Implement attribute read/write. Added examples for this. Added

optional snapshot parameter to h5dsm_file_open.c.  Other minor
fixes/cleanup.

5 files changed, 415 insertions, 12 deletions

diff --git a/examples/h5dsm_attr_read.c b/examples/h5dsm_attr_read.c
new file mode 100644
index 0000000..8909535
--- /dev/null
+++ b/examples/h5dsm_attr_read.c
@@ -0,0 +1,106 @@
+#include "h5dsm_example.h"
+#include <time.h>
+
+int main(int argc, char *argv[]) {
+    uuid_t pool_uuid;
+    char *pool_grp = NULL;
+    hid_t file = -1, obj = -1, attr = -1, fapl = -1;
+    int buf[4][6];
+    int i, j;
+    H5VL_daosm_snap_id_t snap_id;
+
+    (void)MPI_Init(&argc, &argv);
+    (void)daos_init();
+
+    /* Seed random number generator */
+    srand(time(NULL));
+
+    if(argc < 6 || argc > 7)
+        PRINTF_ERROR("argc must be 6 or 7\n");
+
+    /* Parse UUID */
+    if(0 != uuid_parse(argv[1], pool_uuid))
+        ERROR;
+
+    /* Set up FAPL */
+    if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
+        ERROR;
+    if(H5Pset_fapl_daosm(fapl, MPI_COMM_WORLD, MPI_INFO_NULL, pool_uuid, pool_grp) < 0)
+        ERROR;
+
+    /* Open snapshot if specified */
+    if(argc == 7) {
+        snap_id = (H5VL_daosm_snap_id_t)atoi(argv[6]);
+        printf("Opening snapshot %llu\n", (long long unsigned)snap_id);
+        if(H5Pset_daosm_snap_open(fapl, snap_id) < 0)
+            ERROR;
+    } /* end if */
+
+    /* Open file */
+    if((file = H5Fopen(argv[2], H5F_ACC_RDONLY, fapl)) < 0)
+        ERROR;
+
+    /* Open object */
+    if(!strcmp(argv[3], "-d") || !strcmp(argv[3], "-D")) {
+        if((obj = H5Dopen2(file, argv[4], H5P_DEFAULT)) < 0)
+            ERROR;
+    }
+    else {
+        if(strcmp(argv[3], "-g") && strcmp(argv[3], "-G"))
+            PRINTF_ERROR("argv[3] must be -d, -D, -g, or -G\n");
+        if((obj = H5Gopen2(file, argv[4], H5P_DEFAULT)) < 0)
+            ERROR;
+    }
+
+    /* Open attribute */
+    if((attr = H5Aopen(obj, argv[5], H5P_DEFAULT)) < 0)
+        ERROR;
+
+    printf("Reading attribute\n");
+
+    /* Initialize buffer */
+    for(i = 0; i < 4; i++)
+        for(j = 0; j < 6; j++)
+            buf[i][j] = -1;
+
+    /* Read data */
+    if(H5Aread(attr, H5T_NATIVE_INT, buf) < 0)
+        ERROR;
+
+    /* Print buffer */
+    printf("Successfully read data. Buffer is:\n");
+    for(i = 0; i < 4; i++) {
+        for(j = 0; j < 6; j++)
+            printf("%d ", buf[i][j]);
+        printf("\n");
+    }
+
+    /* Close */
+    if(H5Aclose(attr) < 0)
+        ERROR;
+    if(H5Oclose(obj) < 0)
+        ERROR;
+    if(H5Fclose(file) < 0)
+        ERROR;
+    if(H5Pclose(fapl) < 0)
+        ERROR;
+
+    printf("Success\n");
+
+    (void)daos_fini();
+    (void)MPI_Finalize();
+    return 0;
+
+error:
+    H5E_BEGIN_TRY {
+        H5Aclose(attr);
+        H5Oclose(obj);
+        H5Fclose(file);
+        H5Pclose(fapl);
+    } H5E_END_TRY;
+
+    (void)daos_fini();
+    (void)MPI_Finalize();
+    return 1;
+}
+
diff --git a/examples/h5dsm_attr_write.c b/examples/h5dsm_attr_write.c
new file mode 100644
index 0000000..15f5ad1
--- /dev/null
+++ b/examples/h5dsm_attr_write.c
@@ -0,0 +1,100 @@
+#include "h5dsm_example.h"
+#include <time.h>
+
+int main(int argc, char *argv[]) {
+    uuid_t pool_uuid;
+    char *pool_grp = NULL;
+    hid_t file = -1, obj = -1, attr = -1, fapl = -1;
+    H5VL_daosm_snap_id_t snap_id;
+    int buf[4][6];
+    int i, j;
+
+    (void)MPI_Init(&argc, &argv);
+    (void)daos_init();
+
+    /* Seed random number generator */
+    srand(time(NULL));
+
+    if(argc < 6 || argc > 7)
+        PRINTF_ERROR("argc must be 6 or 7\n");
+
+    /* Parse UUID */
+    if(0 != uuid_parse(argv[1], pool_uuid))
+        ERROR;
+
+    /* Set up FAPL */
+    if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
+        ERROR;
+    if(H5Pset_fapl_daosm(fapl, MPI_COMM_WORLD, MPI_INFO_NULL, pool_uuid, pool_grp) < 0)
+        ERROR;
+
+    /* Open file */
+    if((file = H5Fopen(argv[2], H5F_ACC_RDWR, fapl)) < 0)
+        ERROR;
+
+    /* Open object */
+    if(!strcmp(argv[3], "-d") || !strcmp(argv[3], "-D")) {
+        if((obj = H5Dopen2(file, argv[4], H5P_DEFAULT)) < 0)
+            ERROR;
+    }
+    else {
+        if(strcmp(argv[3], "-g") && strcmp(argv[3], "-G"))
+            PRINTF_ERROR("argv[3] must be -d, -D, -g, or -G\n");
+        if((obj = H5Gopen2(file, argv[4], H5P_DEFAULT)) < 0)
+            ERROR;
+    }
+
+    /* Open attribute */
+    if((attr = H5Aopen(obj, argv[5], H5P_DEFAULT)) < 0)
+        ERROR;
+
+    /* Fill and print buffer */
+    printf("Writing data. Buffer is:\n");
+    for(i = 0; i < 4; i++) {
+        for(j = 0; j < 6; j++) {
+            buf[i][j] = rand() % 10;
+            printf("%d ", buf[i][j]);
+        }
+        printf("\n");
+    }
+
+    /* Write data */
+    if(H5Awrite(attr, H5T_NATIVE_INT, buf) < 0)
+        ERROR;
+
+    /* Save snapshot if requested */
+    if(argc == 7) {
+        if(H5VLdaosm_snap_create(file, &snap_id) < 0)
+            ERROR;
+        printf("Saved snapshot: snap_id = %llu\n", (long long unsigned)snap_id);
+    } /* end if */
+
+    /* Close */
+    if(H5Aclose(attr) < 0)
+        ERROR;
+    if(H5Oclose(obj) < 0)
+        ERROR;
+    if(H5Fclose(file) < 0)
+        ERROR;
+    if(H5Pclose(fapl) < 0)
+        ERROR;
+
+    printf("Success\n");
+
+    (void)daos_fini();
+    (void)MPI_Finalize();
+    return 0;
+
+error:
+    H5E_BEGIN_TRY {
+        H5Aclose(attr);
+        H5Oclose(obj);
+        H5Fclose(file);
+        H5Pclose(fapl);
+    } H5E_END_TRY;
+
+    (void)daos_fini();
+    (void)MPI_Finalize();
+    return 1;
+}
+
diff --git a/examples/h5dsm_dset_read.c b/examples/h5dsm_dset_read.c
index 18d41d8..21a811a 100644
--- a/examples/h5dsm_dset_read.c
+++ b/examples/h5dsm_dset_read.c
@@ -44,7 +44,7 @@ int main(int argc, char *argv[]) {
     if((dset = H5Dopen2(file, argv[3], H5P_DEFAULT)) < 0)
         ERROR;
 
-    printf("Reading dataset");
+    printf("Reading dataset\n");
 
     /* Initialize buffer */
     for(i = 0; i < 4; i++)
diff --git a/examples/h5dsm_file_open.c b/examples/h5dsm_file_open.c
index b3846d0..3a1d399 100644
--- a/examples/h5dsm_file_open.c
+++ b/examples/h5dsm_file_open.c
@@ -4,12 +4,13 @@ int main(int argc, char *argv[]) {
     uuid_t pool_uuid;
     char *pool_grp = NULL;
     hid_t file = -1, fapl = -1;
+    H5VL_daosm_snap_id_t snap_id;
 
     (void)MPI_Init(&argc, &argv);
     (void)daos_init();
 
-    if(argc != 3)
-        PRINTF_ERROR("argc != 3\n");
+    if(argc < 3 || argc > 4)
+        PRINTF_ERROR("argc must be 3 or 4\n");
 
     /* Parse UUID */
     if(0 != uuid_parse(argv[1], pool_uuid))
@@ -21,6 +22,14 @@ int main(int argc, char *argv[]) {
     if(H5Pset_fapl_daosm(fapl, MPI_COMM_WORLD, MPI_INFO_NULL, pool_uuid, pool_grp) < 0)
         ERROR;
 
+    /* Open snapshot if specified */
+    if(argc == 4) {
+        snap_id = (H5VL_daosm_snap_id_t)atoi(argv[3]);
+        printf("Opening snapshot %llu\n", (long long unsigned)snap_id);
+        if(H5Pset_daosm_snap_open(fapl, snap_id) < 0)
+            ERROR;
+    } /* end if */
+
     /* Open file */
     if((file = H5Fopen_ff(argv[2], H5F_ACC_RDONLY, fapl, NULL)) < 0)
         ERROR;
diff --git a/src/H5VLdaosm.c b/src/H5VLdaosm.c
index 5338398..9ee7b3a 100644
--- a/src/H5VLdaosm.c
+++ b/src/H5VLdaosm.c
@@ -81,10 +81,10 @@ static void *H5VL_daosm_dataset_create(void *_item,
 static void *H5VL_daosm_dataset_open(void *_item, H5VL_loc_params_t loc_params,
     const char *name, hid_t dapl_id, hid_t dxpl_id, void **req);
 static herr_t H5VL_daosm_dataset_read(void *_dset, hid_t mem_type_id,
-    hid_t mem_space_id, hid_t file_space_id, hid_t plist_id, void *buf,
+    hid_t mem_space_id, hid_t file_space_id, hid_t dxpl_id, void *buf,
     void **req);
 static herr_t H5VL_daosm_dataset_write(void *_dset, hid_t mem_type_id,
-    hid_t mem_space_id, hid_t file_space_id, hid_t plist_id, const void *buf,
+    hid_t mem_space_id, hid_t file_space_id, hid_t dxpl_id, const void *buf,
     void **req);
 /*static herr_t H5VL_daosm_dataset_specific(void *_dset, H5VL_dataset_specific_t specific_type,
                                         hid_t dxpl_id, void **req, va_list arguments);*/
@@ -102,10 +102,10 @@ static void *H5VL_daosm_attribute_create(void *_obj,
     hid_t aapl_id, hid_t dxpl_id, void **req);
 static void *H5VL_daosm_attribute_open(void *_obj, H5VL_loc_params_t loc_params,
     const char *name, hid_t aapl_id, hid_t dxpl_id, void **req);
-/*static herr_t H5VL_daosm_attribute_read(void *_attr, hid_t mem_type_id,
-    hid_t plist_id, void *buf, void **req);
+static herr_t H5VL_daosm_attribute_read(void *_attr, hid_t mem_type_id,
+    void *buf, hid_t dxpl_id, void **req);
 static herr_t H5VL_daosm_attribute_write(void *_attr, hid_t mem_type_id,
-    hid_t plist_id, const void *buf, void **req);*/
+    const void *buf, hid_t dxpl_id, void **req);
 static herr_t H5VL_daosm_attribute_close(void *_attr, hid_t dxpl_id,
     void **req);
 
@@ -155,8 +155,8 @@ static H5VL_class_t H5VL_daosm_g = {
     {                                           /* attribute_cls */
         H5VL_daosm_attribute_create,            /* create */
         H5VL_daosm_attribute_open,              /* open */
-        NULL,//H5VL_iod_attribute_read,                /* read */
-        NULL,//H5VL_iod_attribute_write,               /* write */
+        H5VL_daosm_attribute_read,              /* read */
+        H5VL_daosm_attribute_write,             /* write */
         NULL,//H5VL_iod_attribute_get,                 /* get */
         NULL,//H5VL_iod_attribute_specific,            /* specific */
         NULL,                                   /* optional */
@@ -2799,8 +2799,8 @@ done:
  */
 static herr_t
 H5VL_daosm_dataset_write(void *_dset, hid_t H5_ATTR_UNUSED mem_type_id,
-    hid_t H5_ATTR_UNUSED mem_space_id, hid_t H5_ATTR_UNUSED file_space_id,
-    hid_t H5_ATTR_UNUSED dxpl_id, const void *buf, void H5_ATTR_UNUSED **req)
+    hid_t mem_space_id, hid_t file_space_id, hid_t H5_ATTR_UNUSED dxpl_id,
+    const void *buf, void H5_ATTR_UNUSED **req)
 {
     H5VL_daosm_dset_t *dset = (H5VL_daosm_dset_t *)_dset;
     int ndims;
@@ -3419,6 +3419,194 @@ done:
 
 
 /*-------------------------------------------------------------------------
+ * Function:    H5VL_daosm_attribute_read
+ *
+ * Purpose:     Reads raw data from an attribute into a buffer.
+ *
+ * Return:      Success:        0
+ *              Failure:        -1, attribute not read.
+ *
+ * Programmer:  Neil Fortner
+ *              February, 2017
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5VL_daosm_attribute_read(void *_attr, hid_t H5_ATTR_UNUSED mem_type_id,
+    void *buf, hid_t H5_ATTR_UNUSED dxpl_id, void H5_ATTR_UNUSED **req)
+{
+    H5VL_daosm_attr_t *attr = (H5VL_daosm_attr_t *)_attr;
+    int ndims;
+    hsize_t dim[H5S_MAX_RANK];
+    size_t akey_len;
+    daos_key_t dkey;
+    char *akey = NULL;
+    daos_vec_iod_t iod;
+    daos_recx_t recx;
+    daos_sg_list_t sgl;
+    daos_iov_t sg_iov;
+    char attr_key[] = H5VL_DAOSM_ATTR_KEY;
+    size_t type_size;
+    uint64_t chunk_size;
+    int ret;
+    int i;
+    herr_t ret_value = SUCCEED;
+
+    FUNC_ENTER_NOAPI_NOINIT
+
+    /* Get dataspace extent */
+    if((ndims = H5Sget_simple_extent_ndims(attr->space_id)) < 0)
+        HGOTO_ERROR(H5E_ATTR, H5E_CANTGET, FAIL, "can't get number of dimensions")
+    if(ndims != H5Sget_simple_extent_dims(attr->space_id, dim, NULL))
+        HGOTO_ERROR(H5E_ATTR, H5E_CANTGET, FAIL, "can't get dimensions")
+
+    /* Get datatype size */
+    if((type_size = H5Tget_size(attr->type_id)) == 0)
+        HGOTO_ERROR(H5E_ATTR, H5E_CANTGET, FAIL, "can't get datatype size")
+
+    /* Calculate chunk size */
+    chunk_size = (uint64_t)1;
+    for(i = 0; i < ndims; i++)
+        chunk_size *= (uint64_t)dim[i];
+
+    /* Set up operation to read data */
+    /* Set up dkey */
+    daos_iov_set(&dkey, attr_key, (daos_size_t)(sizeof(attr_key) - 1));
+
+    /* Create akey string (prefix "V-") */
+    akey_len = HDstrlen(attr->name) + 2;
+    if(NULL == (akey = (char *)H5MM_malloc(akey_len + 1)))
+        HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "can't allocate buffer for akey")
+    akey[0] = 'V';
+    akey[1] = '-';
+    (void)HDstrcpy(akey + 2, attr->name);
+
+    /* Set up recx */
+    recx.rx_rsize = (uint64_t)type_size;
+    recx.rx_idx = (uint64_t)0;
+    recx.rx_nr = chunk_size;
+
+    /* Set up iod */
+    HDmemset(&iod, 0, sizeof(iod));
+    daos_iov_set(&iod.vd_name, (void *)akey, (daos_size_t)akey_len);
+    daos_csum_set(&iod.vd_kcsum, NULL, 0);
+    iod.vd_nr = 1u;
+    iod.vd_recxs = &recx;
+
+    /* Set up sgl */
+    daos_iov_set(&sg_iov, (void *)buf, (daos_size_t)(chunk_size * (uint64_t)type_size));
+    sgl.sg_nr.num = 1;
+    sgl.sg_iovs = &sg_iov;
+
+    /* Read data from attribute */
+    if(0 != (ret = daos_obj_fetch(attr->parent->obj_oh, attr->item.file->epoch, &dkey, 1, &iod, &sgl, NULL /*maps*/, NULL /*event*/)))
+        HGOTO_ERROR(H5E_ATTR, H5E_READERROR, FAIL, "can't read data from attribute: %d", ret)
+
+done:
+    /* Free memory */
+    akey = (char *)H5MM_xfree(akey);
+
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5VL_daosm_attribute_read() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5VL_daosm_attribute_write
+ *
+ * Purpose:     Writes raw data from a buffer into an attribute.
+ *
+ * Return:      Success:        0
+ *              Failure:        -1, attribute not written.
+ *
+ * Programmer:  Neil Fortner
+ *              February, 2017
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5VL_daosm_attribute_write(void *_attr, hid_t H5_ATTR_UNUSED mem_type_id,
+    const void *buf, hid_t H5_ATTR_UNUSED dxpl_id, void H5_ATTR_UNUSED **req)
+{
+    H5VL_daosm_attr_t *attr = (H5VL_daosm_attr_t *)_attr;
+    int ndims;
+    hsize_t dim[H5S_MAX_RANK];
+    size_t akey_len;
+    daos_key_t dkey;
+    char *akey = NULL;
+    daos_vec_iod_t iod;
+    daos_recx_t recx;
+    daos_sg_list_t sgl;
+    daos_iov_t sg_iov;
+    char attr_key[] = H5VL_DAOSM_ATTR_KEY;
+    size_t type_size;
+    uint64_t chunk_size;
+    int ret;
+    int i;
+    herr_t ret_value = SUCCEED;
+
+    FUNC_ENTER_NOAPI_NOINIT
+
+    /* Check for write access */
+    if(!(attr->item.file->flags & H5F_ACC_RDWR))
+        HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, FAIL, "no write intent on file")
+
+    /* Get dataspace extent */
+    if((ndims = H5Sget_simple_extent_ndims(attr->space_id)) < 0)
+        HGOTO_ERROR(H5E_ATTR, H5E_CANTGET, FAIL, "can't get number of dimensions")
+    if(ndims != H5Sget_simple_extent_dims(attr->space_id, dim, NULL))
+        HGOTO_ERROR(H5E_ATTR, H5E_CANTGET, FAIL, "can't get dimensions")
+
+    /* Get datatype size */
+    if((type_size = H5Tget_size(attr->type_id)) == 0)
+        HGOTO_ERROR(H5E_ATTR, H5E_CANTGET, FAIL, "can't get datatype size")
+
+    /* Calculate chunk size */
+    chunk_size = (uint64_t)1;
+    for(i = 0; i < ndims; i++)
+        chunk_size *= (uint64_t)dim[i];
+
+    /* Set up operation to write data */
+    /* Set up dkey */
+    daos_iov_set(&dkey, attr_key, (daos_size_t)(sizeof(attr_key) - 1));
+
+    /* Create akey string (prefix "V-") */
+    akey_len = HDstrlen(attr->name) + 2;
+    if(NULL == (akey = (char *)H5MM_malloc(akey_len + 1)))
+        HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "can't allocate buffer for akey")
+    akey[0] = 'V';
+    akey[1] = '-';
+    (void)HDstrcpy(akey + 2, attr->name);
+
+    /* Set up recx */
+    recx.rx_rsize = (uint64_t)type_size;
+    recx.rx_idx = (uint64_t)0;
+    recx.rx_nr = chunk_size;
+
+    /* Set up iod */
+    HDmemset(&iod, 0, sizeof(iod));
+    daos_iov_set(&iod.vd_name, (void *)akey, (daos_size_t)akey_len);
+    daos_csum_set(&iod.vd_kcsum, NULL, 0);
+    iod.vd_nr = 1u;
+    iod.vd_recxs = &recx;
+
+    /* Set up sgl */
+    daos_iov_set(&sg_iov, (void *)buf, (daos_size_t)(chunk_size * (uint64_t)type_size));
+    sgl.sg_nr.num = 1;
+    sgl.sg_iovs = &sg_iov;
+
+    /* Write data to attribute */
+    if(0 != (ret = daos_obj_update(attr->parent->obj_oh, attr->item.file->epoch, &dkey, 1, &iod, &sgl, NULL /*event*/)))
+        HGOTO_ERROR(H5E_ATTR, H5E_WRITEERROR, FAIL, "can't write data to attribute: %d", ret)
+
+done:
+    /* Free memory */
+    akey = (char *)H5MM_xfree(akey);
+
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5VL_daosm_attribute_write() */
+
+
+/*-------------------------------------------------------------------------
  * Function:    H5VL_daosm_attribute_close
  *
  * Purpose:     Closes a daos-m HDF5 attribute.