[svn-r8867] Purpose:

    Bug fix

Description:
    Fix error in chunked dataset I/O where data written out wasn't read
correctly from a chunked, extendible dataset after the dataset was extended.

    Also, fix parallel I/O tests to gather error results from all processes,
in order to detect errors that only occur on one process.

Solution:
    Bypass chunk cache for reads as well as writes, if parallel I/O driver is
used and file is opened for writing.

Platforms tested:
    FreeBSD 4.10 (sleipnir) w/parallel
    Too minor to require h5committest

5 files changed, 210 insertions, 24 deletions

diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 895a7b7..1cd9edc 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -142,18 +142,20 @@ Bug Fixes since HDF5-1.6.0 release
 
     Library
     -------
+        - Fixed bug where incorrect data could be read from a chunked dataset
+            after it was extended.  QAK - 2004/07/12
         - Fixed failure to read data back from file of compound type with
-          variable-length string as field.  SLU - 2004/06/10
+            variable-length string as field.  SLU - 2004/06/10
         - Fixed potential file corruption bug when a block of metadata could
-           overlap the end of the internal metadata accumulator buffer and
-           the buffer would be extended correctly, but would incorrectly 
-           change it's starting address.  QAK - 2004/06/09
+            overlap the end of the internal metadata accumulator buffer and
+            the buffer would be extended correctly, but would incorrectly 
+            change it's starting address.  QAK - 2004/06/09
         - Opaque datatype with no tag failed for some operations.  Fixed.
             SLU - 2004/6/3 
         - Fixed potential file corruption bug where dimensions that were
-           too large (a value greater than could be represented in 32-bits)
-           could cause the incorrect amount of space to be allocated in a
-           file for the raw data for the dataset.  QAK - 2004/06/01
+            too large (a value greater than could be represented in 32-bits)
+            could cause the incorrect amount of space to be allocated in a
+            file for the raw data for the dataset.  QAK - 2004/06/01
 	- Fixed dtypes "sw long double -> double" failure in QSC class
             machines.  AKC - 2004/4/16
         - Fixed problem with fletcher32 filter when converting data of different
diff --git a/src/H5Distore.c b/src/H5Distore.c
index 4520e65..1720a09 100644
--- a/src/H5Distore.c
+++ b/src/H5Distore.c
@@ -1860,10 +1860,20 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a
      * If the chunk is too large to load into the cache and it has no
      * filters in the pipeline (i.e. not compressed) and if the address
      * for the chunk has been defined, then don't load the chunk into the
-     * cache, just write the data to it directly.
+     * cache, just read the data from it directly.
+     *
+     * If MPI based VFD is used, must bypass the
+     * chunk-cache scheme because other MPI processes could be
+     * writing to other elements in the same chunk.  Do a direct
+     * read-through of only the elements requested.
      */
-    if (dset->layout.u.chunk.size>dset->cache.chunk.nbytes && dset->dcpl_cache.pline.nused==0 &&
-            chunk_addr!=HADDR_UNDEF) {
+    if ((dset->layout.u.chunk.size>dset->cache.chunk.nbytes && dset->dcpl_cache.pline.nused==0 && chunk_addr!=HADDR_UNDEF)
+            || (IS_H5FD_MPI(f) && (H5F_ACC_RDWR & H5F_get_intent(f)))) {
+#ifdef H5_HAVE_PARALLEL
+        /* Additional sanity check when operating in parallel */
+        if (chunk_addr==HADDR_UNDEF || dset->dcpl_cache.pline.nused>0)
+            HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to locate raw data chunk");
+#endif /* H5_HAVE_PARALLEL */
         if ((ret_value=H5D_contig_readvv(f, dxpl_id, dset, chunk_addr, (hsize_t)dset->layout.u.chunk.size, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, buf))<0)
             HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read raw data to file");
     } /* end if */
diff --git a/testpar/t_dset.c b/testpar/t_dset.c
index 858f3e3..5ff0a6e 100644
--- a/testpar/t_dset.c
+++ b/testpar/t_dset.c
@@ -12,8 +12,6 @@
  * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-/* $Id$ */
-
 /*
  * Parallel tests for datasets
  */
@@ -1301,6 +1299,174 @@ extend_writeInd(void)
     if (data_array1) free(data_array1);
 }
 
+/*
+ * Example of using the parallel HDF5 library to create an extendable dataset
+ * and perform I/O on it in a way that verifies that the chunk cache is
+ * bypassed for parallel I/O.
+ */
+
+void
+extend_writeInd2(void)
+{
+    char *filename;
+    hid_t fid;                  /* HDF5 file ID */
+    hid_t fapl;			/* File access templates */
+    hid_t fs;   		/* File dataspace ID */
+    hid_t ms;   		/* Memory dataspace ID */
+    hid_t dataset;		/* Dataset ID */
+    hbool_t use_gpfs = FALSE;   /* Use GPFS hints */
+    hsize_t orig_size=10;   	/* Original dataset dim size */
+    hsize_t new_size=20;   	/* Extended dataset dim size */
+    hsize_t one=1;
+    hsize_t max_size = H5S_UNLIMITED;	/* dataset maximum dim size */
+    hsize_t chunk_size = 16384;	/* chunk size */
+    hid_t dcpl;	       		/* dataset create prop. list */
+    int   written[10],          /* Data to write */
+        retrieved[10];          /* Data read in */
+    int mpi_size, mpi_rank;     /* MPI settings */
+    int i;                      /* Local index variable */
+    herr_t ret;         	/* Generic return value */
+
+    filename = (char *) GetTestParameters();
+    if (VERBOSE_MED)
+	printf("Extend independent write test #2 on file %s\n", filename);
+
+    /* set up MPI parameters */
+    MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
+    MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
+
+    /* -------------------
+     * START AN HDF5 FILE
+     * -------------------*/
+    /* setup file access template */
+    fapl = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
+    VRFY((fapl >= 0), "create_faccess_plist succeeded");
+
+    /* create the file collectively */
+    fid=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,fapl);
+    VRFY((fid >= 0), "H5Fcreate succeeded");
+
+    /* Release file-access template */
+    ret=H5Pclose(fapl);
+    VRFY((ret >= 0), "H5Pclose succeeded");
+
+
+    /* --------------------------------------------------------------
+     * Define the dimensions of the overall datasets and create them.
+     * ------------------------------------------------------------- */
+
+    /* set up dataset storage chunk sizes and creation property list */
+    dcpl = H5Pcreate(H5P_DATASET_CREATE);
+    VRFY((dcpl >= 0), "H5Pcreate succeeded");
+    ret = H5Pset_chunk(dcpl, 1, &chunk_size);
+    VRFY((ret >= 0), "H5Pset_chunk succeeded");
+
+    /* setup dimensionality object */
+    fs = H5Screate_simple (1, &orig_size, &max_size);
+    VRFY((fs >= 0), "H5Screate_simple succeeded");
+
+    /* create an extendible dataset collectively */
+    dataset = H5Dcreate(fid, DATASETNAME1, H5T_NATIVE_INT, fs, dcpl);
+    VRFY((dataset >= 0), "H5Dcreate succeeded");
+
+    /* release resource */
+    ret=H5Pclose(dcpl);
+    VRFY((ret >= 0), "H5Pclose succeeded");
+
+
+    /* -------------------------
+     * Test writing to dataset
+     * -------------------------*/
+    /* create a memory dataspace independently */
+    ms = H5Screate_simple(1, &orig_size, &max_size);
+    VRFY((ms >= 0), "H5Screate_simple succeeded");
+
+    /* put some trivial data in the data_array */
+    for (i=0; i<(int)orig_size; i++)
+        written[i] = i;
+    MESG("data array initialized");
+    if (VERBOSE_MED) {
+	MESG("writing at offset zero: ");
+        for (i=0; i<(int)orig_size; i++)
+            printf("%s%d", i?", ":"", written[i]);
+        printf("\n");
+    }
+    ret = H5Dwrite(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, written);
+    VRFY((ret >= 0), "H5Dwrite succeeded");
+
+    /* -------------------------
+     * Read initial data from dataset.
+     * -------------------------*/
+    ret = H5Dread(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, retrieved);
+    VRFY((ret >= 0), "H5Dread succeeded");
+    for (i=0; i<(int)orig_size; i++)
+        if(written[i]!=retrieved[i]) {
+            printf("Line #%d: written!=retrieved: written[%d]=%d, retrieved[%d]=%d\n",__LINE__,
+                i,written[i], i,retrieved[i]);
+            nerrors++;
+        }
+    if (VERBOSE_MED){
+	MESG("read at offset zero: ");
+        for (i=0; i<(int)orig_size; i++)
+            printf("%s%d", i?", ":"", retrieved[i]);
+        printf("\n");
+    }
+
+    /* -------------------------
+     * Extend the dataset & retrieve new dataspace
+     * -------------------------*/
+    ret =H5Dextend(dataset, &new_size);
+    VRFY((ret >= 0), "H5Dextend succeeded");
+    ret=H5Sclose(fs);
+    VRFY((ret >= 0), "H5Sclose succeeded");
+    fs = H5Dget_space(dataset);
+    VRFY((fs >= 0), "H5Dget_space succeeded");
+
+    /* -------------------------
+     * Write to the second half of the dataset
+     * -------------------------*/
+    for (i=0; i<(int)orig_size; i++)
+        written[i] = orig_size + i;
+    MESG("data array re-initialized");
+    if (VERBOSE_MED) {
+	MESG("writing at offset 10: ");
+        for (i=0; i<(int)orig_size; i++)
+            printf("%s%d", i?", ":"", written[i]);
+        printf("\n");
+    }
+    ret = H5Sselect_hyperslab(fs, H5S_SELECT_SET, (hssize_t *)&orig_size, NULL, &one, &orig_size);
+    VRFY((ret >= 0), "H5Sselect_hyperslab succeeded");
+    ret = H5Dwrite(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, written);
+    VRFY((ret >= 0), "H5Dwrite succeeded");
+
+    /* -------------------------
+     * Read the new data
+     * -------------------------*/
+    ret = H5Dread(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, retrieved);
+    VRFY((ret >= 0), "H5Dread succeeded");
+    for (i=0; i<(int)orig_size; i++)
+        if(written[i]!=retrieved[i]) {
+            printf("Line #%d: written!=retrieved: written[%d]=%d, retrieved[%d]=%d\n",__LINE__,
+                i,written[i], i,retrieved[i]);
+            nerrors++;
+        }
+    if (VERBOSE_MED){
+	MESG("read at offset 10: ");
+        for (i=0; i<(int)orig_size; i++)
+            printf("%s%d", i?", ":"", retrieved[i]);
+        printf("\n");
+    }
+
+
+    /* Close dataset collectively */
+    ret=H5Dclose(dataset);
+    VRFY((ret >= 0), "H5Dclose succeeded");
+
+    /* Close the file collectively */
+    ret = H5Fclose(fid);
+    VRFY((ret >= 0), "H5Fclose succeeded");
+}
+
 /* Example of using the parallel HDF5 library to read an extendible dataset */
 void
 extend_readInd(void)
diff --git a/testpar/testphdf5.c b/testpar/testphdf5.c
index 990095e..551a02a 100644
--- a/testpar/testphdf5.c
+++ b/testpar/testphdf5.c
@@ -12,8 +12,6 @@
  * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-/* $Id$ */
-
 /*
  * Main driver of the Parallel HDF5 tests
  */
@@ -434,6 +432,8 @@ int main(int argc, char **argv)
 	    "dataset collective write", filenames[1]);
     AddTest("indwriteext", extend_writeInd, NULL, 
 	    "extendible dataset independent write", filenames[2]);
+    AddTest("indwriteext2", extend_writeInd2, NULL, 
+	    "extendible dataset independent write #2", filenames[2]);
     AddTest("collwriteext", extend_writeAll, NULL, 
 	    "extendible dataset collective write", filenames[2]);
 
@@ -482,7 +482,7 @@ int main(int argc, char **argv)
     if (CleanUp && !getenv("HDF5_NOCLEANUP"))
         TestCleanup();
 
-    nerrors = GetTestNumErrs();
+    nerrors += GetTestNumErrs();
 
     }
 
@@ -526,6 +526,9 @@ int main(int argc, char **argv)
 	MPI_BANNER("extendible dataset independent write...");
 	extend_writeInd(filenames[2]);
 
+	MPI_BANNER("extendible dataset independent write #2...");
+	extend_writeInd2(filenames[2]);
+
 	MPI_BANNER("extendible dataset collective write...");
 	extend_writeAll(filenames[2]);
     }
@@ -600,22 +603,28 @@ finish:
      * and exit.
      */
     MPI_Barrier(MPI_COMM_WORLD);
+
+    /* Gather errors from all processes */
+    {
+        int temp;
+        MPI_Reduce(&nerrors, &temp, 1, MPI_INT, MPI_MAX, 0, MPI_COMM_WORLD);
+        if(mpi_rank==0)
+            nerrors=temp;
+    }
+
     if (MAINPROCESS){		/* only process 0 reports */
 	printf("===================================\n");
-	if (nerrors){
+	if (nerrors)
 	    printf("***PHDF5 tests detected %d errors***\n", nerrors);
-	}
-	else{
+	else
 	    printf("PHDF5 tests finished with no errors\n");
-	}
 	printf("===================================\n");
     }
-    if (dowrite){
+    if (dowrite)
 	h5_cleanup(FILENAME, fapl);
-    } else {
+    else
 	/* h5_cleanup would have closed fapl.  Now must do it explicitedly */
 	H5Pclose(fapl);
-    }
 
     /* close HDF5 library */
     H5close();
diff --git a/testpar/testphdf5.h b/testpar/testphdf5.h
index 968ee28..8fb6b39 100644
--- a/testpar/testphdf5.h
+++ b/testpar/testphdf5.h
@@ -12,8 +12,6 @@
  * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-/* $Id$ */
-
 #ifndef PHDF5TEST_H
 #define PHDF5TEST_H
 
@@ -153,6 +151,7 @@ void test_split_comm_access(void);
 void dataset_writeInd(void);
 void dataset_writeAll(void);
 void extend_writeInd(void);
+void extend_writeInd2(void);
 void extend_writeAll(void);
 void dataset_readInd(void);
 void dataset_readAll(void);