Merge pull request #5 from NCAR/master

Updating my fork

doc/source/mach_walkthrough.txt

@@ -349,7 +349,7 @@ with: <pre>tar zxf parallel-netcdf-1.6.1.tar.gz</pre>
 
 <p>Build with:
 <pre>cd parallel-netcdf-1.6.1
-FC=mpifort CC=mpicc ./configure --prefix=/usr/local
+FC=mpifort CC=mpicc CFLAGS=-fPIC ./configure --prefix=/usr/local
 make all check
 sudo make install </pre>
 
@@ -371,16 +371,29 @@ sudo make install </pre>
 
 <p>Download the netcdf C library from the <a
 href="http://www.unidata.ucar.edu/downloads/netcdf/index.jsp">NetCDF download
-page</a>. (These instructions were tested using version 4.3.3.1). Untar
-with: <pre>tar zxf netcdf-4.3.3.1.tar.gz</pre>
+page</a>. (These instructions were tested using version 4.4.0). Untar
+with: <pre>tar zxf netcdf-c-4.4.0.tar.gz</pre>
 
 
 <p>Build with:
-<pre>cd netcdf-4.3.3.1
+<pre>cd netcdf-c-4.4.0
 CC=mpicc ./configure --with-zlib=/usr/local --prefix=/usr/local --with-szlib=/usr/local --with-hdf5=/usr/local --enable-pnetcdf --enable-parallel-tests --enable-logging
 make all check
 sudo make install </pre>
 
+<li>Installing NetCDF-4 Fortran Library
+
+<p>Download the netcdf Fortran library from the <a
+href="http://www.unidata.ucar.edu/downloads/netcdf/index.jsp">NetCDF download
+page</a>. (These instructions were tested using version 4.4.3). Untar
+with: <pre>tar zxf netcdf-fortran-4.4.3.tar.gz</pre>
+
+
+<p>Build with:
+<pre>cd netcdf-fortran-4.4.3
+F77=mpif77 F90=mpif90  ./configure --with-zlib=/usr/local --prefix=/usr/local --with-szlib=/usr/local --with-hdf5=/usr/local --enable-pnetcdf --enable-parallel-tests --enable-logging
+make all check
+sudo make install </pre>
 
 <li>Installing ParallelIO Library
 

examples/c/example1.c

@@ -10,6 +10,7 @@
  * processors.
  */
 
+#include <getopt.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <unistd.h>
@@ -280,6 +281,9 @@ int check_file(int ntasks, char *filename) {
 	/** Used for command line processing. */
 	int c;
 
+	/** Return value. */
+	int ret;
+
 	/* Parse command line. */
 	while ((c = getopt(argc, argv, "v")) != -1)
 	    switch (c)
@@ -293,7 +297,6 @@ int check_file(int ntasks, char *filename) {
 
 #ifdef TIMING    
 	/* Initialize the GPTL timing library. */
-	int ret;
 	if ((ret = GPTLinitialize ()))
 	    return ret;
 #endif    

examples/c/example2.c

@@ -21,6 +21,7 @@
  * </pre>
  */
 
+#include <getopt.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <unistd.h>
@@ -437,6 +438,8 @@ int main(int argc, char* argv[])
     /** Needed for command line processing. */
     int c;
 
+    int ret;
+
     /* Parse command line. */
     while ((c = getopt(argc, argv, "v")) != -1)
 	switch (c)
@@ -450,7 +453,6 @@ int main(int argc, char* argv[])
 
 #ifdef TIMING    
     /* Initialize the GPTL timing library. */
-    int ret;
     if ((ret = GPTLinitialize ()))
 	return ret;
 #endif    

examples/c/examplePio.c

@@ -10,6 +10,7 @@
  * processors.
  */
 
+#include <getopt.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <unistd.h>

src/clib/bget.c

@@ -397,6 +397,7 @@
     BGET CONFIGURATION
     ==================
 */
+//#define PIO_USE_MALLOC 1
 #ifdef PIO_USE_MALLOC
 #include <stdlib.h>
 #endif
@@ -610,11 +611,13 @@ void *bget(requested_size)
 #endif
 
 #ifdef PIO_USE_MALLOC
-    if(requested_size>maxsize){
-      maxsize=requested_size;
-      printf("%s %d %d\n",__FILE__,__LINE__,maxsize);
-    }
-    return(malloc(requested_size));
+    //    if(requested_size>maxsize){
+    //   maxsize=requested_size;
+    //   printf("%s %d %d\n",__FILE__,__LINE__,maxsize);
+    // }
+    buf = malloc(requested_size);
+    //    printf("bget allocate %ld %x\n",requested_size,buf);
+    return(buf);
 #endif 
 
 
@@ -875,6 +878,7 @@ void brel(buf)
     struct bfhead *b, *bn;
 
 #ifdef PIO_USE_MALLOC
+    //    printf("bget free %d %x\n",__LINE__,buf);
     free(buf);
     return;
 #endif    

src/clib/ncparser.pl

@@ -301,7 +301,7 @@
 		  print F "    if(name != NULL){ \n";
 		  print F "      int slen;\n";
 		  print F "      if(ios->iomaster)\n";
-		  print F "        slen = (int) strlen(name);\n";
+		  print F "        slen = (int) strlen(name) + 1;\n";
 		  print F "      mpierr = MPI_Bcast(&slen, 1, MPI_INT, ios->ioroot, ios->my_comm);\n";
 		  print F "      mpierr = MPI_Bcast(name, slen, MPI_CHAR, ios->ioroot, ios->my_comm);\n    }\n";
 
@@ -316,15 +316,15 @@
 		  print F  "    if(name != NULL){ \n";
 		  print F "      int slen;\n";
 		  print F "      if(ios->iomaster)\n";
-		  print F "        slen = (int) strlen(name);\n";
+		  print F "        slen = (int) strlen(name) + 1;\n";
 		  print F "      mpierr = MPI_Bcast(&slen, 1, MPI_INT, ios->ioroot, ios->my_comm);\n";
 		  print F "      mpierr = MPI_Bcast(name, slen, MPI_CHAR, ios->ioroot, ios->my_comm);\n    }\n";
 		  print F "      if(lenp != NULL) mpierr = MPI_Bcast(lenp , 1, MPI_OFFSET, ios->ioroot, ios->my_comm);\n";
 	      }elsif($func =~ /inq_dimname/ || $func =~ /inq_varname/ || $func =~ /inq_attname/){
 		  print F "    if(name != NULL){\n";
 		  print F "      int slen;\n";
 		  print F "      if(ios->iomaster)\n";
-		  print F "        slen = (int) strlen(name);\n";
+		  print F "        slen = (int) strlen(name) + 1;\n";
 		  print F "      mpierr = MPI_Bcast(&slen, 1, MPI_INT, ios->ioroot, ios->my_comm);\n";
 		  print F "      mpierr = MPI_Bcast(name, slen, MPI_CHAR, ios->ioroot, ios->my_comm);\n    }\n";
 	      }elsif($func =~ /inq_vardimid/){

src/clib/pio.h

@@ -366,19 +366,17 @@ int PIOc_def_var_deflate(int ncid, int varid, int shuffle, int deflate,
 int PIOc_inq_var_deflate(int ncid, int varid, int *shufflep,
 			 int *deflatep, int *deflate_levelp);
 int PIOc_inq_var_szip(int ncid, int varid, int *options_maskp, int *pixels_per_blockp);
-int PIOc_def_var_fletcher32(int ncid, int varid, int fletcher32);
-int PIOc_inq_var_fletcher32(int ncid, int varid, int *fletcher32p);
-int PIOc_def_var_chunking(int ncid, int varid, int storage, const size_t *chunksizesp);
-int PIOc_inq_var_chunking(int ncid, int varid, int *storagep, size_t *chunksizesp);
+int PIOc_def_var_chunking(int ncid, int varid, int storage, const PIO_Offset *chunksizesp);
+int PIOc_inq_var_chunking(int ncid, int varid, int *storagep, PIO_Offset *chunksizesp);
 int PIOc_def_var_fill(int ncid, int varid, int no_fill, const void *fill_value);
 int PIOc_inq_var_fill(int ncid, int varid, int *no_fill, void *fill_valuep);
 int PIOc_def_var_endian(int ncid, int varid, int endian);
 int PIOc_inq_var_endian(int ncid, int varid, int *endianp);
-int PIOc_set_chunk_cache(int iotype, int io_rank, size_t size, size_t nelems, float preemption);
-int PIOc_get_chunk_cache(int iotype, int io_rank, size_t *sizep, size_t *nelemsp, float *preemptionp);
-int PIOc_set_var_chunk_cache(int ncid, int varid, size_t size, size_t nelems,
+int PIOc_set_chunk_cache(int iosysid, int iotype, PIO_Offset size, PIO_Offset nelems, float preemption);
+int PIOc_get_chunk_cache(int iosysid, int iotype, PIO_Offset *sizep, PIO_Offset *nelemsp, float *preemptionp);
+int PIOc_set_var_chunk_cache(int ncid, int varid, PIO_Offset size, PIO_Offset nelems,
 			     float preemption);
-int PIOc_get_var_chunk_cache(int ncid, int varid, size_t *sizep, size_t *nelemsp,
+int PIOc_get_var_chunk_cache(int ncid, int varid, PIO_Offset *sizep, PIO_Offset *nelemsp,
 			     float *preemptionp);
 int PIOc_inq_var (int ncid, int varid, char *name, nc_type *xtypep, int *ndimsp, int *dimidsp, int *nattsp); 
 int PIOc_inq_varname (int ncid, int varid, char *name); 
@@ -601,6 +599,7 @@ int PIOc_set_blocksize(const int newblocksize);
   int PIOc_get_varm_short (int ncid, int varid, const PIO_Offset start[], const PIO_Offset count[], const PIO_Offset stride[], const PIO_Offset imap[], short *buf);  
   int PIOc_get_varm_ulonglong (int ncid, int varid, const PIO_Offset start[], const PIO_Offset count[], const PIO_Offset stride[], const PIO_Offset imap[], unsigned long long *buf);  
   int PIOc_get_var_schar (int ncid, int varid, signed char *buf); 
+  int PIOc_iotype_available(const int iotype);
 
 #if defined(__cplusplus)
 }