STR)/linux86-64/7.1/lib \

File src/enzo/Make.mach.orange

View file
+#=======================================================================
+#
+# FILE:        Make.mach.orange
+#
+# DESCRIPTION: Makefile settings for SLAC's orange
+#
+# AUTHOR:      Matthew Turk
+#
+# DATE:        2009-03-21
+#
+#=======================================================================
+
+MACH_TEXT  = Orange
+MACH_VALID = 1
+MACH_FILE  = Make.mach.orange
+
+#-----------------------------------------------------------------------
+# Commands to run test executables
+#-----------------------------------------------------------------------
+
+
+#-----------------------------------------------------------------------
+# Install paths (local variables)
+#-----------------------------------------------------------------------
+
+LOCAL_MPI_INSTALL    = /afs/slac/Packages/OpenMPI/
+LOCAL_MPI_INSTALL    = /afs/slac/package/OpenMPI/1.2.5/amd64_linux26
+LOCAL_HDF5_INSTALL   = /u/ki/mturk/Research/local/yt-x86_64/
+LOCAL_PYTHON_INSTALL = /u/ki/mturk/Research/local/yt-x86_64/
+
+#-----------------------------------------------------------------------
+# Compiler settings
+#-----------------------------------------------------------------------
+
+MACH_CPP       = /usr/bin/cpp 
+
+# With MPI
+
+MACH_CC_MPI    = $(LOCAL_MPI_INSTALL)/bin/mpicc
+MACH_CXX_MPI   = $(LOCAL_MPI_INSTALL)/bin/mpic++ -DMPICH_IGNORE_CXX_SEEK
+MACH_FC_MPI    = $(LOCAL_MPI_INSTALL)/bin/mpif90
+MACH_F90_MPI   = $(LOCAL_MPI_INSTALL)/bin/mpif90
+MACH_LD_MPI    = $(LOCAL_MPI_INSTALL)/bin/mpicc
+
+# Without MPI
+
+MACH_CC_NOMPI  = icc
+MACH_CXX_NOMPI = icc
+MACH_FC_NOMPI  = ifort
+MACH_F90_NOMPI = ifort
+MACH_LD_NOMPI  = icc
+
+#-----------------------------------------------------------------------
+# Machine-dependent defines
+#-----------------------------------------------------------------------
+
+#MACH_DEFINES   = -DXT3 -DNO_IO_LOG -DSYSCALL -DENZO_ANALYSIS
+#MACH_DEFINES   = -DXT3 -DNO_IO_LOG -DSYSCALL -DHAVE_SPRNG
+#MACH_DEFINES   = -DXT3 -DNO_IO_LOG -DSYSCALL -DSFGEN_PERF -DHAVE_SPRNG -DUSE_STOCHASTIC_FORCING
+MACH_DEFINES = -DLINUX -DH5_USE_16_API #-DEMBEDDED_PYTHON
+
+#-----------------------------------------------------------------------
+# Compiler flag settings
+#-----------------------------------------------------------------------
+
+MACH_CPPFLAGS = -P -traditional
+MACH_CFLAGS   = 
+MACH_CXXFLAGS = 
+MACH_FFLAGS   = 
+MACH_F90FLAGS = 
+MACH_LDFLAGS  = -Wl
+#,-static 
+
+#-----------------------------------------------------------------------
+# Precision-related flags
+#-----------------------------------------------------------------------
+
+MACH_FFLAGS_INTEGER_32 = -i4
+MACH_FFLAGS_INTEGER_64 = -i8
+MACH_FFLAGS_REAL_32    = -r4
+MACH_FFLAGS_REAL_64    = -r8
+
+#-----------------------------------------------------------------------
+# Optimization flags
+#-----------------------------------------------------------------------
+
+# *** WARNING *** WARNING *** WARNING *** WARNING *** WARNING ***
+#
+#  Use optimization -O2 or greater with PGI compilers at your own
+#  risk!  Older versions of Grid_PPMDirectEuler.C compiled with -O2
+#  led to incorrect results on many test problems, and CURRENT
+#  (-r1995) versions of ffte4X.src and ZeusSource.C lead to incorrect
+#  results for ZeldovichPancake and ExtremeAdvectionTest tests,
+#  respectively.  jobordner@ucsd.edu
+#
+# *** WARNING *** WARNING *** WARNING *** WARNING *** WARNING ***
+
+MACH_OPT_WARN        = 
+MACH_OPT_DEBUG       = -g
+MACH_OPT_HIGH        = -O2
+MACH_OPT_AGGRESSIVE  = -O3
+
+#-----------------------------------------------------------------------
+# Includes
+#-----------------------------------------------------------------------
+
+LOCAL_INCLUDES_MPI    = 
+LOCAL_INCLUDES_HDF5   = -I$(LOCAL_HDF5_INSTALL)/include
+LOCAL_INCLUDES_IOBUF  = -I$(IOBUF_INC)
+LOCAL_INCLUDES_PYTHON = -I$(LOCAL_PYTHON_INSTALL)/include/python2.6/ \
+                        -I$(LOCAL_PYTHON_INSTALL)/lib/python2.6/site-packages/numpy/core/include
+
+MACH_INCLUDES         = $(LOCAL_INCLUDES_HDF5) $(LOCAL_INCLUDES_SPRNG) #$(LOCAL_INCLUDES_PYTHON)
+#MACH_INCLUDES         = $(LOCAL_INCLUDES_HDF5)
+
+MACH_INCLUDES_MPI     = $(LOCAL_INCLUDES_MPI)
+MACH_INCLUDES_HYPRE   = $(LOCAL_INCLUDES_HYPRE)
+MACH_INCLUDES_JBPERF  = $(LOCAL_INCLUDES_JBPERF)
+
+#-----------------------------------------------------------------------
+# Libraries
+#-----------------------------------------------------------------------
+#
+# make sure to "load module iobuf" before compiling, only then IOBUF environment
+# variables will be properly set
+#
+
+LOCAL_LIBS_MPI    = 
+LOCAL_LIBS_HDF5   = -L$(LOCAL_HDF5_INSTALL)/lib -lhdf5 -lz 
+LOCAL_LIBS_PYTHON  = $(LOCAL_PYTHON_INSTALL)/lib/python2.6/config/libpython2.6.a
+
+LOCAL_LIBS_MACH   =  -L$(INT_DIR)/fc/lib/ \
+                     -limf -lifcore -lifport \
+                     -L$(INT_DIR)/cc/lib/ \
+                     -lstdc++ -lg2c
+
+MACH_LIBS         = $(LOCAL_LIBS_HDF5) $(LOCAL_LIBS_MACH) #$(LOCAL_LIBS_PYTHON)
+MACH_LIBS_MPI     = $(LOCAL_LIBS_MPI)

File src/enzo/Make.mach.red

View file
+#=======================================================================
+#
+# FILE:        Make.mach.red
+#
+# DESCRIPTION: Makefile settings for SLAC's red
+#
+# AUTHOR:      Matthew Turk
+#
+# DATE:        2009-06-03
+#
+#=======================================================================
+
+MACH_TEXT  = Red
+MACH_VALID = 1
+MACH_FILE  = Make.mach.red
+
+#-----------------------------------------------------------------------
+# Commands to run test executables
+#-----------------------------------------------------------------------
+
+
+#-----------------------------------------------------------------------
+# Install paths (local variables)
+#-----------------------------------------------------------------------
+
+LOCAL_MPI_INSTALL    = /usr
+LOCAL_HDF5_INSTALL   = /u/ki/mturk/Research/local/yt-ia64/
+LOCAL_PYTHON_INSTALL = /u/ki/mturk/Research/local/yt-ia64/
+LOCAL_INT_INSTALL     = /afs/slac.stanford.edu/package/intel_tools/compiler9.0/@sys/
+
+#-----------------------------------------------------------------------
+# Compiler settings
+#-----------------------------------------------------------------------
+
+MACH_CPP       = /usr/bin/cpp 
+
+# With MPI
+
+MACH_CC_MPI    = $(LOCAL_INT_INSTALL)/cc/bin/icc
+MACH_CXX_MPI   = $(LOCAL_INT_INSTALL)/cc/bin/icc
+MACH_FC_MPI    = $(LOCAL_INT_INSTALL)/fc/bin/ifort
+MACH_F90_MPI   = $(LOCAL_INT_INSTALL)/fc/bin/ifort
+MACH_LD_MPI    = $(LOCAL_INT_INSTALL)/cc/bin/icc
+
+# Without MPI
+
+MACH_CC_NOMPI  = $(LOCAL_INT_INSTALL)/icc
+MACH_CXX_NOMPI = $(LOCAL_INT_INSTALL)/icc
+MACH_FC_NOMPI  = $(LOCAL_INT_INSTALL)/ifort
+MACH_F90_NOMPI = $(LOCAL_INT_INSTALL)/ifort
+MACH_LD_NOMPI  = $(LOCAL_INT_INSTALL)/icc
+
+#-----------------------------------------------------------------------
+# Machine-dependent defines
+#-----------------------------------------------------------------------
+
+MACH_DEFINES = -DLINUX -DH5_USE_16_API -DOPTIMIZED_CTP -DENABLE_LOAD_BALANCE \
+	-DSIB1 -DSIB2 -DSIB3 -DSIB4 -DSIB5
+	#-DEMBEDDED_PYTHON
+
+#-----------------------------------------------------------------------
+# Compiler flag settings
+#-----------------------------------------------------------------------
+
+MACH_CPPFLAGS = -P -traditional
+MACH_CFLAGS   = -ftz -IPF_fp_speculationfast -IPF_fma -mp -cxxlib-icc 
+MACH_CXXFLAGS = -ftz -IPF_fp_speculationfast -IPF_fma -mp -cxxlib-icc 
+MACH_FFLAGS   = -IPF_fp_speculationfast -IPF_fma -mp -132 -ftz
+MACH_F90LAGS  = -IPF_fp_speculationfast -IPF_fma -mp -132 -ftz
+MACH_LDFLAGS  = -ftz
+#,-static 
+
+#-----------------------------------------------------------------------
+# Precision-related flags
+#-----------------------------------------------------------------------
+
+MACH_FFLAGS_INTEGER_32 = -i4
+MACH_FFLAGS_INTEGER_64 = -i8
+MACH_FFLAGS_REAL_32    = -r4
+MACH_FFLAGS_REAL_64    = -r8
+
+#-----------------------------------------------------------------------
+# Optimization flags
+#-----------------------------------------------------------------------
+
+# *** WARNING *** WARNING *** WARNING *** WARNING *** WARNING ***
+#
+#  Use optimization -O2 or greater with PGI compilers at your own
+#  risk!  Older versions of Grid_PPMDirectEuler.C compiled with -O2
+#  led to incorrect results on many test problems, and CURRENT
+#  (-r1995) versions of ffte4X.src and ZeusSource.C lead to incorrect
+#  results for ZeldovichPancake and ExtremeAdvectionTest tests,
+#  respectively.  jobordner@ucsd.edu
+#
+# *** WARNING *** WARNING *** WARNING *** WARNING *** WARNING ***
+
+MACH_OPT_WARN        = 
+MACH_OPT_DEBUG       = -g
+MACH_OPT_HIGH        = -O2
+MACH_OPT_AGGRESSIVE  = -O3
+
+#-----------------------------------------------------------------------
+# Includes
+#-----------------------------------------------------------------------
+
+LOCAL_INCLUDES_MPI    = -I$(LOCAL_MPI_INSTALL)/include
+LOCAL_INCLUDES_HDF5   = -I$(LOCAL_HDF5_INSTALL)/include
+LOCAL_INCLUDES_PYTHON = -I$(LOCAL_PYTHON_INSTALL)/include/python2.6/ \
+                        -I$(LOCAL_PYTHON_INSTALL)/lib/python2.6/site-packages/numpy/core/include
+
+MACH_INCLUDES         = $(LOCAL_INCLUDES_HDF5) #$(LOCAL_INCLUDES_PYTHON)
+
+MACH_INCLUDES_MPI     = $(LOCAL_INCLUDES_MPI)
+MACH_INCLUDES_HYPRE   = $(LOCAL_INCLUDES_HYPRE)
+MACH_INCLUDES_JBPERF  = $(LOCAL_INCLUDES_JBPERF)
+
+#-----------------------------------------------------------------------
+# Libraries
+#-----------------------------------------------------------------------
+#
+# make sure to "load module iobuf" before compiling, only then IOBUF environment
+# variables will be properly set
+#
+
+LOCAL_LIBS_MPI    = -L$(LOCAL_MPI_INSTALL)/lib -lmpi -lmpi++
+LOCAL_LIBS_HDF5   = -L$(LOCAL_HDF5_INSTALL)/lib -lhdf5 -lz 
+LOCAL_LIBS_PYTHON  = $(LOCAL_PYTHON_INSTALL)/lib/python2.6/config/libpython2.6.a -lpthread -lutil
+
+LOCAL_LIBS_MACH   =  -L$(LOCAL_INT_INSTALL)/fc/lib/ \
+                     -limf -lifcore -lifport \
+                     -L$(LOCAL_INT_INSTALL)/cc/lib/ \
+                     -lifcore -lifport -limf -lcprts \
+                     -lstdc++ -lg2c
+
+MACH_LIBS         = $(LOCAL_LIBS_HDF5) $(LOCAL_LIBS_MACH) #$(LOCAL_LIBS_PYTHON)
+MACH_LIBS_MPI     = $(LOCAL_LIBS_MPI)

File src/enzo/Options.C

View file
     fprintf(opf, " 64 bit Integer initial conditions\n");
 #endif
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
     fprintf(opf, " Float precision is 32 bits\n");
 #endif
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
     fprintf(opf, " Float precision is 64 bits\n");
 #endif
 
-#ifdef p4
+#ifdef CONFIG_PFLOAT_4
     fprintf(opf, " Position and time precision is 32 bits - NOT SUPPORTED!\n");
 #endif
 
-#ifdef p8
+#ifdef CONFIG_PFLOAT_8
     fprintf(opf, " Position and time precision is 64 bits\n");
 #endif
 
-#ifdef p16
+#ifdef CONFIG_PFLOAT_16
     fprintf(opf, " Position and time precision is 128 bits\n");
 #endif
 

File src/enzo/ReadParameterFile.C

View file
         return FAIL;
       }
     }
+
+    ret += sscanf(line, "LoadBalancing = %"ISYM, &LoadBalancing);
  
     if (sscanf(line, "TimeActionType[%"ISYM"] = %"ISYM, &dim, &int_dummy) == 2) {
       ret++; TimeActionType[dim] = int_dummy;
     if (sscanf(line, "CoolDataParameterFile = %s", dummy) == 1)
       CoolData.ParameterFilename = dummy;
 
+    ret += sscanf(line, "OutputCoolingTime = %"ISYM, &OutputCoolingTime);
+    ret += sscanf(line, "OutputTemperature = %"ISYM, &OutputTemperature);
+
     ret += sscanf(line, "ZEUSQuadraticArtificialViscosity = %"FSYM,
 		  &ZEUSQuadraticArtificialViscosity);
     ret += sscanf(line, "ZEUSLinearArtificialViscosity = %"FSYM,

File src/enzo/RebuildHierarchy.C

View file
       FastSiblingLocatorFinalize(&ChainingMesh);
  
       /* Redistribute grids over processors to Load balance. */
-#ifdef ENABLE_LOAD_BALANCE 
-      TIME_MSG("Load balancing");
-      CommunicationLoadBalanceGrids(SubgridHierarchyPointer, subgrids, 
-				    MoveParticles);
-      TIME_MSG("Finished load balancing");
-#endif
+      switch( LoadBalancing ){
+      case 1:
+	TIME_MSG("Load balancing");
+	CommunicationLoadBalanceGrids(SubgridHierarchyPointer, subgrids, 
+				      MoveParticles);
+	TIME_MSG("Finished load balancing");
+	break;
+      default:
+	
+	break;
+      }
+
 
       /* If this is the finest level with static subgrids, the grids
 	 should be distributed enough to collect the particles on each

File src/enzo/SetDefaultGlobalValues.C

View file
  
   MetaData.LocalDir            = NULL;
   MetaData.GlobalDir           = NULL;
+
+  LoadBalancing = 1; //On, memory equalization method
  
   for (i = 0; i < MAX_TIME_ACTIONS; i++) {
     TimeActionType[i]      = 0;
   CoolData.alpha0             = 1.5;               // radiation spectral slope
   CoolData.f3                 = 1.0e-21;           // radiation normalization
   CoolData.ParameterFilename  = NULL;
- 
+
+  OutputCoolingTime = 0;
+  OutputTemperature = 0;
+
   ZEUSLinearArtificialViscosity    = 0.0;
   ZEUSQuadraticArtificialViscosity = 2.0;
   UseMinimumPressureSupport        = FALSE;

File src/enzo/Star_ActivateNewStar.C

View file
   int StarType;
   FILE *fptr;
   if (this->IsUnborn()) {  // unborn
-    StarType = abs(type);
+    StarType = ABS(type);
     switch (StarType) {
     case PopII:
       if (Mass > StarClusterMinimumMass) {

File src/enzo/Star_FindFeedbackSphere.C

View file
 
   SphereContained = TRUE;
   SkipMassRemoval = FALSE;
-  StarType = abs(this->type);
+  StarType = ABS(this->type);
   for (dim = 0; dim < MAX_DIMENSION; dim++)
     AvgVelocity[dim] = 0.0;
 

File src/enzo/WriteParameterFile.C

View file
   for (dim = 0; dim < MAX_CUBE_DUMPS; dim++)
     if (CubeDumps[dim] != NULL)
       fprintf(fptr, "CubeDump[%"ISYM"]            = %s\n", dim, CubeDumps[dim]);
+
+  fprintf(fptr,"LoadBalancing         = %"ISYM"\n",LoadBalancing);
  
   for (dim = 0; dim < MAX_TIME_ACTIONS; dim++)
     if (TimeActionType[dim] > 0) {
 
   if (CoolData.ParameterFilename != NULL)
     fprintf(fptr, "CoolDataParameterFile = %s\n\n", CoolData.ParameterFilename);
+
+  fprintf(fptr, "OutputCoolingTime              = %"ISYM"\n", OutputCoolingTime);
+  fprintf(fptr, "OutputTemperature              = %"ISYM"\n", OutputTemperature);
  
   fprintf(fptr, "ZEUSLinearArtificialViscosity    = %"GSYM"\n",
 	  ZEUSLinearArtificialViscosity);

File src/enzo/acml_st1.src

View file
 
 #ifdef XT3
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
 
       subroutine acml_st1(x, n1, idir)
 
 
 #endif
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
 
       subroutine acml_st1(x, n1, idir)
 

File src/enzo/cray_x1_fft64.src

View file
 #include "error.def"
 #ifdef CRAYX1
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
 
       subroutine cray_1d(x, rank, n1, n2, n3, idir)
 
 
 #endif
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
 
       subroutine cray_1d(x, rank, n1, n2, n3, idir)
 

File src/enzo/cray_x1_st1_fft64.src

View file
 
 #ifdef CRAYX1
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
 
       subroutine cray_st1(x, n1, idir)
 
 
 #endif
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
 
       subroutine cray_st1(x, n1, idir)
 

File src/enzo/fft90.src90

View file
   PRIVATE
   PUBLIC:: fft, fftn, fftkind
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
   REAL*4 :: TYPE_DUMMY
 #endif
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
   REAL*8 :: TYPE_DUMMY
 #endif
 

File src/enzo/ffte4X.src

View file
 
       implicit none
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
       REAL*4 :: TYPE_DUMMY
 #endif
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
       REAL*8 :: TYPE_DUMMY
 #endif
 

File src/enzo/fortran.def

View file
 #define MAX_ANY_SINGLE_DIRECTION 3079
 
-#ifdef p4
+#ifdef CONFIG_PFLOAT_4
 #define tiny 1.0e-20
 #define huge 1.0e+20
 #define REALSUB real
 #endif
 
-#ifdef p8
+#ifdef CONFIG_PFLOAT_8
 #define tiny 1.0e-20
 #define huge 1.0e+20
 #define REALSUB real*8
 #endif
 
-#ifdef p16
+#ifdef CONFIG_PFLOAT_16
 #define tiny 1.0e-20
 #define huge 1.0e+20
 #define REALSUB real*16

File src/enzo/global_data.h

View file
 # define EXTERN extern
 #endif
 
+/* Load Balancing.  Currently only memory count method implemented
+                          0 = off
+                          1 = Equalize processor memory count */
+EXTERN int LoadBalancing;
+
 /* debugging, extraction flags */
 
 EXTERN int debug;
 
 EXTERN int CellFlaggingMethod[MAX_FLAGGING_METHODS];
 
+
 /* Velocity to limit timesteps */
 
 EXTERN float TimestepSafetyVelocity;
 EXTERN int RadiationFieldLevelRecompute;
 EXTERN int RadiationXRaySecondaryIon;
 
+/* Output cooling time with grid data. */
+
+EXTERN int OutputCoolingTime;
+
+/* Output temperature with grid data. */
+
+EXTERN int OutputTemperature;
+
 /* ZEUS Hydro artificial viscosity parameters (C1, C2 of Stone & Norman). */
 
 EXTERN float ZEUSLinearArtificialViscosity;

File src/enzo/ibm_fft64.src

View file
 
 #ifdef SP2
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
 
       subroutine ibm_1d(x, rank, n1, n2, n3, idir)
 
 
 
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
 
       subroutine ibm_1d(x, rank, n1, n2, n3, idir)
 

File src/enzo/ibm_st1_fft64.src

View file
 
 #ifdef SP2
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
 
       subroutine ibm_st1(x, n1, idir)
 
 
 
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
 
       subroutine ibm_st1(x, n1, idir)
 

File src/enzo/macros_and_parameters.h

View file
 #define ABS(A) labs((long_int) (A))
 #endif
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
 #define Eflt float
 #define FSYM "f"
 #define FloatDataType MPI_FLOAT
 #endif
 #endif
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
 #define Eflt double
 #define FSYM "lf"
 #define FloatDataType MPI_DOUBLE
 #endif
 #endif
 
-#ifdef p4
+#ifdef CONFIG_PFLOAT_4
 #define FLOAT float
 #define PSYM "f"
 #define GSYM "g"
 #define HDF5_FILE_PREC HDF5_FILE_R4
 #endif
 
-#ifdef p8
+#ifdef CONFIG_PFLOAT_8
 #define FLOAT double
 #define PSYM "lf"
 #define GSYM "g"
 #define HDF5_FILE_PREC HDF5_FILE_R8
 #endif
 
-#ifdef p16
+#ifdef CONFIG_PFLOAT_16
 #define FLOAT long_double
 #define PSYM "Lf"
 #define GSYM "g"

File src/enzo/mkl_st1.src

View file
 
 #ifdef MKL
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
 
       subroutine mkl_st1(x, n1, idir)
 
 
 #endif
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
 
       subroutine mkl_st1(x, n1, idir)
 

File src/enzo/multi_cool.src

View file
       integer itmax, ijk
       parameter (itmax = 10000, ijk = MAX_ANY_SINGLE_DIRECTION)
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
       real tolerance
       parameter (tolerance = 1.0e-05)
 #endif
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
       real tolerance
       parameter (tolerance = 1.0e-10)
 #endif

File src/enzo/sgi_st1_fft64.src

View file
 
 #ifdef ALTIX
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
 
 
       subroutine sgi_st1(x, n1, idir)
 
 
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
 
       subroutine sgi_st1(x, n1, idir)
 

File src/enzo/solve_cool.src

View file
       integer itmax, ijk
       parameter (itmax = 5000, ijk = MAX_ANY_SINGLE_DIRECTION)
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
       real tolerance
       parameter (tolerance = 1.0e-05)
 #endif
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
       real tolerance
       parameter (tolerance = 1.0e-10)
 #endif

File src/enzo/solve_rate.src

View file
       integer itmax, ijk
       parameter (itmax = 5000, ijk = MAX_ANY_SINGLE_DIRECTION)
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
       real tolerance
       parameter (tolerance = 1.0e-05)
 #endif
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
       real tolerance
       parameter (tolerance = 1.0e-10)
 #endif

File src/enzo/solve_rate_cool.src

View file
       integer itmax, ijk
       parameter (itmax = 10000, ijk = MAX_ANY_SINGLE_DIRECTION)
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
       real tolerance
       parameter (tolerance = 1.0e-05)
 #endif
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
       real tolerance
       parameter (tolerance = 1.0e-10)
 #endif

File src/enzo/twoshock.src

View file
 
 !     Tolerance can be relaxed to reduce the cost of this routine
 
-#ifdef r4
+#ifdef CONFIG_BFLOAT_4
       real tolerance
       parameter (tolerance = 1.0e-07)
 #endif
 
-#ifdef r8
+#ifdef CONFIG_BFLOAT_8
       real tolerance
       parameter (tolerance = 1.0e-14)
 #endif

File src/yt/CREDITS

-YT is increasingly a group project.
-
-Lead Developer:                     Matthew Turk (matthewturk@gmail.com)
-Orion Support:                      Jeff Oishi (jsoishi@gmail.com)
-Cosmology & Fragmentation Analysis: Britton Smith (brittonsmith@gmail.com)
-Galaxy Merger Trees:                Stephen Skory (sskory@physics.ucsd.edu)
-
-We also include the Delaunay Triangulation module written by Robert Kern of
-Enthought.
-
-Thanks to everyone for all your contributions!

File src/yt/LICENSE.txt

-                    GNU GENERAL PUBLIC LICENSE
-                       Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
-                            Preamble
-
-  The GNU General Public License is a free, copyleft license for
-software and other kinds of works.
-
-  The licenses for most software and other practical works are designed
-to take away your freedom to share and change the works.  By contrast,
-the GNU General Public License is intended to guarantee your freedom to
-share and change all versions of a program--to make sure it remains free
-software for all its users.  We, the Free Software Foundation, use the
-GNU General Public License for most of our software; it applies also to
-any other work released this way by its authors.  You can apply it to
-your programs, too.
-
-  When we speak of free software, we are referring to freedom, not
-price.  Our General Public Licenses are designed to make sure that you
-have the freedom to distribute copies of free software (and charge for
-them if you wish), that you receive source code or can get it if you
-want it, that you can change the software or use pieces of it in new
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-
-  To protect your rights, we need to prevent others from denying you
-these rights or asking you to surrender the rights.  Therefore, you have
-certain responsibilities if you distribute copies of the software, or if
-you modify it: responsibilities to respect the freedom of others.
-
-  For example, if you distribute copies of such a program, whether
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-
-  Developers that use the GNU GPL protect your rights with two steps:
-(1) assert copyright on the software, and (2) offer you this License
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