Merge of branch cdo-pio into trunk cdi

.gitattributes

@@ -250,8 +250,31 @@ tables/remo -text
 tables/wmo_001 -text
 tests/Makefile.am -text
 tests/Makefile.in -text
+tests/cksum.c -text
+tests/cksum.h -text
+tests/cksum_read.c -text
+tests/cksum_write.c -text
+tests/ensure_array_size.c -text
+tests/ensure_array_size.h -text
+tests/pio_cksum_asynch.in -text
+tests/pio_cksum_fpguard.in -text
+tests/pio_cksum_mpinonb.in -text
+tests/pio_cksum_writer.in -text
+tests/pio_write.c -text
+tests/pio_write_run.in -text
+tests/stream_cksum.c -text
+tests/stream_cksum.h -text
+tests/test_cksum_extra.in -text
+tests/test_cksum_grib.in -text
+tests/test_cksum_ieg.in -text
+tests/test_cksum_nc.in -text
+tests/test_cksum_nc2.in -text
+tests/test_cksum_nc4.in -text
+tests/test_cksum_service.in -text
 tests/test_grib.c -text
 tests/test_grib.sh -text
+tests/var_cksum.c -text
+tests/var_cksum.h -text
 util/mpi_launch_poe -text
 util/serialrun.in -text
 util/sunf95preproc-wrapper -text

tests/Makefile.am

 ## Process this file with automake to produce Makefile.in
 #
-TESTS = test_grib.sh
-check_PROGRAMS = test_grib
+TESTS = test_grib.sh test_cksum_grib test_cksum_nc test_cksum_extra \
+	test_cksum_service test_cksum_nc2 test_cksum_nc4 test_cksum_ieg \
+	pio_write_run pio_cksum_mpinonb pio_cksum_fpguard \
+	pio_cksum_asynch pio_cksum_writer
+check_PROGRAMS = test_grib cksum_write cksum_read pio_write
 #
 test_grib_SOURCES = test_grib.c
+cksum_write_SOURCES = cksum_write.c cksum.c cksum.h
+cksum_read_SOURCES = cksum_read.c \
+	var_cksum.c var_cksum.h \
+	stream_cksum.c stream_cksum.h \
+	cksum.c cksum.h \
+	ensure_array_size.h ensure_array_size.c
+pio_write_SOURCES = pio_write.c cksum.h cksum.c
 #
-LDADD = -L../src -lcdi -lm
-AM_LDFLAGS = -L$(top_srcdir)/src
+LDADD = ../src/libcdi.la -lm
 INCLUDES   = -I$(top_srcdir)/src
 #
 EXTRA_DIST = $(TESTS)

tests/cksum.c

+#include <inttypes.h>
+#include <stdlib.h>
+#include <sys/types.h>
+
+static const uint32_t crctab[] = {
+  0x00000000,
+  0x04c11db7, 0x09823b6e, 0x0d4326d9, 0x130476dc, 0x17c56b6b,
+  0x1a864db2, 0x1e475005, 0x2608edb8, 0x22c9f00f, 0x2f8ad6d6,
+  0x2b4bcb61, 0x350c9b64, 0x31cd86d3, 0x3c8ea00a, 0x384fbdbd,
+  0x4c11db70, 0x48d0c6c7, 0x4593e01e, 0x4152fda9, 0x5f15adac,
+  0x5bd4b01b, 0x569796c2, 0x52568b75, 0x6a1936c8, 0x6ed82b7f,
+  0x639b0da6, 0x675a1011, 0x791d4014, 0x7ddc5da3, 0x709f7b7a,
+  0x745e66cd, 0x9823b6e0, 0x9ce2ab57, 0x91a18d8e, 0x95609039,
+  0x8b27c03c, 0x8fe6dd8b, 0x82a5fb52, 0x8664e6e5, 0xbe2b5b58,
+  0xbaea46ef, 0xb7a96036, 0xb3687d81, 0xad2f2d84, 0xa9ee3033,
+  0xa4ad16ea, 0xa06c0b5d, 0xd4326d90, 0xd0f37027, 0xddb056fe,
+  0xd9714b49, 0xc7361b4c, 0xc3f706fb, 0xceb42022, 0xca753d95,
+  0xf23a8028, 0xf6fb9d9f, 0xfbb8bb46, 0xff79a6f1, 0xe13ef6f4,
+  0xe5ffeb43, 0xe8bccd9a, 0xec7dd02d, 0x34867077, 0x30476dc0,
+  0x3d044b19, 0x39c556ae, 0x278206ab, 0x23431b1c, 0x2e003dc5,
+  0x2ac12072, 0x128e9dcf, 0x164f8078, 0x1b0ca6a1, 0x1fcdbb16,
+  0x018aeb13, 0x054bf6a4, 0x0808d07d, 0x0cc9cdca, 0x7897ab07,
+  0x7c56b6b0, 0x71159069, 0x75d48dde, 0x6b93dddb, 0x6f52c06c,
+  0x6211e6b5, 0x66d0fb02, 0x5e9f46bf, 0x5a5e5b08, 0x571d7dd1,
+  0x53dc6066, 0x4d9b3063, 0x495a2dd4, 0x44190b0d, 0x40d816ba,
+  0xaca5c697, 0xa864db20, 0xa527fdf9, 0xa1e6e04e, 0xbfa1b04b,
+  0xbb60adfc, 0xb6238b25, 0xb2e29692, 0x8aad2b2f, 0x8e6c3698,
+  0x832f1041, 0x87ee0df6, 0x99a95df3, 0x9d684044, 0x902b669d,
+  0x94ea7b2a, 0xe0b41de7, 0xe4750050, 0xe9362689, 0xedf73b3e,
+  0xf3b06b3b, 0xf771768c, 0xfa325055, 0xfef34de2, 0xc6bcf05f,
+  0xc27dede8, 0xcf3ecb31, 0xcbffd686, 0xd5b88683, 0xd1799b34,
+  0xdc3abded, 0xd8fba05a, 0x690ce0ee, 0x6dcdfd59, 0x608edb80,
+  0x644fc637, 0x7a089632, 0x7ec98b85, 0x738aad5c, 0x774bb0eb,
+  0x4f040d56, 0x4bc510e1, 0x46863638, 0x42472b8f, 0x5c007b8a,
+  0x58c1663d, 0x558240e4, 0x51435d53, 0x251d3b9e, 0x21dc2629,
+  0x2c9f00f0, 0x285e1d47, 0x36194d42, 0x32d850f5, 0x3f9b762c,
+  0x3b5a6b9b, 0x0315d626, 0x07d4cb91, 0x0a97ed48, 0x0e56f0ff,
+  0x1011a0fa, 0x14d0bd4d, 0x19939b94, 0x1d528623, 0xf12f560e,
+  0xf5ee4bb9, 0xf8ad6d60, 0xfc6c70d7, 0xe22b20d2, 0xe6ea3d65,
+  0xeba91bbc, 0xef68060b, 0xd727bbb6, 0xd3e6a601, 0xdea580d8,
+  0xda649d6f, 0xc423cd6a, 0xc0e2d0dd, 0xcda1f604, 0xc960ebb3,
+  0xbd3e8d7e, 0xb9ff90c9, 0xb4bcb610, 0xb07daba7, 0xae3afba2,
+  0xaafbe615, 0xa7b8c0cc, 0xa379dd7b, 0x9b3660c6, 0x9ff77d71,
+  0x92b45ba8, 0x9675461f, 0x8832161a, 0x8cf30bad, 0x81b02d74,
+  0x857130c3, 0x5d8a9099, 0x594b8d2e, 0x5408abf7, 0x50c9b640,
+  0x4e8ee645, 0x4a4ffbf2, 0x470cdd2b, 0x43cdc09c, 0x7b827d21,
+  0x7f436096, 0x7200464f, 0x76c15bf8, 0x68860bfd, 0x6c47164a,
+  0x61043093, 0x65c52d24, 0x119b4be9, 0x155a565e, 0x18197087,
+  0x1cd86d30, 0x029f3d35, 0x065e2082, 0x0b1d065b, 0x0fdc1bec,
+  0x3793a651, 0x3352bbe6, 0x3e119d3f, 0x3ad08088, 0x2497d08d,
+  0x2056cd3a, 0x2d15ebe3, 0x29d4f654, 0xc5a92679, 0xc1683bce,
+  0xcc2b1d17, 0xc8ea00a0, 0xd6ad50a5, 0xd26c4d12, 0xdf2f6bcb,
+  0xdbee767c, 0xe3a1cbc1, 0xe760d676, 0xea23f0af, 0xeee2ed18,
+  0xf0a5bd1d, 0xf464a0aa, 0xf9278673, 0xfde69bc4, 0x89b8fd09,
+  0x8d79e0be, 0x803ac667, 0x84fbdbd0, 0x9abc8bd5, 0x9e7d9662,
+  0x933eb0bb, 0x97ffad0c, 0xafb010b1, 0xab710d06, 0xa6322bdf,
+  0xa2f33668, 0xbcb4666d, 0xb8757bda, 0xb5365d03, 0xb1f740b4
+};
+
+
+uint32_t
+memcrc(const unsigned char *b, size_t n)
+{
+/*  Input arguments:
+ *  const char*   b == byte sequence to checksum
+ *  size_t        n == length of sequence
+ */
+
+
+  register uint32_t i, c, s = 0;
+
+
+  for (i = n; i > 0; --i) {
+    c = (uint32_t)(*b++);
+    s = (s << 8) ^ crctab[(s >> 24) ^ c];
+  }
+
+
+  /* Extend with the length of the string. */
+  while (n != 0) {
+    c = n & 0377;
+    n >>= 8;
+    s = (s << 8) ^ crctab[(s >> 24) ^ c];
+  }
+
+
+  return ~s;
+}
+
+void
+memcrc_r(uint32_t *state, const unsigned char *block, size_t block_len)
+{
+/*  Input arguments:
+ *  const char*   b == byte sequence to checksum
+ *  size_t        n == length of sequence
+ */
+
+
+  register uint32_t i, c, s = *state;
+  register size_t n = block_len;
+  register const unsigned char *b = block;
+
+  for (i = n; i > 0; --i) {
+    c = (uint32_t)(*b++);
+    s = (s << 8) ^ crctab[(s >> 24) ^ c];
+  }
+
+  *state = s;
+}
+
+unsigned long
+memcrc_finish(uint32_t *state, off_t total_size)
+{
+  register uint32_t c, s = *state;
+  register off_t n = total_size;
+
+  /* Extend with the length of the string. */
+  while (n != 0) {
+    c = n & 0377;
+    n >>= 8;
+    s = (s << 8) ^ crctab[(s >> 24) ^ c];
+  }
+
+  return ~s;
+}

tests/cksum.h

+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <inttypes.h>
+
+void
+memcrc_r(uint32_t *state, const unsigned char *block, size_t block_len);
+
+unsigned long
+memcrc_finish(uint32_t *state, off_t total_size);
+
+uint32_t
+memcrc(const unsigned char *b, size_t n);
+

tests/cksum_read.c

+#ifndef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <assert.h>
+#include <inttypes.h>
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "ensure_array_size.h"
+#include "var_cksum.h"
+#include "stream_cksum.h"
+
+static struct cksum_table *
+read_table(const char *table_fname, size_t *table_len)
+{
+  struct cksum_table *table = NULL;
+  FILE *tablefp;
+  size_t table_size = 0, table_used = 0;
+  unsigned long cksum_temp;
+  int code;
+
+  if (!(tablefp = fopen(table_fname, "r")))
+    {
+      perror("failed to open table file");
+      *table_len = -1;
+      return NULL;
+    }
+  while (fscanf(tablefp, "%08lx %d\n", &cksum_temp, &code) == 2)
+    {
+      ENSURE_ARRAY_SIZE(table, table_size, table_used + 1);
+      table[table_used].code = code;
+      table[table_used].cksum = cksum_temp;
+      ++table_used;
+    }
+  fclose(tablefp);
+  *table_len = table_used;
+  return table;
+}
+
+
+int main(int argc, char *argv[])
+{
+  char *fname = "example.grb", *table_fname = "example.cksum";
+
+  if (argc > 1)
+    fname = argv[1];
+  if (argc > 2)
+    table_fname = argv[2];
+
+  // compute checksums from data file
+  size_t nvars;
+  struct cksum_table *file_vars = cksum_stream(fname, &nvars);
+  if (!file_vars)
+    exit(EXIT_FAILURE);
+  // check checksums from table file
+  int retcode;
+  {
+    size_t num_ref_entries;
+    struct cksum_table *ref_var_table
+      = read_table(table_fname, &num_ref_entries);
+    if (num_ref_entries == -1)
+      exit(EXIT_FAILURE);
+    retcode
+      = compare_checksums(file_vars, nvars, "file",
+                          ref_var_table, num_ref_entries, "reference table");
+    free(ref_var_table);
+  }
+
+  return retcode;
+}
+
+/*
+ * Local Variables:
+ * c-file-style: "Java"
+ * c-basic-offset: 2
+ * indent-tabs-mode: nil
+ * show-trailing-whitespace: t
+ * require-trailing-newline: t
+ * End:
+ */

tests/cksum_write.c

+#include <errno.h>
+#include <inttypes.h>
+#include <limits.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+
+#include "cdi.h"
+
+#include "cksum.h"
+
+static int
+parse_intarg(const char msg[])
+{
+  char *end;
+  long temp = strtol(optarg, &end, 0);
+  if ((errno == ERANGE && (temp == LONG_MAX || temp == LONG_MIN))
+      || (errno != 0 && temp == 0)) {
+    perror(msg);
+    exit(EXIT_FAILURE);
+  }
+  if (temp > INT_MAX || temp < INT_MIN)
+  {
+    fprintf(stderr, "range error: %ld\n", temp);
+    exit(EXIT_FAILURE);
+  }
+  return (int)temp;
+}
+
+static inline double
+sign_flat(double v)
+{
+  if (v == 0.0)
+    return 0.0;
+  return v;
+}
+
+static char *
+fname_create(const char *prefix, const char *suffix)
+{
+  size_t prefix_len, suffix_len;
+  char *fname;
+  if (!(fname =malloc((prefix_len = strlen(prefix)) + 1
+                      + (suffix_len = strlen(suffix)) + 1)))
+    {
+      perror("cannot create string");
+      exit(EXIT_FAILURE);
+    }
+  strcpy(fname, prefix);
+  fname[prefix_len] = '.';
+  strcpy(fname + prefix_len + 1, suffix);
+  return fname;
+}
+
+static const struct {
+  char suffix[4];
+  int type, defaultDT, defaultGrid;
+} suffix2type[] = {
+  { "nc", FILETYPE_NC, DATATYPE_FLT64, GRID_LONLAT },
+  { "grb",  FILETYPE_GRB, DATATYPE_PACK24, GRID_LONLAT },
+  { "nc2", FILETYPE_NC2, DATATYPE_FLT64, GRID_LONLAT },
+  { "nc4", FILETYPE_NC4, DATATYPE_FLT64, GRID_LONLAT },
+  { "ext", FILETYPE_EXT, DATATYPE_FLT64, GRID_GENERIC, },
+  { "svc", FILETYPE_SRV, DATATYPE_FLT64, GRID_GENERIC, },
+  { "ieg", FILETYPE_IEG, DATATYPE_FLT64, GRID_LONLAT },
+};
+
+enum {
+  nvars = 2,
+};
+
+static const int varCodes[nvars] = { 42, 55 };
+
+int
+main(int argc, char *argv[])
+{
+  int gridID, zaxisID[nvars], taxisID;
+  int vlistID, varID[nvars], streamID, tsID;
+  int nlon = 12, //!< Number of longitudes
+    nlat = 6, //!< Number of latitudes
+    nlev = 5, //!< Number of levels
+    nts = 3; //!< Number of time steps
+  int i, j, k, nmiss = 0;
+  double *lons, *lats, *var[nvars], *levs, mscale, mrscale;
+  size_t varSize[nvars];
+  char *varName[nvars] = { "varname1", "varname2" };
+  const char *suffix = "grb", *prefix = "example";
+  int grid = GRID_LONLAT;
+  int filetype = FILETYPE_GRB, datatype = DATATYPE_PACK24;
+  {
+    int opt;
+    while ((opt = getopt(argc, argv, "f:m:n:o:t:")) != -1)
+      switch (opt) {
+      case 'f':
+        {
+          int found = 0;
+          for (i = 0;
+               i < sizeof (suffix2type) / sizeof (suffix2type[0]);
+               ++i)
+            if (!strcmp(optarg, suffix2type[i].suffix))
+              {
+                found = 1;
+                filetype = suffix2type[i].type;
+                suffix = suffix2type[i].suffix;
+                datatype = suffix2type[i].defaultDT;
+                break;
+              }
+          if (!found)
+            {
+              fprintf(stderr, "Unsupported format requested: %s\n", optarg);
+              exit(EXIT_FAILURE);
+            }
+        }
+        break;
+      case 'm':
+        nlon = parse_intarg("error parsing number of longitudes");
+        break;
+      case 'n':
+        nlat = parse_intarg("error parsing number of latitudes");
+        break;
+      case 'o':
+        nlev = parse_intarg("error parsing number of levels");
+        break;
+      case 't':
+        nts = parse_intarg("error parsing number of timesteps");
+        break;
+      default: /* '?' */
+        fprintf(stderr, "Usage: %s [-m nlon] [-n nlat] [-o nlev] [-t nts]\n",
+                argv[0]);
+        exit(EXIT_FAILURE);
+      }
+  }
+
+  lons = malloc(nlon * sizeof (lons[0]));
+  for (i = 0; i < nlon; ++i)
+    lons[i] = ((double)(i * 360))/nlon;
+  lats = malloc(nlat * sizeof (lats[0]));
+  for (i = 0; i < nlat; ++i)
+    lats[i] = ((double)(i * 180))/nlat - 90.0;
+  levs = malloc(nlev * sizeof (levs[0]));
+  for (i = 0; i < nlev; ++i)
+    levs[i] = 101300 - 3940.3 * (exp(1.3579 * (double)(i)/(nlev - 1)) - 1.0);
+
+  varSize[0] = nlon * nlat;
+  varSize[1] = nlon * nlat * nlev;
+
+  // Create a regular lon/lat grid
+  gridID = gridCreate(grid, nlon*nlat);
+  gridDefXsize(gridID, nlon);
+  gridDefYsize(gridID, nlat);
+  gridDefXvals(gridID, lons);
+  gridDefYvals(gridID, lats);
+
+  // Create a surface level Z-axis
+  zaxisID[0] = zaxisCreate(ZAXIS_SURFACE, 1);
+
+  // Create a pressure level Z-axis
+  zaxisID[1] = zaxisCreate(ZAXIS_PRESSURE, nlev);
+  zaxisDefLevels(zaxisID[1], levs);
+
+  // Create a Time axis
+  taxisID = taxisCreate(TAXIS_ABSOLUTE);
+
+  // Create a variable list
+  vlistID = vlistCreate();
+
+  for (i = 0; i < nvars; ++i)
+    {
+      // Define the variables
+      varID[i] = vlistDefVar(vlistID, gridID, zaxisID[i], TIME_VARIABLE);
+      // Define the variable names,
+      vlistDefVarName(vlistID, varID[i], varName[i]);
+      // the codes
+      vlistDefVarCode(vlistID, varID[i], varCodes[i]);
+      // and set the data type
+      vlistDefVarDatatype(vlistID, varID[i], datatype);
+      // create memory for variables
+      var[i] = malloc(varSize[i] * sizeof (var[i][0]));
+
+    }
+
+  {
+    int mant_bits;
+    switch (datatype)
+      {
+      case DATATYPE_PACK8:
+        mant_bits = 7;
+        break;
+      case DATATYPE_PACK16:
+        mant_bits = 15;
+        break;
+      case DATATYPE_PACK24:
+        mant_bits = 23;
+        break;
+      case DATATYPE_FLT32:
+        mant_bits = 24;
+        break;
+      case DATATYPE_FLT64:
+        mant_bits = 53;
+        break;
+      case DATATYPE_INT8:
+      case DATATYPE_INT16:
+      case DATATYPE_INT32:
+      default:
+        fprintf(stderr, "Unexpected or unusable content format: %d\n",
+                datatype);
+        exit(EXIT_FAILURE);
+      }
+    mscale = INT64_C(1) << mant_bits;
+    mrscale = 1.0/mscale;
+  }
+
+  // Assign the Time axis to the variable list
+  vlistDefTaxis(vlistID, taxisID);
+
+  // Create a dataset in netCDF fromat
+  {
+    char *fname = fname_create(prefix, suffix);
+    if ((streamID = streamOpenWrite(fname, filetype)) < 0)
+      {
+        fprintf(stderr, "error opening output file %s: %s\n",
+                fname, cdiStringError(streamID));
+        exit(EXIT_FAILURE);
+      }
+    free(fname);
+  }
+
+  // Assign the variable list to the dataset
+  streamDefVlist(streamID, vlistID);
+
+  {
+    uint32_t checksum_state[nvars] = { 0, 0 };
+    // Loop over the number of time steps
+    for ( tsID = 0; tsID < nts; tsID++ )
+      {
+        // Set the verification date to 1985-01-01 + tsID
+        taxisDefVdate(taxisID, 19850101+tsID);
+        // Set the verification time to 12:00:00
+        taxisDefVtime(taxisID, 120000);
+        // Define the time step
+        streamDefTimestep(streamID, tsID);
+
+        // Init var1 and var2
+        for (j = 0; j < nlat; j++)
+          for (i = 0; i < nlon; i++)
+            var[0][i+j*nlon]
+              = sign_flat(round(
+                   (sin(2.0 * M_PI * (lons[(i + tsID)%nlon] - lons[0])
+                        / (lons[nlon-1] - lons[0]))
+                    * cos(2.0 * M_PI * (lats[j] - lats[0])
+                          / (lons[nlat-1] - lats[0]))
+                    ) * mscale)) * mrscale;
+        for (k = 0; k < nlev; ++k)
+          for (j = 0; j < nlat; j++)
+            for (i = 0; i < nlon; i++)
+              var[1][i+j*nlon+k*nlon*nlat]
+                = sign_flat(round(
+                     (cos(2.0 * M_PI * (lons[(i + tsID)%nlon] - lons[0])
+                          / (lons[nlon-1] - lons[0]))
+                      * sin(2.0 * M_PI * (lats[j] - lats[0])
+                            / (lons[nlat-1] - lats[0]))
+                      ) * mscale)) * mrscale;
+
+        memcrc_r(&checksum_state[0], (const unsigned char *)var[0],
+                 varSize[0] * sizeof (var[0][0]));
+        memcrc_r(&checksum_state[1], (const unsigned char *)var[1],
+                 varSize[1] * sizeof (var[1][0]));
+
+        // Write var1 and var2
+        streamWriteVar(streamID, varID[0], var[0], nmiss);
+        streamWriteVar(streamID, varID[1], var[1], nmiss);
+      }
+    // write checksums to table file
+    {
+      FILE *tablefp;
+      {
+        char *fname = fname_create(prefix, "cksum");
+        if (!(tablefp = fopen(fname, "w")))
+          {
+            perror("failed to open table file");
+            exit(EXIT_FAILURE);
+          }
+        free(fname);
+      }
+      for (i = 0; i < nvars; ++i)
+        {
+          uint32_t cksum;
+          int code;
+          cksum = memcrc_finish(&checksum_state[i],
+                                (off_t)varSize[i] * sizeof (var[i][0]) * nts);
+          code = vlistInqVarCode(vlistID, varID[i]);
+          if (fprintf(tablefp, "%08lx %d\n", (unsigned long)cksum, code) < 0)
+            {
+              perror("failed to write table file");
+              exit(EXIT_FAILURE);
+            }
+        }
+      fclose(tablefp);
+    }
+  }
+
+  // Close the output stream
+  streamClose(streamID);
+
+  // Destroy the objects
+  vlistDestroy(vlistID);
+  taxisDestroy(taxisID);
+  zaxisDestroy(zaxisID[0]);
+  zaxisDestroy(zaxisID[1]);
+  gridDestroy(gridID);
+
+  return 0;
+}
+
+/*
+ * Local Variables:
+ * c-file-style: "Java"
+ * c-basic-offset: 2
+ * indent-tabs-mode: nil
+ * show-trailing-whitespace: t
+ * require-trailing-newline: t
+ * End:
+ */

tests/ensure_array_size.c

+#include <stdlib.h>
+
+#include "ensure_array_size.h"
+#include "pio_util.h"
+