fix compiler warnings

include/Cubism/GridMorton.h

@@ -106,7 +106,6 @@ protected:
 
     TBlock& operator()( int ix,  int iy = 0,  int iz = 0) const
     {
-        const int N = this->N;
         const int NX = this->NX;
         const int NY = this->NY;
         const int NZ = this->NZ;
@@ -129,7 +128,7 @@ protected:
         assert(iflat >= 0 && iflat < f2m.size());
 
         const unsigned int idx = f2m[iflat];
-        assert(idx >= 0 && idx < N);
+        assert(idx >= 0 && idx < this->N);
 
         return *(this->_linaccess(idx));
     }

include/Cubism/HDF5SubdomainDumper.h

@@ -232,6 +232,7 @@ namespace SubdomainTypes
             }
 
         Subdomain(const Subdomain& c) = default;
+        virtual ~Subdomain() = default;
 
         inline int id() const { return m_id; }
         inline const int (&bbox_start() const)[3] { return m_bbox_start; }

include/Cubism/Histogram.h

@@ -23,7 +23,6 @@ class Histogram
     std::map<std::string,std::vector<float> > mk2t;
     bool isroot;
     bool bInitialized;
-    int reportID;
 
     void _print2file(std::string sKernel, std::vector<float> & buf);
     void _print_statistcis(std::string sKernel, std::vector<float> & buf);

include/Cubism/Indexers.h

@@ -19,22 +19,22 @@ class Indexer
 {
 protected:
     const unsigned int sizeX, sizeY, sizeZ, sizeTotal;
-    
-public:	
-    Indexer(const unsigned int sizeX, const unsigned int sizeY, const unsigned int sizeZ):
-    sizeX(sizeX), sizeY(sizeY), sizeZ(sizeZ), sizeTotal(sizeX*sizeY*sizeZ)
+
+public:
+    Indexer(const unsigned int sizeX_, const unsigned int sizeY_, const unsigned int sizeZ_):
+    sizeX(sizeX_), sizeY(sizeY_), sizeZ(sizeZ_), sizeTotal(sizeX_*sizeY_*sizeZ_)
     {
     }
-    
+
     virtual unsigned int encode(unsigned int ix, unsigned int iy, unsigned int iz) const
     {
         const unsigned int retval = ix + sizeX*(iy + iz*sizeY);
 
         assert(retval < sizeTotal && retval>=0);
 
-        return retval; 
+        return retval;
     }
-    
+
     virtual void decode(unsigned int code, unsigned int& ix, unsigned int& iy, unsigned int& iz) const
     {
         ix = code % sizeX;
@@ -47,33 +47,33 @@ class IndexerMorton : public Indexer
 {
     unsigned int depth;
 public:
-    IndexerMorton(const unsigned int sizeX, const unsigned int sizeY, const unsigned int sizeZ):
-    Indexer(sizeX, sizeY, sizeZ)
+    IndexerMorton(const unsigned int sizeX_, const unsigned int sizeY_, const unsigned int sizeZ_):
+    Indexer(sizeX_, sizeY_, sizeZ_)
     {
         depth = (unsigned int) fmin(10., ceil(log2((double)fmax(sizeX,fmax(sizeY,sizeZ)))));
     }
-    
+
     unsigned int encode(unsigned int ix, unsigned int iy, unsigned int iz) const
     {
         unsigned int idx=0;
-        
+
         for(unsigned int counter=0;counter<depth;++counter)
         {
             const unsigned int bitmask = 1 << counter;
             const unsigned int idx0 = ix&bitmask;
             const unsigned int idx1 = iy&bitmask;
             const unsigned int idx2 = iz&bitmask;
-            
+
             idx |= ((idx0<<2*counter) | (idx1<<(2*counter+1)) | (idx2<<(2*counter+2)));
         }
-        
-        return idx; 
+
+        return idx;
     }
-    
+
     void decode(unsigned int code, unsigned int& ix, unsigned int& iy, unsigned int& iz) const
     {
         ix=iy=iz=0;
-        
+
         for(unsigned int counter=0;counter<depth;++counter)
         {
             const unsigned int bitmask_x = 1 << (counter*3+0);

include/Cubism/LosslessCompression.h

@@ -14,6 +14,8 @@
 
 #include "Common.h"
 
+#define DBG 0
+
 CUBISM_NAMESPACE_BEGIN
 
 extern "C"
@@ -48,7 +50,7 @@ inline size_t
 ZZcompress(unsigned char *buf, size_t len, int layout[4], size_t *max)
 {
 #if 1
-    int zbufsize = 0;
+    size_t zbufsize = 0;
     char *zbuf = NULL;
     zbufsize = len + 4096;
     zbuf = (char *)malloc(zbufsize);

include/Cubism/PlainBinDumper_MPI.h

@@ -13,6 +13,7 @@
 #include <iostream>
 #include <string>
 #include <sstream>
+#include <cstdlib>
 #include <mpi.h>
 
 #include "Common.h"
@@ -110,7 +111,8 @@ void PlainReadBin_MPI(MPI_Comm comm, TReal **buffer, long *bytes, const std::str
 #if DBG
     printf("Reading %ld bytes of binary data\n", lbytes);
 #endif
-    unsigned char *tmp = (unsigned char *) malloc(lbytes);
+    unsigned long *tmp = nullptr;
+    posix_memalign((void**)&tmp, 16, lbytes);
 
     long base = MAX_MPI_PROCS*sizeof(tag);	// Header
     MPI_File_read_at(file_id, base + offset, (char *)tmp, lbytes, MPI_CHAR, &status);
@@ -119,6 +121,7 @@ void PlainReadBin_MPI(MPI_Comm comm, TReal **buffer, long *bytes, const std::str
     *bytes = lbytes;
 
     MPI_File_close(&file_id);
+    free(tmp);
 }
 
 CUBISM_NAMESPACE_END

include/Cubism/ZBinDumper.h

@@ -17,6 +17,8 @@
 #include "BlockInfo.h"
 #include "LosslessCompression.h"
 
+#define DBG 0
+
 CUBISM_NAMESPACE_BEGIN
 
 typedef struct _header_serial {
@@ -43,7 +45,6 @@ void DumpZBin(const TGrid &grid,
     filename << dump_path << "/" << f_name;
 
     FILE *file_id;
-    int status;
 
     static const int NCHANNELS = TStreamer::NCHANNELS;
     const int NX = grid.getBlocksPerDimension(0) * B::sizeX;
@@ -119,13 +120,13 @@ void DumpZBin(const TGrid &grid,
                    compressed_bytes);
 
         tag.size[ichannel] = compressed_bytes;
-        size_t wb_data = fwrite(array_all, 1, compressed_bytes, file_id);
+        fwrite(array_all, 1, compressed_bytes, file_id);
     }
 
     fseek(file_id, 0, SEEK_SET);
-    size_t wb_header = fwrite(&tag.size[0], 1, sizeof(tag), file_id);
+    fwrite(&tag.size[0], 1, sizeof(tag), file_id);
 
-    status = fclose(file_id);
+    fclose(file_id);
 
     delete[] array_all;
 }
@@ -142,7 +143,6 @@ void ReadZBin(TGrid &grid,
     std::ostringstream filename;
     filename << read_path << "/" << f_name;
 
-    int status;
     FILE *file_id;
 
     const int NX = grid.getBlocksPerDimension(0) * B::sizeX;
@@ -168,7 +168,7 @@ void ReadZBin(TGrid &grid,
     size_t local_bytes = local_count * sizeof(Real);
 
     header_serial tag;
-    size_t rb_header = fread(&tag.size[0], 1, sizeof(tag), file_id);
+    fread(&tag.size[0], 1, sizeof(tag), file_id);
 
 #if DBG
     printf("HEADER(%d):\n", rank);
@@ -191,10 +191,12 @@ void ReadZBin(TGrid &grid,
 #endif
         unsigned char *tmp = (unsigned char *)malloc(compressed_bytes + 4096);
 
-        size_t rb_data = fread(tmp, 1, compressed_bytes, file_id);
+        fread(tmp, 1, compressed_bytes, file_id);
 
         int layout[4] = {NX, NY, NZ, 1};
+#if DBG
         size_t decompressed_bytes =
+#endif
             ZZdecompress<typename TGrid::Real>(tmp,
                                                compressed_bytes,
                                                layout,
@@ -227,7 +229,7 @@ void ReadZBin(TGrid &grid,
         }
     } /* ichannel */
 
-    status = fclose(file_id);
+    fclose(file_id);
     delete [] array_all;
 }
 

include/Cubism/ZBinDumper_MPI.h

@@ -19,6 +19,8 @@
 #include "BlockInfo.h"
 #include "LosslessCompression.h"
 
+#define DBG 0
+
 CUBISM_NAMESPACE_BEGIN
 
 #define MAX_MPI_PROCS (16 * 1024) // header: 0.25MB* 8
@@ -246,13 +248,13 @@ void ReadZBin_MPI(TGrid &grid,
     //	size_t local_count = NX * NY * NZ * NCHANNELS;
     size_t local_count = NX * NY * NZ * 1;
     size_t local_bytes = local_count * sizeof(Real);
-    long offset;
 
     header tag;
     MPI_File_read_at(
         file_id, rank * sizeof(tag), &tag, 2 * 8, MPI_LONG, &status);
 
 #if DBG
+    long offset;
     printf("HEADER(%d):\n", rank);
     for (int i = 0; i < NCHANNELS; i++) {
         printf("channel %d: %ld %ld\n", i, tag.offset[i], tag.size[i]);
@@ -289,7 +291,9 @@ void ReadZBin_MPI(TGrid &grid,
 
         //	int layout[4] = {NCHANNELS, NX, NY, NZ};
         int layout[4] = {NX, NY, NZ, 1};
+#if DBG
         size_t decompressed_bytes =
+#endif
             ZZdecompress<typename TGrid::Real>(tmp,
                                                compressed_bytes,
                                                layout,

src/Histogram.cpp

@@ -67,7 +67,7 @@ void Histogram::_print2file(string sKernel, vector<float> & buf)
     sprintf(f_name_ascii, "hist_%s", sKernel.c_str());
 
     FILE * pFile_ascii = fopen(f_name_ascii, "a");
-    for(int i=0; i<buf.size(); ++i)
+    for(size_t i=0; i<buf.size(); ++i)
         fprintf(pFile_ascii, "%e\n", buf[i]);
     fclose (pFile_ascii);
 }