Synchronize with develop

.github/workflows/dependencies-macos.sh

@@ -2,9 +2,7 @@
 
 set -eu -o pipefail
 
-export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=FALSE
-
-brew install open-mpi automake
+brew install open-mpi automake m4 libtool
 
 # libfabric
 wget https://github.com/ofiwg/libfabric/archive/refs/tags/v1.15.2.tar.gz

.github/workflows/gitlab-develop.yml

@@ -0,0 +1,28 @@
+name: GitLab
+
+on:
+  push:
+    branches:
+      - develop
+
+jobs:
+  sync-with-gitlab:
+    runs-on: ubuntu-latest
+    timeout-minutes: 2
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup git
+        run: |
+          git config --global user.name "PDC BOT"
+          git config --global user.email "pdc@example.com"
+
+      - name: Update branch
+        run: |
+          git fetch origin develop
+          git remote add gitlab https://${{ secrets.GITLAB_TOKEN_NAME }}:${{ secrets.GITLAB_TOKEN }}@${{ secrets.GITLAB_URL }}
+          git checkout develop
+          git push -f gitlab -u develop

.github/workflows/gitlab-stable.yml

@@ -0,0 +1,28 @@
+name: GitLab
+
+on:
+  push:
+    branches:
+      - stable
+
+jobs:
+  sync-with-gitlab:
+    runs-on: ubuntu-latest
+    timeout-minutes: 2
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup git
+        run: |
+          git config --global user.name "PDC BOT"
+          git config --global user.email "pdc@example.com"
+
+      - name: Update branch
+        run: |
+          git fetch stable
+          git remote add gitlab https://${{ secrets.GITLAB_TOKEN_NAME }}:${{ secrets.GITLAB_TOKEN }}@${{ secrets.GITLAB_URL }}
+          git checkout stable
+          git push -f gitlab -u stable

.github/workflows/macos.yml

@@ -33,4 +33,4 @@ jobs:
           sudo sh -c 'echo "`ipconfig getifaddr en0` PDC" >> /etc/hosts'
           sudo scutil --set HostName PDC
           export HG_TRANSPORT="sockets"
-          ctest -L serial
+          ctest -L serial --output-on-failure

.github/workflows/ubuntu-cache.yml

@@ -28,4 +28,4 @@ jobs:
 
       - name: Test PDC
         working-directory: build
-        run: ctest -L serial
+        run: ctest -L serial --output-on-failure

.github/workflows/ubuntu-no-cache.yaml

@@ -28,4 +28,4 @@ jobs:
 
       - name: Test PDC
         working-directory: build
-        run: ctest -L serial
+        run: ctest -L serial --output-on-failure

docs/source/api.rst

@@ -205,7 +205,8 @@ PDC object APIs
 		* pdc: PDC class ID, returned from PDCInit
 	* Output:
 		* Local object ID
-	* Open a PDC ID created previously by name.
+	* Open a PDC ID created previously by name, if an object is just created or already opened,
+          return the same obj_id. Each open requires a close.
 	* For developers: see pdc_obj.c. Need to communicate with servers for metadata of the object.
 
 * perr_t PDCobj_close(pdcid_t obj_id)

src/api/pdc_client_connect.c

@@ -43,6 +43,7 @@
 #include "pdc_transforms_common.h"
 #include "pdc_client_connect.h"
 #include "pdc_logger.h"
+#include "pdc_malloc.h"
 
 #include "mercury.h"
 #include "mercury_macros.h"
@@ -1354,7 +1355,7 @@ PDC_Client_mercury_init(hg_class_t **hg_class, hg_context_t **hg_context, int po
 {
     perr_t ret_value = SUCCEED;
     char   na_info_string[NA_STRING_INFO_LEN];
-    char   hostname[HOSTNAME_LEN];
+    char * hostname;
     int    local_server_id;
     /* Set the default mercury transport
      * but enable overriding that to any of:
@@ -1378,14 +1379,19 @@ PDC_Client_mercury_init(hg_class_t **hg_class, hg_context_t **hg_context, int po
     if ((hg_transport = getenv("HG_TRANSPORT")) == NULL) {
         hg_transport = default_hg_transport;
     }
-    memset(hostname, 0, sizeof(hostname));
-    gethostname(hostname, sizeof(hostname));
+    if ((hostname = getenv("HG_HOST")) == NULL) {
+        hostname = PDC_malloc(HOSTNAME_LEN);
+        memset(hostname, 0, HOSTNAME_LEN);
+        gethostname(hostname, HOSTNAME_LEN - 1);
+    }
     sprintf(na_info_string, "%s://%s:%d", hg_transport, hostname, port);
     if (pdc_client_mpi_rank_g == 0) {
-        LOG_INFO("==PDC_CLIENT: using %.7s\n", na_info_string);
+        LOG_INFO("==PDC_CLIENT: using %s\n", na_info_string);
         fflush(stdout);
     }
 
+    free(hostname);
+
 // gni starts here
 #ifdef PDC_HAS_CRAY_DRC
     /* Acquire credential */
@@ -3047,30 +3053,10 @@ pack_region_metadata(int ndim, uint64_t *offset, uint64_t *size, region_info_tra
 
     FUNC_ENTER(NULL);
     transfer->ndim = ndim;
-    if (ndim >= 1) {
-        transfer->start_0 = offset[0];
-        transfer->count_0 = size[0];
-    }
-    else {
-        transfer->start_0 = 0;
-        transfer->count_0 = 0;
-    }
-    if (ndim >= 2) {
-        transfer->count_1 = size[1];
-        transfer->start_1 = offset[1];
-    }
-    else {
-        transfer->start_1 = 0;
-        transfer->count_1 = 0;
-    }
-    if (ndim >= 3) {
-        transfer->count_2 = size[2];
-        transfer->start_2 = offset[2];
-    }
-    else {
-        transfer->start_2 = 0;
-        transfer->count_2 = 0;
-    }
+
+    PDC_copy_region_desc(offset, transfer->start, ndim, ndim);
+    PDC_copy_region_desc(size, transfer->count, ndim, ndim);
+
     fflush(stdout);
     FUNC_LEAVE(ret_value);
 }
@@ -3521,16 +3507,9 @@ PDC_Client_transfer_request(void *buf, pdcid_t obj_id, uint32_t data_server_id,
     in.access_type = access_type;
     in.remote_unit = unit;
     in.obj_id      = obj_id;
-    in.obj_ndim    = obj_ndim;
-    if (in.obj_ndim >= 1) {
-        in.obj_dim0 = obj_dims[0];
-    }
-    if (in.obj_ndim >= 2) {
-        in.obj_dim1 = obj_dims[1];
-    }
-    if (in.obj_ndim >= 3) {
-        in.obj_dim2 = obj_dims[2];
-    }
+
+    in.obj_ndim = obj_ndim;
+    PDC_copy_region_desc(obj_dims, in.obj_dims, in.obj_ndim, in.obj_ndim);
 
     // Compute metadata server id
     meta_server_id = PDC_get_server_by_obj_id(obj_id, pdc_server_num_g);
@@ -6586,8 +6565,8 @@ PDC_Client_read_with_storage_meta(int nobj, region_storage_meta_t **all_storage_
         prev_fname = fname;
 
         // TODO: currently assumes 1d data and 1 storage region per object
-        storage_start = all_storage_meta[i]->region_transfer.start_0;
-        storage_count = all_storage_meta[i]->region_transfer.count_0;
+        storage_start = all_storage_meta[i]->region_transfer.start[0];
+        storage_count = all_storage_meta[i]->region_transfer.count[0];
         req_start     = storage_start;
         req_count     = storage_count;
         file_offset   = all_storage_meta[i]->offset;

src/api/pdc_obj/pdc_obj.c

@@ -535,9 +535,29 @@ PDCobj_open_common(const char *obj_name, pdcid_t pdc, int is_col)
     pdcid_t               obj_prop;
     size_t                i;
     uint32_t              metadata_server_id;
+    obj_handle *          oh;
+    struct pdc_obj_info * info;
+    int                   is_opened = 0;
 
     FUNC_ENTER(NULL);
 
+    // Search if the object has already been opened
+    oh = PDCobj_iter_start(pdc);
+    while (!PDCobj_iter_null(oh)) {
+        info = PDCobj_iter_get_info(oh);
+        if (strcmp(obj_name, info->name) == 0) {
+            is_opened = 1;
+            break;
+        }
+        oh = PDCobj_iter_next(oh, pdc);
+    }
+
+    if (is_opened) {
+        ret_value = info->local_id;
+        PDC_inc_ref(info->local_id);
+        goto done;
+    }
+
     p = (struct _pdc_obj_info *)PDC_malloc(sizeof(struct _pdc_obj_info));
     if (!p)
         PGOTO_ERROR(0, "PDC object memory allocation failed");

src/api/pdc_region/include/pdc_region.h

@@ -27,10 +27,13 @@
 
 #include "pdc_public.h"
 #include "pdc_obj.h"
+
 #ifdef ENABLE_MPI
 #include "mpi.h"
 #endif
 
+#define DIM_MAX 4
+
 /**************************/
 /* Library Public Struct */
 /**************************/
@@ -46,6 +49,13 @@ struct pdc_region_info {
     size_t                unit;
 };
 
+// Similar structure PDC_region_info_t defined in pdc_obj_pkg.h
+typedef struct region_info_transfer_t {
+    size_t   ndim;
+    uint64_t start[DIM_MAX];
+    uint64_t count[DIM_MAX];
+} region_info_transfer_t;
+
 typedef enum {
     PDC_TRANSFER_STATUS_COMPLETE  = 0,
     PDC_TRANSFER_STATUS_PENDING   = 1,
@@ -253,4 +263,129 @@ perr_t PDCreg_obtain_lock(pdcid_t obj_id, pdcid_t reg_id, pdc_access_t access_ty
  */
 perr_t PDCreg_release_lock(pdcid_t obj_id, pdcid_t reg_id, pdc_access_t access_type);
 
+/**
+ * @brief Check if two region info transfers are identical.
+ *
+ * Compares two region info transfer structures (`reg1` and `reg2`) to determine if they
+ * are equal. The comparison checks if all bytes within the structures match.
+ *
+ * @param reg1 [IN] Pointer to the first region info transfer to compare.
+ * @param reg2 [IN] Pointer to the second region info transfer to compare.
+ *
+ * @return 1 if the region info transfers are identical, -1 otherwise.
+ */
+pbool_t PDC_region_info_transfer_t_is_equal(const region_info_transfer_t *reg1,
+                                            const region_info_transfer_t *reg2);
+
+/**
+ * @brief Copy a region info transfer to another region.
+ *
+ * Copies the data from one region info transfer structure (`src_reg`) to another (`dest_reg`).
+ *
+ * @param src_reg [IN] Pointer to the source region info transfer to copy from.
+ * @param dest_reg [OUT] Pointer to the destination region info transfer to copy to.
+ *
+ * @return Non-negative on success, negative on failure.
+ */
+perr_t PDC_copy_region_info_transfer_t(const region_info_transfer_t *src_reg,
+                                       region_info_transfer_t *      dest_reg);
+
+/**
+ * @brief Calculate the size of a region descriptor in bytes.
+ *
+ * This function computes the size of the region described by `src_reg` in bytes by
+ * multiplying the size of each dimension by the element size (`unit`).
+ * The size in bytes is computed as the product of all dimensions, scaled by `unit`.
+ *
+ * @param src_reg [IN] Pointer to the source region descriptor (in elements)
+ * @param unit [IN] Size of each element in bytes
+ * @param ndim [IN] Number of dimensions in the region descriptor
+ *
+ * @return The size of the region in bytes.
+ */
+uint64_t PDC_get_region_desc_size_bytes(uint64_t *src_reg, int unit, int ndim);
+
+/**
+ * @brief Calculate the size of a region descriptor in elements from region desccriptor in bytes.
+ *
+ * This function computes the size of the region described by `src_reg` in terms of the
+ * number of elements by dividing the given byte size by the element size (`unit`).
+ *
+ * @param src_reg [IN] Pointer to the source region descriptor (in bytes)
+ * @param unit [IN] Size of each element in bytes
+ * @param ndim [IN] Number of dimensions in the region descriptor
+ *
+ * @return The size of the region in terms of the number of elements.
+ */
+uint64_t PDC_get_region_desc_size_from_bytes_to_elements(const uint64_t *src_reg, int unit, int ndim);
+
+/**
+ * @brief Calculate the total size of a region descriptor in elements.
+ *
+ * This function computes the total size of the region described by `src_reg`,
+ * by multiplying the dimensions of the region. The size is returned in terms
+ * of the number of elements, not bytes.
+ *
+ * @param src_reg [IN] Pointer to the source region descriptor (in elements)
+ * @param ndim [IN] Number of dimensions in the region descriptor
+ *
+ * @return The total size of the region in terms of the number of elements.
+ */
+uint64_t PDC_get_region_desc_size(const uint64_t *src_reg, int ndim);
+
+/**
+ * @brief Convert a region descriptor from byte units to element units.
+ *
+ * Copies the region dimensions from the source descriptor to the destination descriptor,
+ * converting each dimension from bytes to elements by dividing by the element size.
+ * For each dimension i:
+ * dest_reg[i] = src_reg[i] / unit
+ *
+ * Both source and destination pointers must be non-null.
+ *
+ * @param src_reg [IN] Pointer to the source region descriptor (in bytes)
+ * @param dest_reg [OUT] Pointer to the destination region descriptor (in elements)
+ * @param unit [IN] Size of each element in bytes
+ * @param ndim [IN] Number of dimensions in the region
+ *
+ * @return Non-negative on success, negative on failure.
+ */
+perr_t PDC_copy_region_desc_bytes_to_elements(const uint64_t *src_reg, uint64_t *dest_reg, int unit,
+                                              int ndim);
+
+/**
+ * @brief Copy a region descriptor from source to destination without unit scaling.
+ *
+ * Copies each dimension from the source region descriptor to the destination region
+ * descriptor without applying any scaling. The number of dimensions may differ between
+ * source and destination, in which case only the common number of dimensions is copied.
+ *
+ * Validates that both source and destination pointers are not NULL.
+ *
+ * @param src_reg [IN] Pointer to the source region descriptor
+ * @param dest_reg [OUT] Pointer to the destination region descriptor
+ * @param src_ndim [IN] Number of dimensions in the source region
+ * @param dest_ndim [IN] Number of dimensions in the destination region
+ *
+ * @return Non-negative on success, negative on failure.
+ */
+perr_t PDC_copy_region_desc(const uint64_t *src_reg, uint64_t *dest_reg, int src_ndim, int dest_ndim);
+
+/**
+ * @brief Copy a region descriptor from element units to byte units.
+ *
+ * Sets each dimension of the destination region descriptor equal to the
+ * corresponding dimension of the source descriptor multiplied by the element size in bytes.
+ * For the i-th dimension: dest_reg[i] = src_reg[i] * unit
+ *
+ * @param src_reg [IN] Pointer to the source region descriptor (in elements)
+ * @param dest_reg [OUT] Pointer to the destination region descriptor (in bytes)
+ * @param unit [IN] Size of each element in bytes
+ * @param dest_ndim [IN] Number of dimensions in the destination region
+ *
+ * @return Non-negative on success, negative on failure.
+ */
+perr_t PDC_copy_region_desc_elements_to_bytes(const uint64_t *src_reg, uint64_t *dest_reg, int unit,
+                                              int dest_ndim);
+
 #endif /* PDC_REGION_H */

src/commons/CMakeLists.txt

@@ -74,6 +74,7 @@ install(
     ${PDC_SOURCE_DIR}/src/commons/utils/include/pdc_id_pkg.h
     ${PDC_SOURCE_DIR}/src/commons/utils/include/pdc_malloc.h
     ${PDC_SOURCE_DIR}/src/commons/utils/include/pdc_linkedlist.h
+    ${PDC_SOURCE_DIR}/src/commons/logging/include/pdc_logger.h
   DESTINATION
     ${PDC_INSTALL_INCLUDE_DIR}
   COMPONENT