Merge pull request #755 from CamStan/main

Merge dev into main for release 1.0.1

Author: adammoody

.github/workflows/build-and-test.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-latest ]
+        os: [ ubuntu-20.04 ]
         compiler: [ gcc ]
         gcc: [ 7, 8, 9, 10, 11 ]
 
@@ -37,7 +37,15 @@ jobs:
       CXX: g++-${{ matrix.gcc }}
 
     steps:
-    - uses: actions/checkout@v2
+    - name: Push checkout
+      if: github.event_name == 'push'
+      uses: actions/checkout@v2
+
+    - name: PR checkout
+      if: github.event_name == 'pull_request'
+      uses: actions/checkout@v2
+      with:
+        ref: ${{ github.event.pull_request.head.sha }}
 
     - name: Set up GCC
       uses: egor-tensin/setup-gcc@v1

Makefile.am

@@ -5,8 +5,10 @@ CONFIG = ordered
 ACLOCAL_AMFLAGS = -I m4
 
 pkgconfigdir = @pkgconfigdir@
-pkgconfig_DATA = client/unifyfs.pc \
-		 client/unifyfs-api.pc
+pkgconfig_DATA = \
+  client/unifyfs.pc \
+  client/unifyfs-api.pc \
+  client/unifyfs-static.pc
 
 CLEANFILES =
 

client/src/Makefile.am

@@ -13,6 +13,10 @@ if USE_PMPI_WRAPPERS
 lib_LTLIBRARIES += libunifyfs_mpi_gotcha.la
 endif #USE_PMPI_WRAPPERS
 
+if ENABLE_LD_PRELOAD
+lib_LTLIBRARIES += libunifyfs_preload_gotcha.la
+endif #ENABLE_LD_PRELOAD
+
 if HAVE_FORTRAN
 lib_LTLIBRARIES += libunifyfsf.la
 endif #HAVE_FORTRAN
@@ -40,15 +44,13 @@ CLIENT_COMMON_CPPFLAGS = \
 
 CLIENT_COMMON_CFLAGS = \
   $(AM_CFLAGS) \
-  $(UNIFYFS_COMMON_FLAGS) \
-  $(MPI_CFLAGS)
+  $(UNIFYFS_COMMON_FLAGS)
 
 CLIENT_COMMON_LDFLAGS = \
   -version-info $(LIBUNIFYFS_LT_VERSION)
 
 CLIENT_COMMON_LIBADD = \
   $(UNIFYFS_COMMON_LIBS) \
-  $(MPI_CLDFLAGS) \
   -lm -lrt -lcrypto -lpthread
 
 if HAVE_SPATH
@@ -96,6 +98,8 @@ PMPI_SRC_FILES = \
   pmpi_wrappers.c \
   pmpi_wrappers.h
 
+PRELOAD_SRC_FILES = \
+  preload.c
 
 # Per-target flags begin here
 
@@ -118,8 +122,8 @@ libunifyfs_la_SOURCES  = \
 
 if USE_PMPI_WRAPPERS
 libunifyfs_mpi_la_CPPFLAGS = $(CLIENT_COMMON_CPPFLAGS)
-libunifyfs_mpi_la_CFLAGS   = $(CLIENT_COMMON_CFLAGS)
-libunifyfs_mpi_la_LDFLAGS  = $(CLIENT_COMMON_LDFLAGS)
+libunifyfs_mpi_la_CFLAGS   = $(CLIENT_COMMON_CFLAGS) $(MPI_CFLAGS)
+libunifyfs_mpi_la_LDFLAGS  = $(CLIENT_COMMON_LDFLAGS) $(MPI_CLDFLAGS)
 libunifyfs_mpi_la_LIBADD   = libunifyfs.la
 libunifyfs_mpi_la_SOURCES  = $(PMPI_SRC_FILES)
 endif #USE_PMPI_WRAPPERS
@@ -137,10 +141,18 @@ libunifyfs_gotcha_la_SOURCES  = \
   $(POSIX_CLIENT_SRC_FILES) \
   gotcha_map_unifyfs_list.c
 
+if ENABLE_LD_PRELOAD
+libunifyfs_preload_gotcha_la_CPPFLAGS = $(CLIENT_COMMON_CPPFLAGS)
+libunifyfs_preload_gotcha_la_CFLAGS   = $(CLIENT_COMMON_CFLAGS)
+libunifyfs_preload_gotcha_la_LDFLAGS  = $(CLIENT_COMMON_LDFLAGS)
+libunifyfs_preload_gotcha_la_LIBADD   = libunifyfs_gotcha.la
+libunifyfs_preload_gotcha_la_SOURCES  = $(PRELOAD_SRC_FILES)
+endif #ENABLE_LD_PRELOAD
+
 if USE_PMPI_WRAPPERS
 libunifyfs_mpi_gotcha_la_CPPFLAGS = $(CLIENT_COMMON_CPPFLAGS)
-libunifyfs_mpi_gotcha_la_CFLAGS   = $(CLIENT_COMMON_CFLAGS)
-libunifyfs_mpi_gotcha_la_LDFLAGS  = $(CLIENT_COMMON_LDFLAGS)
+libunifyfs_mpi_gotcha_la_CFLAGS   = $(CLIENT_COMMON_CFLAGS) $(MPI_CFLAGS)
+libunifyfs_mpi_gotcha_la_LDFLAGS  = $(CLIENT_COMMON_LDFLAGS) $(MPI_CLDFLAGS)
 libunifyfs_mpi_gotcha_la_LIBADD   = libunifyfs_gotcha.la
 libunifyfs_mpi_gotcha_la_SOURCES  = $(PMPI_SRC_FILES)
 endif #USE_PMPI_WRAPPERS

client/src/client_read.c

@@ -419,17 +419,41 @@ void service_local_reqs(
             /* copy data from local write log into user buffer */
             off_t log_offset = ext_log_pos + ext_byte_offset;
             size_t nread = 0;
-            int rc = unifyfs_logio_read(client->state.logio_ctx, log_offset,
-                                        cover_length, req_ptr, &nread);
-            if (rc == UNIFYFS_SUCCESS) {
-                /* update bytes we have filled in the request buffer */
-                update_read_req_coverage(req, req_byte_offset, nread);
+            /* we need to use the logio_ctx from correct client */
+            logio_context* logio_ctx = NULL;
+            if (next->client_id == client->state.client_id) {
+                logio_ctx = client->state.logio_ctx;
+            } else if (client->logio_ctx_ptrs[next->client_id] != NULL) {
+                logio_ctx = client->logio_ctx_ptrs[next->client_id];
             } else {
-                LOGERR("local log read failed for offset=%zu size=%zu",
-                       (size_t)log_offset, cover_length);
-                req->errcode = rc;
+                size_t shmem_size = 0;
+                if (client->state.logio_ctx->shmem != NULL) {
+                    shmem_size = client->state.logio_ctx->shmem->size;
+                }
+                char* spill_dir = NULL;
+                if (client->state.logio_ctx->spill_sz > 0) {
+                    spill_dir = client->cfg.logio_spill_dir;
+                }
+                unifyfs_logio_init(client->state.app_id,
+                                   next->client_id,
+                                   shmem_size,
+                                   client->state.logio_ctx->spill_sz,
+                                   spill_dir,
+                                   &client->logio_ctx_ptrs[next->client_id]);
+                logio_ctx = client->logio_ctx_ptrs[next->client_id];
+            }
+            if (NULL != logio_ctx) {
+                int rc = unifyfs_logio_read(logio_ctx, log_offset,
+                                            cover_length, req_ptr, &nread);
+                if (rc == UNIFYFS_SUCCESS) {
+                    /* update bytes we have filled in the request buffer */
+                    update_read_req_coverage(req, req_byte_offset, nread);
+                } else {
+                    LOGERR("local log read failed for offset=%zu size=%zu",
+                           (size_t) log_offset, cover_length);
+                    req->errcode = rc;
+                }
             }
-
             /* get the next element in the tree */
             next = seg_tree_iter(extents, next);
         }
@@ -560,7 +584,7 @@ static void update_read_req_result(unifyfs_client* client,
  */
 int process_gfid_reads(unifyfs_client* client,
                        read_req_t* in_reqs,
-                       int in_count)
+                       size_t in_count)
 {
     if (0 == in_count) {
         return UNIFYFS_SUCCESS;
@@ -597,9 +621,76 @@ int process_gfid_reads(unifyfs_client* client,
     /* this records the pointer to the temp request array if
      * we allocate one, we should free this later if not NULL */
     read_req_t* reqs = NULL;
+    if (client->use_node_local_extents) {
+        extents_list_t* list = calloc(1, sizeof(struct extents_list));
+        struct extents_list* cur = list;
+        int num_request_selected = 0;
+        for (int i = 0; i < in_count; ++i) {
+            int fid = unifyfs_fid_from_gfid(client, in_reqs[i].gfid);
+            /* get meta for this file id */
+            unifyfs_filemeta_t* meta = unifyfs_get_meta_from_fid(client, fid);
+            if (meta != NULL) {
+                if (!meta->attrs.is_laminated || !meta->needs_reads_sync) {
+                    /* do not proceed for this request as
+                     * it is not a laminated file or has already been synced.*/
+                    continue;
+                }
+                num_request_selected++;
+                off_t filesize_offt = unifyfs_gfid_filesize(client,
+                                                            in_reqs[i].gfid);
+                cur->value.file_pos = 0;
+                cur->value.length = filesize_offt - 1;
+                cur->value.gfid = in_reqs[i].gfid;
+                if (i < in_count - 1) {
+                    cur->next = calloc(1, sizeof(struct extents_list));
+                    cur->next->next = NULL;
+                    cur = cur->next;
+                } else {
+                    cur->next = NULL;
+                }
+                meta->needs_reads_sync = 0;
+            }
+        }
+        if (num_request_selected > 0) {
+            /* There are files which are laminated and
+             * require sync of extents */
+            size_t extent_count = 0;
+            unifyfs_client_index_t* extents = NULL;
+            int rc =
+                  invoke_client_node_local_extents_get_rpc(client,
+                                                           num_request_selected,
+                                                           list,
+                                                           &extent_count,
+                                                           &extents);
+            if (rc == UNIFYFS_SUCCESS && extent_count != 0) {
+                for (int j = 0; j < extent_count; ++j) {
+                    if (extents[j].log_app_id ==
+                        client->state.app_id) {
+                        int fid = unifyfs_fid_from_gfid(client,
+                                                        extents[j].gfid);
+                        /* get meta for this file id */
+                        unifyfs_filemeta_t* meta = unifyfs_get_meta_from_fid(
+                                client,
+                                fid);
+                        if (meta != NULL) {
+                            seg_tree_add(&meta->extents,
+                                         extents[j].file_pos,
+                                         extents[j].file_pos +
+                                         extents[j].length - 1,
+                                         extents[j].log_pos,
+                                         extents[j].log_client_id);
+                        }
+                    }
+                }
+            }
+            if (extents != NULL) {
+                free(extents);
+            }
+        }
+    }
 
     /* attempt to complete requests locally if enabled */
-    if (client->use_local_extents) {
+    if (client->use_local_extents || client->use_node_local_extents) {
         /* allocate space to make local and server copies of the requests,
          * each list will be at most in_count long */
         size_t reqs_size = 2 * in_count;
@@ -743,7 +834,7 @@ int process_gfid_reads(unifyfs_client* client,
     /* if we attempted to service requests from our local extent map,
      * then we need to copy the resulting read requests from the local
      * and server arrays back into the user's original array */
-    if (client->use_local_extents) {
+    if (client->use_local_extents || client->use_node_local_extents) {
         /* TODO: would be nice to copy these back into the same order
          * in which we received them. */
 

client/src/client_read.h

@@ -111,6 +111,6 @@ void update_read_req_coverage(read_req_t* req,
 /* process a set of client read requests */
 int process_gfid_reads(unifyfs_client* client,
                        read_req_t* in_reqs,
-                       int in_count);
+                       size_t in_count);
 
 #endif // UNIFYFS_CLIENT_READ_H

client/src/gotcha_map_unifyfs_list.c

@@ -61,6 +61,13 @@ UNIFYFS_DEF(unlink, int,
 UNIFYFS_DEF(remove, int,
             (const char* path),
             (path))
+UNIFYFS_DEF(utimensat, int,
+            (int dirfd, const char* pathname, const struct timespec times[2],
+             int flags),
+            (dirfd, pathname, times, flags))
+UNIFYFS_DEF(futimens, int,
+            (int fd, const struct timespec times[2]),
+            (fd, times))
 
 UNIFYFS_DEF(stat, int,
             (const char* path, struct stat* buf),
@@ -144,6 +151,12 @@ UNIFYFS_DEF(pwrite64, ssize_t,
 UNIFYFS_DEF(close, int,
             (int fd),
             (fd))
+UNIFYFS_DEF(dup, int,
+            (int fd),
+            (fd))
+UNIFYFS_DEF(dup2, int,
+            (int fd, int desired_fd),
+            (fd, desired_fd))
 UNIFYFS_DEF(fchdir, int,
             (int fd),
             (fd))
@@ -349,6 +362,8 @@ struct gotcha_binding_t unifyfs_wrappers[] = {
     { "truncate", UNIFYFS_WRAP(truncate), &wrappee_handle_truncate },
     { "unlink", UNIFYFS_WRAP(unlink), &wrappee_handle_unlink },
     { "remove", UNIFYFS_WRAP(remove), &wrappee_handle_remove },
+    { "utimensat", UNIFYFS_WRAP(utimensat), &wrappee_handle_utimensat },
+    { "futimens", UNIFYFS_WRAP(futimens), &wrappee_handle_futimens },
     { "stat", UNIFYFS_WRAP(stat), &wrappee_handle_stat },
     { "fstat", UNIFYFS_WRAP(fstat), &wrappee_handle_fstat },
     { "__xstat", UNIFYFS_WRAP(__xstat), &wrappee_handle___xstat },
@@ -386,6 +401,8 @@ struct gotcha_binding_t unifyfs_wrappers[] = {
     { "munmap", UNIFYFS_WRAP(munmap), &wrappee_handle_munmap },
     { "mmap64", UNIFYFS_WRAP(mmap64), &wrappee_handle_mmap64 },
     { "close", UNIFYFS_WRAP(close), &wrappee_handle_close },
+    { "dup", UNIFYFS_WRAP(dup), &wrappee_handle_dup },
+    { "dup2", UNIFYFS_WRAP(dup2), &wrappee_handle_dup2 },
     { "opendir", UNIFYFS_WRAP(opendir), &wrappee_handle_opendir },
     { "fdopendir", UNIFYFS_WRAP(fdopendir), &wrappee_handle_fdopendir },
     { "closedir", UNIFYFS_WRAP(closedir), &wrappee_handle_closedir },