Use PDC_malloc, PDC_free, PDC_calloc, and PDC_realloc (#260)

* checkpoint

* replace free with PDC_free and calloc with PDC_calloc

* Committing clang-format changes

* fix more mallocs to PDC_malloc

* more PDC_free fixes

* Committing clang-format changes

* Update ubuntu-cache.yml

* remove eno1

* fix realloc

* Committing clang-format changes

* Update ubuntu-no-cache.yaml

* Fix several bugs with error checking with object dim allocation

* Committing clang-format changes

* fix bug

* Committing clang-format changes

* Update ubuntu-no-cache.yaml

* Update ubuntu-cache.yml

* Set default value of ndim to 1 in PDCprop_create when using PDC_OBJ_CREATE

* Committing clang-format changes

* Malloc when defaulting to ndim size 1.
Only free hostname when we PDC_malloc the memory
because pointers returned by getenv are not malloced
and could point to static memory.

* Committing clang-format changes

* Update README.md

minor change to trigger the pipeline

---------

Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Jean Luca Bez <[email protected]>
Co-authored-by: Jean Luca Bez <[email protected]>

README.md

@@ -15,7 +15,7 @@ Proactive Data Containers (PDC) software provides an object-focused data managem
 
 Full documentation of PDC with installation instructions, code examples for using PDC API, and research publications are available at [pdc.readthedocs.io](https://pdc.readthedocs.io)
 
-More information and publications on PDC is available at https://sdm.lbl.gov/pdc
+More information and publications on PDC are available at https://sdm.lbl.gov/pdc
 
 If you use PDC in your research, please use the following citations:
 

src/api/pdc.c

@@ -130,8 +130,8 @@ PDC_class__close(struct _pdc_class *p)
     PDC_timing_finalize();
 #endif
 
-    free(p->name);
-    p = (struct _pdc_class *)(intptr_t)PDC_free(p);
+    p->name = (char *)PDC_free(p->name);
+    p       = (struct _pdc_class *)(intptr_t)PDC_free(p);
 
     FUNC_LEAVE(ret_value);
 }

src/api/pdc_analysis/pdc_analysis.c

@@ -101,7 +101,8 @@ iterator_init(pdcid_t objectId, pdcid_t reg_id, int blocks, struct _pdc_iterator
             }
         }
         iter->totalElements = 1;
-        if ((iter->srcDims = (size_t *)calloc(obj_prop_ptr->obj_prop_pub->ndim, sizeof(size_t))) != NULL) {
+        if ((iter->srcDims = (size_t *)PDC_calloc(obj_prop_ptr->obj_prop_pub->ndim, sizeof(size_t))) !=
+            NULL) {
             iter->ndim = obj_prop_ptr->obj_prop_pub->ndim;
             for (i = 0; i < iter->ndim; i++) {
                 iter->srcDims[i] = (size_t)obj_prop_ptr->obj_prop_pub->dims[i];
@@ -336,13 +337,13 @@ PDC_get_argv0_()
         procpath = strdup(fullPath);
         shellcmd = fopen(procpath, "r");
         if (shellcmd == NULL) {
-            free(procpath);
+            procpath = (char *)PDC_free(procpath);
             PGOTO_ERROR(NULL, "fopen failed!");
         }
         else {
             cmdLength = fread(fullPath, 1, sizeof(fullPath), shellcmd);
             if (procpath)
-                free(procpath);
+                procpath = (char *)PDC_free(procpath);
             if (cmdLength > 0) {
                 _argv0 = strdup(fullPath);
                 /* truncate the cmdline if any whitespace (space or tab) */
@@ -366,7 +367,7 @@ PDC_get_argv0_()
                 /* Get rid of the copy (strdup) of fullPath now in _argv0.
                  * and replace it with the next (modified/fully_qualified?) version.
                  */
-                free(_argv0);
+                _argv0 = (char *)PDC_free(_argv0);
                 _argv0 = next;
             }
         }
@@ -460,7 +461,7 @@ PDCobj_analysis_register(char *func, pdcid_t iterIn, pdcid_t iterOut)
     thisFtn->ftnPtr = (int (*)())ftnPtr;
     thisFtn->n_args = 2;
     /* Allocate for iterator ids and region ids */
-    if ((thisFtn->object_id = (pdcid_t *)calloc(4, sizeof(pdcid_t))) != NULL) {
+    if ((thisFtn->object_id = (pdcid_t *)PDC_calloc(4, sizeof(pdcid_t))) != NULL) {
         thisFtn->object_id[0] = iterIn;
         thisFtn->object_id[1] = iterOut;
     }
@@ -497,11 +498,11 @@ PDCobj_analysis_register(char *func, pdcid_t iterIn, pdcid_t iterOut)
 
 done:
     if (applicationDir)
-        free(applicationDir);
+        applicationDir = (char *)PDC_free(applicationDir);
     if (userdefinedftn)
-        free(userdefinedftn);
+        userdefinedftn = (char *)PDC_free(userdefinedftn);
     if (loadpath)
-        free(loadpath);
+        loadpath = (char *)PDC_free(loadpath);
 
     fflush(stdout);
     FUNC_LEAVE(ret_value);
@@ -556,7 +557,7 @@ PDCobj_data_getNextBlock(pdcid_t iter, void **nextBlock, size_t *dims)
         if (thisIter->srcStart == NULL) {
             if (execution_locus == SERVER_MEMORY) {
                 if ((thisIter->srcNext = PDC_Server_get_region_data_ptr(thisIter->objectId)) == NULL)
-                    thisIter->srcNext = malloc(thisIter->totalElements * thisIter->element_size);
+                    thisIter->srcNext = PDC_malloc(thisIter->totalElements * thisIter->element_size);
                 if ((thisIter->srcStart = thisIter->srcNext) == NULL)
                     PGOTO_ERROR(0, "==PDC_ANALYSIS_SERVER: Unable to allocate iterator storage");
 

src/api/pdc_analysis/pdc_analysis_and_transforms_connect.c

@@ -63,7 +63,7 @@ PDC_Client_send_iter_recv_id(pdcid_t iter_id, pdcid_t *meta_id)
         hg_atomic_init32(atomic_work_todo_g, 0);
     }
 
-    my_rpc_state_p = (struct _pdc_my_rpc_state *)calloc(1, sizeof(struct _pdc_my_rpc_state));
+    my_rpc_state_p = (struct _pdc_my_rpc_state *)PDC_calloc(1, sizeof(struct _pdc_my_rpc_state));
     if (my_rpc_state_p == NULL)
         PGOTO_ERROR(FAIL, "PDC_Client_send_iter_recv_id(): Could not allocate my_rpc_state");
 
@@ -130,7 +130,7 @@ PDC_Client_send_iter_recv_id(pdcid_t iter_id, pdcid_t *meta_id)
 done:
     fflush(stdout);
     HG_Destroy(my_rpc_state_p->handle);
-    free(my_rpc_state_p);
+    my_rpc_state_p = (struct _pdc_my_rpc_state *)PDC_free(my_rpc_state_p);
 
     FUNC_LEAVE(ret_value);
 }
@@ -183,7 +183,7 @@ PDC_Client_register_obj_analysis(struct _pdc_region_analysis_ftn_info *thisFtn,
         hg_atomic_init32(atomic_work_todo_g, 0);
     }
 
-    my_rpc_state_p = (struct _pdc_my_rpc_state *)calloc(1, sizeof(struct _pdc_my_rpc_state));
+    my_rpc_state_p = (struct _pdc_my_rpc_state *)PDC_calloc(1, sizeof(struct _pdc_my_rpc_state));
     if (my_rpc_state_p == NULL)
         PGOTO_ERROR(FAIL, "PDC_Client_register_obj_analysis(): Could not allocate my_rpc_state");
 
@@ -250,7 +250,7 @@ PDC_Client_register_obj_analysis(struct _pdc_region_analysis_ftn_info *thisFtn,
 done:
     fflush(stdout);
     HG_Destroy(my_rpc_state_p->handle);
-    free(my_rpc_state_p);
+    my_rpc_state_p = (struct _pdc_my_rpc_state *)PDC_free(my_rpc_state_p);
 
     FUNC_LEAVE(ret_value);
 }
@@ -301,7 +301,7 @@ PDC_Client_register_region_transform(const char *func, const char *loadpath,
         hg_atomic_init32(atomic_work_todo_g, 0);
     }
 
-    my_rpc_state_p = (struct _pdc_my_rpc_state *)calloc(1, sizeof(struct _pdc_my_rpc_state));
+    my_rpc_state_p = (struct _pdc_my_rpc_state *)PDC_calloc(1, sizeof(struct _pdc_my_rpc_state));
     if (my_rpc_state_p == NULL)
         PGOTO_ERROR(FAIL, "Could not allocate my_rpc_state");
 
@@ -345,7 +345,7 @@ PDC_Client_register_region_transform(const char *func, const char *loadpath,
     if (object_info)
         PDC_free_obj_info(object_info);
     HG_Destroy(my_rpc_state_p->handle);
-    free(my_rpc_state_p);
+    my_rpc_state_p = (struct _pdc_my_rpc_state *)PDC_free(my_rpc_state_p);
 
     FUNC_LEAVE(ret_value);
 }

src/api/pdc_analysis/pdc_analysis_common.c

@@ -34,6 +34,7 @@
 #include "pdc_analysis_and_transforms_common.h"
 #include "pdc_client_server_common.h"
 #include "pdc_analysis_pkg.h"
+#include "pdc_malloc.h"
 #include "pdc_region.h"
 #include "pdc_server_analysis.h"
 #include "pdc_logger.h"
@@ -90,7 +91,7 @@ pdc_analysis_registry_init_(size_t newSize)
     FUNC_ENTER(NULL);
 
     if (pdc_region_analysis_registry == NULL) {
-        new_registry = (struct _pdc_region_analysis_ftn_info **)calloc(sizeof(void *), newSize);
+        new_registry = (struct _pdc_region_analysis_ftn_info **)PDC_calloc(sizeof(void *), newSize);
         if (new_registry) {
             hg_atomic_init32(&registered_analysis_ftn_count_g, 0);
             pdc_region_analysis_registry = new_registry;
@@ -99,11 +100,12 @@ pdc_analysis_registry_init_(size_t newSize)
         }
     }
     else if (newSize > analysis_registry_size) {
-        new_registry = (struct _pdc_region_analysis_ftn_info **)calloc(sizeof(void *), newSize);
+        new_registry = (struct _pdc_region_analysis_ftn_info **)PDC_calloc(sizeof(void *), newSize);
         if (new_registry) {
             size_t copysize = analysis_registry_size * sizeof(void *);
             memcpy(new_registry, pdc_region_analysis_registry, copysize);
-            free(pdc_region_analysis_registry);
+            pdc_region_analysis_registry =
+                (struct _pdc_region_analysis_ftn_info **)PDC_free(pdc_region_analysis_registry);
             pdc_region_analysis_registry = new_registry;
             analysis_registry_size       = newSize;
             PGOTO_DONE(newSize);
@@ -125,7 +127,7 @@ pdc_transform_registry_init_(size_t newSize)
     FUNC_ENTER(NULL);
 
     if (pdc_region_transform_registry == NULL) {
-        new_registry = (struct _pdc_region_transform_ftn_info **)calloc(sizeof(void *), newSize);
+        new_registry = (struct _pdc_region_transform_ftn_info **)PDC_calloc(sizeof(void *), newSize);
         if (new_registry) {
             hg_atomic_init32(&registered_transform_ftn_count_g, 0);
             pdc_region_transform_registry = new_registry;
@@ -134,11 +136,12 @@ pdc_transform_registry_init_(size_t newSize)
         }
     }
     else if (newSize > transform_registry_size) {
-        new_registry = (struct _pdc_region_transform_ftn_info **)calloc(sizeof(void *), newSize);
+        new_registry = (struct _pdc_region_transform_ftn_info **)PDC_calloc(sizeof(void *), newSize);
         if (new_registry) {
             copysize = transform_registry_size * sizeof(void *);
             memcpy(new_registry, pdc_region_transform_registry, copysize);
-            free(pdc_region_transform_registry);
+            pdc_region_transform_registry =
+                (struct _pdc_region_transform_ftn_info **)PDC_free(pdc_region_transform_registry);
             pdc_region_transform_registry = new_registry;
             transform_registry_size       = newSize;
             PGOTO_DONE(newSize);
@@ -161,11 +164,12 @@ pdc_analysis_registry_finalize_()
     if ((pdc_region_analysis_registry != NULL) && (analysis_registry_size > 0)) {
         while (hg_atomic_get32(&i) > 0) {
             if (pdc_region_analysis_registry[i - 1])
-                free(pdc_region_analysis_registry[i - 1]);
-            pdc_region_analysis_registry[i - 1] = NULL;
+                pdc_region_analysis_registry[i - 1] =
+                    (struct _pdc_region_analysis_ftn_info *)PDC_free(pdc_region_analysis_registry[i - 1]);
             hg_atomic_decr32(&i);
         }
-        free(pdc_region_analysis_registry);
+        pdc_region_analysis_registry =
+            (struct _pdc_region_analysis_ftn_info **)PDC_free(pdc_region_analysis_registry);
         analysis_registry_size = 0;
         hg_atomic_init32(&registered_analysis_ftn_count_g, 0);
     }
@@ -250,12 +254,12 @@ PDCiter_get_nextId(void)
     FUNC_ENTER(NULL);
 
     if (PDC_Block_iterator_cache == NULL) {
-        PDC_Block_iterator_cache =
-            (struct _pdc_iterator_info *)calloc(iterator_cache_entries, sizeof(struct _pdc_iterator_info));
+        PDC_Block_iterator_cache = (struct _pdc_iterator_info *)PDC_calloc(iterator_cache_entries,
+                                                                           sizeof(struct _pdc_iterator_info));
         if (PDC_Block_iterator_cache == NULL)
             PGOTO_ERROR(-1, "calloc failed");
 
-        i_cache_freed = (int *)calloc(iterator_cache_entries, sizeof(int));
+        i_cache_freed = (int *)PDC_calloc(iterator_cache_entries, sizeof(int));
         /* Index 0 is NOT-USED other than to indicate an empty iterator */
         hg_atomic_init32(&i_cache_index, 1);
         hg_atomic_init32(&i_free_index, 0);
@@ -274,15 +278,15 @@ PDCiter_get_nextId(void)
         /* Realloc the cache and free list */
         previous_i_cache_freed   = i_cache_freed;
         previous_state           = PDC_Block_iterator_cache;
-        PDC_Block_iterator_cache = (struct _pdc_iterator_info *)calloc(iterator_cache_entries * 2,
-                                                                       sizeof(struct _pdc_iterator_info));
+        PDC_Block_iterator_cache = (struct _pdc_iterator_info *)PDC_calloc(iterator_cache_entries * 2,
+                                                                           sizeof(struct _pdc_iterator_info));
         memcpy(PDC_Block_iterator_cache, previous_state,
                iterator_cache_entries * sizeof(struct _pdc_iterator_info));
-        i_cache_freed = (int *)calloc(iterator_cache_entries * 2, sizeof(int));
+        i_cache_freed = (int *)PDC_calloc(iterator_cache_entries * 2, sizeof(int));
         memcpy(i_cache_freed, previous_i_cache_freed, iterator_cache_entries * sizeof(int));
         iterator_cache_entries *= 2;
-        free(previous_i_cache_freed);
-        free(previous_state);
+        previous_i_cache_freed = (int *)PDC_free(previous_i_cache_freed);
+        previous_state         = (struct _pdc_iterator_info *)PDC_free(previous_state);
     }
 
     ret_value = nextId;
@@ -492,11 +496,11 @@ HG_TEST_RPC_CB(analysis_ftn, handle)
          * Otherwise, go ahead and register...
          */
         if (nulliter_count < 2) {
-            if ((thisFtn = (struct _pdc_region_analysis_ftn_info *)calloc(
+            if ((thisFtn = (struct _pdc_region_analysis_ftn_info *)PDC_calloc(
                      sizeof(struct _pdc_region_analysis_ftn_info), 1)) != NULL) {
                 thisFtn->ftnPtr    = (int (*)())ftnPtr;
                 thisFtn->n_args    = 2;
-                thisFtn->object_id = (pdcid_t *)calloc(2, sizeof(pdcid_t));
+                thisFtn->object_id = (pdcid_t *)PDC_calloc(2, sizeof(pdcid_t));
                 registrationId     = PDC_add_analysis_ptr_to_registry_(thisFtn);
                 out.remote_ftn_id  = registrationId;
             }
@@ -601,10 +605,11 @@ PDC_free_analysis_registry()
 
     if (pdc_region_analysis_registry && (registered_analysis_ftn_count_g > 0)) {
         for (index = 0; index < registered_analysis_ftn_count_g; index++) {
-            free(pdc_region_analysis_registry[index]);
+            pdc_region_analysis_registry[index] =
+                (struct _pdc_region_analysis_ftn_info *)PDC_free(pdc_region_analysis_registry[index]);
         }
-        free(pdc_region_analysis_registry);
-        pdc_region_analysis_registry = NULL;
+        pdc_region_analysis_registry =
+            (struct _pdc_region_analysis_ftn_info **)PDC_free(pdc_region_analysis_registry);
     }
 
     FUNC_LEAVE_VOID;
@@ -619,10 +624,11 @@ PDC_free_transform_registry()
 
     if (pdc_region_transform_registry && (registered_transform_ftn_count_g > 0)) {
         for (index = 0; index < registered_transform_ftn_count_g; index++) {
-            free(pdc_region_transform_registry[index]);
+            pdc_region_transform_registry[index] =
+                (struct _pdc_region_transform_ftn_info *)PDC_free(pdc_region_transform_registry[index]);
         }
-        free(pdc_region_transform_registry);
-        pdc_region_transform_registry = NULL;
+        pdc_region_transform_registry =
+            (struct _pdc_region_transform_ftn_info **)PDC_free(pdc_region_transform_registry);
     }
 
     FUNC_LEAVE_VOID;
@@ -635,8 +641,7 @@ PDC_free_iterator_cache()
     FUNC_ENTER(NULL);
 
     if (PDC_Block_iterator_cache != NULL)
-        free(PDC_Block_iterator_cache);
-    PDC_Block_iterator_cache = NULL;
+        PDC_Block_iterator_cache = (struct _pdc_iterator_info *)PDC_free(PDC_Block_iterator_cache);
 
     FUNC_LEAVE_VOID;
 }

src/api/pdc_analysis/pdc_hist_pkg.c

@@ -2,6 +2,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include "pdc_logger.h"
+#include "pdc_malloc.h"
 
 #define MACRO_SAMPLE_MIN_MAX(TYPE, n, data, sample_pct, min, max)                                            \
     ({                                                                                                       \
@@ -123,11 +124,11 @@ PDC_create_hist(pdc_var_type_t dtype, int nbin, double min, double max)
     bin_incr = floor_power_of_2((max - min) / (nbin - 2)); // Excluding first and last bin (open ended)
     nbin     = ceil((max - min) / bin_incr);
 
-    hist        = (pdc_histogram_t *)malloc(sizeof(pdc_histogram_t));
+    hist        = (pdc_histogram_t *)PDC_malloc(sizeof(pdc_histogram_t));
     hist->incr  = bin_incr;
     hist->dtype = dtype;
-    hist->range = (double *)calloc(sizeof(double), nbin * 2);
-    hist->bin   = (uint64_t *)calloc(sizeof(uint64_t), nbin);
+    hist->range = (double *)PDC_calloc(sizeof(double), nbin * 2);
+    hist->bin   = (uint64_t *)PDC_calloc(sizeof(uint64_t), nbin);
     hist->nbin  = nbin;
 
     min_bin = floor(min);
@@ -292,9 +293,9 @@ PDC_free_hist(pdc_histogram_t *hist)
     if (NULL == hist)
         PGOTO_DONE_VOID;
 
-    free(hist->range);
-    free(hist->bin);
-    free(hist);
+    hist->range = (double *)PDC_free(hist->range);
+    hist->bin   = (uint64_t *)PDC_free(hist->bin);
+    hist        = (pdc_histogram_t *)PDC_free(hist);
 
 done:
     fflush(stdout);
@@ -337,11 +338,11 @@ PDC_dup_hist(pdc_histogram_t *hist)
         PGOTO_DONE(NULL);
 
     nbin       = hist->nbin;
-    res        = (pdc_histogram_t *)malloc(sizeof(pdc_histogram_t));
+    res        = (pdc_histogram_t *)PDC_malloc(sizeof(pdc_histogram_t));
     res->dtype = hist->dtype;
     res->nbin  = nbin;
-    res->range = (double *)calloc(sizeof(double), nbin * 2);
-    res->bin   = (uint64_t *)calloc(sizeof(uint64_t), nbin);
+    res->range = (double *)PDC_calloc(sizeof(double), nbin * 2);
+    res->bin   = (uint64_t *)PDC_calloc(sizeof(uint64_t), nbin);
     res->incr  = hist->incr;
 
     memcpy(res->range, hist->range, sizeof(double) * nbin * 2);
@@ -434,10 +435,10 @@ PDC_copy_hist(pdc_histogram_t *to, pdc_histogram_t *from)
     to->incr  = from->incr;
     to->dtype = from->dtype;
     if (NULL == to->range)
-        to->range = (double *)calloc(sizeof(double), nbin * 2);
+        to->range = (double *)PDC_calloc(sizeof(double), nbin * 2);
     memcpy(to->range, from->range, sizeof(double) * nbin * 2);
     if (NULL == to->bin)
-        to->bin = (uint64_t *)calloc(sizeof(uint64_t), nbin);
+        to->bin = (uint64_t *)PDC_calloc(sizeof(uint64_t), nbin);
     memcpy(to->bin, from->bin, sizeof(uint64_t) * nbin);
     to->nbin = from->nbin;