Merge pull request #468 from lukemartinlogan/master

Final stage-in release commits

CMakeLists.txt

@@ -417,6 +417,7 @@ if(CMAKE_PROJECT_NAME STREQUAL HERMES AND BUILD_TESTING)
   endif()
   enable_testing()
   add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/test)
+  add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/data_stager/test)
 endif()
 
 if(HERMES_ENABLE_STDIO_ADAPTER OR HERMES_ENABLE_POSIX_ADAPTER OR

adapter/adapter_generator/adapter_generator/create_interceptor.py

@@ -156,6 +156,7 @@ def _CreateH(self, namespace, includes, path):
         # Create the class definition
         self.h_lines.append(f"namespace hermes::adapter::{namespace} {{")
         self.h_lines.append(f"")
+        self.h_lines.append(f"/** Pointers to the real {namespace} API */")
         self.h_lines.append(f"class API {{")
 
         # Create class function pointers
@@ -175,6 +176,8 @@ def _CreateH(self, namespace, includes, path):
         self.h_lines.append(f"}};")
         self.h_lines.append(f"}}  // namespace hermes::adapter::{namespace}")
         self.h_lines.append("")
+        self.h_lines.append("#undef REQUIRE_API")
+        self.h_lines.append("")
         self.h_lines.append(f"#endif  // HERMES_ADAPTER_{namespace.upper()}_H")
         self.h_lines.append("")
 
@@ -183,23 +186,26 @@ def _CreateH(self, namespace, includes, path):
 
     def require_api(self):
         self.h_lines.append(f"#define REQUIRE_API(api_name) \\")
-        self.h_lines.append(f"  if (real_api->api_name == nullptr) {{ \\")
+        self.h_lines.append(f"  if (api_name == nullptr) {{ \\")
         self.h_lines.append(f"    LOG(FATAL) << \"HERMES Adapter failed to map symbol: \" \\")
         self.h_lines.append(f"    #api_name << std::endl; \\")
-        self.h_lines.append(f"    exit(1);")
+        self.h_lines.append(f"    std::exit(1); \\")
+        self.h_lines.append(f"   }}")
 
     def add_typedef(self, api):
         self.h_lines.append(f"typedef {api.ret} (*{api.type})({api.get_args()});")
 
     def add_intercept_api(self, api):
-        self.h_lines.append(f"  {api.ret} (*{api.real_name})({api.get_args()}) = nullptr;")
+        self.h_lines.append(f"  /** {api.real_name} */")
+        self.h_lines.append(f"  {api.type} {api.real_name} = nullptr;")
 
     def init_api(self, api):
         self.h_lines.append(f"    if (is_intercepted) {{")
         self.h_lines.append(f"      {api.real_name} = ({api.type})dlsym(RTLD_NEXT, \"{api.name}\");")
         self.h_lines.append(f"    }} else {{")
         self.h_lines.append(f"      {api.real_name} = ({api.type})dlsym(RTLD_DEFAULT, \"{api.name}\");")
         self.h_lines.append(f"    }}")
+        self.h_lines.append(f"    REQUIRE_API({api.real_name})")
 
     def save(self, path, text):
         if path is None:

adapter/adapter_generator/posix.py

@@ -16,12 +16,14 @@
     Api("ssize_t pwrite64(int fd, const void *buf, size_t count, off64_t offset)"),
     Api("off_t lseek(int fd, off_t offset, int whence)"),
     Api("off64_t lseek64(int fd, off64_t offset, int whence)"),
-    Api("int __fxstat(int version, int fd, struct stat *buf)"),
+    Api("int __fxstat(int __ver, int __filedesc, struct stat *__stat_buf)"),
     Api("int fsync(int fd)"),
     Api("int close(int fd)"),
 ]
 
 includes = [
+    "<sys/types.h>",
+    "<sys/stat.h>",
     "<unistd.h>",
     "<fcntl.h>",
     "\"interceptor.h\"",

adapter/constants.h

@@ -81,6 +81,7 @@ const char kPathDelimiter = ',';
 const char* kAdapterDefaultMode = "DEFAULT";
 const char* kAdapterBypassMode = "BYPASS";
 const char* kAdapterScratchMode = "SCRATCH";
+const char* kAdapterWorkflowMode = "WORKFLOW";
 
 /**
  * If the \c HERMES_STOP_DAEMON environment variable is unset or has a non-zero

adapter/enumerations.h

@@ -14,8 +14,9 @@
 #define HERMES_ADAPTER_ENUMERATIONS_H
 enum class AdapterMode {
   kDefault = 0, /**< All/given files are stored on file close or flush. */
-  kBypass = 1,  /**< All/given files are not buffered. */
-  kScratch = 2  /**< All/given files are ignored on file close or flush. */
+  kBypass = 1, /**< All/given files are not buffered. */
+  kScratch = 2, /**< All/given files are ignored on file close or flush. */
+  kWorkflow = 3 /**< Keep data in hermes until user stages out. */
 };
 
 enum class FlushingMode {

adapter/filesystem/filesystem.cc

@@ -70,13 +70,18 @@ void Filesystem::Open(AdapterStat &stat, File &f, const std::string &path) {
         u8 c;
         stat.st_bkid =
             std::make_shared<hapi::Bucket>(path_str, mdm->GetHermes());
-        stat.st_bkid->Put(stat.main_lock_blob, &c, 1);
+        if (!stat.st_bkid->ContainsBlob(stat.main_lock_blob)) {
+          stat.st_bkid->Put(stat.main_lock_blob, &c, 1);
+        }
       }
       MPI_Barrier(stat.comm);
       if (rank != 0) {
         stat.st_bkid =
             std::make_shared<hapi::Bucket>(path_str, mdm->GetHermes());
       }
+
+      // Create a vbucket for storing all modified blobs (per-rank)
+
     } else {
       stat.st_bkid =
           std::make_shared<hapi::Bucket>(path_str, mdm->GetHermes());
@@ -138,7 +143,7 @@ size_t Filesystem::Write(File &f, AdapterStat &stat, const void *ptr,
   std::shared_ptr<hapi::Bucket> &bkt = stat.st_bkid;
   std::string filename = bkt->GetName();
   LOG(INFO) << "Write called for filename: " << filename << " on offset: "
-            << stat.st_ptr << " and size: " << total_size << std::endl;
+            << off << " and size: " << total_size << std::endl;
 
   size_t ret;
   auto mdm = Singleton<MetadataManager>::GetInstance();
@@ -484,9 +489,7 @@ size_t Filesystem::_ReadNew(BlobPlacementIter &ri) {
 
   if (ri.opts_.dpe_ != PlacementPolicy::kNone) {
     LOG(INFO) << "Placing the read blob in the hierarchy" << std::endl;
-    IoOptions opts(ri.opts_);
-    opts.seek_ = false;
-    opts.with_fallback_ = false;
+    IoOptions opts = IoOptions::PlaceInHermes(ri.opts_);
     Write(ri.f_, ri.stat_,
           ri.blob_.data() + ri.p_.blob_off_,
           ri.p_.bucket_off_,
@@ -623,6 +626,7 @@ int Filesystem::Sync(File &f, AdapterStat &stat) {
     return 0;
   }
   if (IsAsyncFlush(filename)) {
+    LOG(INFO) << "Asynchronous flushing enabled" << std::endl;
     stat.st_vbkt->WaitForBackgroundFlush();
     return 0;
   }
@@ -654,6 +658,23 @@ int Filesystem::Sync(File &f, AdapterStat &stat) {
   return _RealSync(f);
 }
 
+void SaveModifiedBlobSet(AdapterStat &stat) {
+  int rank = 0;
+  auto mdm = Singleton<MetadataManager>::GetInstance();
+  if (mdm->is_mpi) {
+    MPI_Comm_rank(stat.comm, &rank);
+  }
+  auto filename = stat.st_bkid->GetName();
+  const auto &blob_names = stat.st_blobs;
+  std::string vbucket_name = filename + "#" +
+                             std::to_string(rank) + "#sync";
+  hapi::VBucket file_vbucket(vbucket_name, mdm->GetHermes());
+  auto offset_map = std::unordered_map<std::string, hermes::u64>();
+  for (const auto &blob_name : blob_names) {
+    file_vbucket.Link(blob_name, filename);
+  }
+}
+
 int Filesystem::Close(File &f, AdapterStat &stat, bool destroy) {
   hapi::Context ctx;
   int rank = 0;
@@ -678,19 +699,22 @@ int Filesystem::Close(File &f, AdapterStat &stat, bool destroy) {
     }
     MPI_Barrier(stat.comm);
   }
-  if (INTERCEPTOR_LIST->adapter_mode == AdapterMode::kScratch) {
+  if (INTERCEPTOR_LIST->adapter_mode == AdapterMode::kScratch ||
+      INTERCEPTOR_LIST->adapter_mode == AdapterMode::kWorkflow) {
     destroy = false;
   }
 
-  Sync(f, stat);
+  Sync(f, stat);  // TODO(llogan): should wait until hermes destroyed to flush
   auto filename = stat.st_bkid->GetName();
   if (mdm->is_mpi) { MPI_Barrier(stat.comm); }
   if (IsAsyncFlush(filename)) {
     stat.st_vbkt->Destroy();
   }
   mdm->Delete(f);
   if (mdm->is_mpi) { MPI_Barrier(stat.comm); }
-  if (destroy) { stat.st_bkid->Destroy(ctx); }
+  if (destroy) {
+    stat.st_bkid->Destroy(ctx);
+  }
   if (stat.amode & MPI_MODE_DELETE_ON_CLOSE) {
     stdfs::remove(filename);
   }

adapter/filesystem/filesystem.h

@@ -200,6 +200,18 @@ struct IoOptions {
     opts.seek_ = seek;
     return opts;
   }
+
+  /**
+   * Ensure that I/O goes only to Hermes, and does not fall back to PFS.
+   *
+   * @param orig_opts The original options to modify
+   * */
+  static IoOptions PlaceInHermes(IoOptions &orig_opts) {
+    IoOptions opts(orig_opts);
+    opts.seek_ = false;
+    opts.with_fallback_ = false;
+    return opts;
+  }
 };
 
 /**
@@ -337,10 +349,12 @@ class Filesystem {
      * well-defined.
      * */
     if (bucket_exists) {
+      size_t orig = stat.st_size;
       size_t bkt_size = stat.st_bkid->GetTotalBlobSize();
-      stat.st_size = std::max(bkt_size, stat.st_size);
+      stat.st_size = std::max(bkt_size, orig);
       LOG(INFO) << "Since bucket exists, should reset its size to: "
-                << stat.st_size << std::endl;
+                << bkt_size << " or " << orig
+                << ", winner: " << stat.st_size << std::endl;
     }
     if (stat.is_append) {
       stat.st_ptr = stat.st_size;

adapter/interceptor.h

@@ -130,6 +130,8 @@ struct InterceptorList {
         adapter_mode = AdapterMode::kBypass;
       } else if (strcmp(kAdapterScratchMode, adapter_mode_str) == 0) {
         adapter_mode = AdapterMode::kScratch;
+      } else if (strcmp(kAdapterWorkflowMode, adapter_mode_str) == 0) {
+        adapter_mode = AdapterMode::kWorkflow;
       } else {
         // TODO(hari): @errorhandling throw error.
         return;
@@ -157,7 +159,8 @@ struct InterceptorList {
      check if \a path file path persists
    */
   bool Persists(std::string path) {
-    if (adapter_mode == AdapterMode::kDefault) {
+    if (adapter_mode == AdapterMode::kDefault ||
+        adapter_mode == AdapterMode::kWorkflow) {
       if (adapter_paths.empty()) {
         return true;
       } else {

adapter/mapper/abstract_mapper.h

@@ -60,14 +60,15 @@ struct BlobPlacement {
   }
 
   /** decode \a blob_name BLOB name by splitting it into index, offset, size,
-      and rank. */
-  void DecodeBlobNamePerProc(const std::string &blob_name) {
-    auto str_split = hermes::adapter::StringSplit(blob_name.data(), '#');
+        and rank. */
+  void DecodeBlobNameLogEntry(const std::string &blob_name) {
+    auto str_split =
+        hermes::adapter::StringSplit(blob_name.data(), '#');
     std::stringstream(str_split[0]) >> page_;
     std::stringstream(str_split[1]) >> blob_off_;
     std::stringstream(str_split[2]) >> blob_size_;
     std::stringstream(str_split[3]) >> rank_;
-    std::stringstream(str_split[4]) >> rank_;
+    std::stringstream(str_split[4]) >> time_;
   }
 };