New parameter to remove rootdir at the end

.gitlab-ci.yml

@@ -87,6 +87,8 @@ gkfwd:
       -DGKFS_INSTALL_TESTS:BOOL=ON
       -DGKFS_ENABLE_FORWARDING:BOOL=ON
       -DGKFS_ENABLE_AGIOS:BOOL=ON
+      -DGKFS_ENABLE_PARALLAX:BOOL=OFF
+      -DGKFS_ENABLE_ROCKSDB:BOOL=ON
       -DCMAKE_INSTALL_PREFIX=${INSTALL_PATH}
       ${CI_PROJECT_DIR}
     - make -j$(nproc) install

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 Support for different databases backend
 New Docker Images and scripts (0.9.1)
 ([!110](https://storage.bsc.es/gitlab/hpc/gekkofs/-/merge_requests/110)).
+- Added `--clean-rootdir-finish` argument to remove rootdir/metadir at the end.
 
 ## [0.9.0] - 2022-02-22
 ### New

README.md

@@ -104,15 +104,12 @@ Options:
                               Libfabric must have enabled support verbs or psm2.
   --auto-sm                   Enables intra-node communication (IPCs) via the `na+sm` (shared memory) protocol, instead of using the RPC protocol. (Default off)
   -c,--clean-rootdir          Cleans Rootdir >before< launching the deamon
+  -f, --clean-rootdir-finish Cleans Rootdir >After< the deamon finishes
   --version                   Print version and exit.
 
   --dbbackend               'rocksdb' (default) or 'parallaxdb' can be specified as
                             metadata backend, in that case a file in 'metadir' named
                             rocksdbx is created. Parallaxdb support is experimental.
-  --keepmd                  'parallaxdb' specific, persist the metadata file
-                            (default off, file is deleted at the end)
-  --reusemd                 'parallaxdb' specific, do not recreate the 
-                            metadata file, (default re/create)
   --kreonsize               'parallaxdb' specific, size of the metadata file in GB. Minimal is 8 GB
                             (default 8, 8 GB)
   --version                 Print version and exit.
@@ -239,7 +236,7 @@ Finally, modify `guided_config.txt` to your distribution requirements.
 ### Metadata Backends
 There are two different metadata backends in GekkoFS. The default one uses `rocksdb`, however an alternative based on `PARALLAX` from `FORTH` 
 is available.
-To enable it use the `-DGKFS_ENABLE_PARALLAX:BOOL=ON` option, you can also disable `rocksdb` with `-DGKFS_ENABLE_ROCKSDB:BOOL=ON`.
+To enable it use the `-DGKFS_ENABLE_PARALLAX:BOOL=ON` option, you can also disable `rocksdb` with `-DGKFS_ENABLE_ROCKSDB:BOOL=OFF`.
 
 Once it is enabled, `--dbbackend` option will be functional.
 

docs/sphinx/users/building.rst

@@ -108,6 +108,11 @@ dependencies:
 - `AGIOS <https://github.com/francielizanon/agios>`_ (commit c26a654 or
   newer) to enable the :code:`GekkoFWD` I/O forwarding mode.
 
+- `PARALLAX` There are two different metadata backends in GekkoFS. The default one uses `rocksdb`, however an alternative based on `PARALLAX` from `FORTH` 
+is available. To enable it, use the `-DGKFS_ENABLE_PARALLAX:BOOL=ON` option, you can also disable `rocksdb` with `-DGKFS_ENABLE_ROCKSDB:BOOL=OFF`.
+  Once it is enabled, `--dbbackend` option will be functional.
+
+
 .. _step_by_step_installation:
 
 Step-by-step installation

docs/sphinx/users/running.md

@@ -74,6 +74,12 @@ Further options are available
                                Libfabric must have enabled support verbs or psm2.
    --auto-sm                   Enables intra-node communication (IPCs) via the `na+sm` (shared memory) protocol, instead of using the RPC protocol. (Default off)
    -c,--clean-rootdir          Cleans Rootdir >before< launching the deamon
+   -f,--clean-rootdir-finish   Cleans Rootdir >after< finishing the deamon
+    --dbbackend               'rocksdb' (default) or 'parallaxdb' can be specified as
+                                metadata backend, in that case a file in 'metadir' named
+                                rocksdbx is created. Parallaxdb support is experimental.
+    --kreonsize               'parallaxdb' specific, size of the metadata file in GB. Minimal is 8 GB
+                              (default 8, 8 GB)
    --version                   Print version and exit.
 ````
 

include/client/preload_util.hpp

@@ -32,7 +32,6 @@
 
 #include <client/preload.hpp>
 #include <common/metadata.hpp>
-#include <optional>
 #include <string>
 #include <iostream>
 #include <map>

include/daemon/backend/metadata/db.hpp

@@ -37,11 +37,13 @@
 #include <daemon/backend/exceptions.hpp>
 #include <tuple>
 #include <daemon/backend/metadata/metadata_backend.hpp>
+#ifdef GKFS_ENABLE_ROCKSDB
 #include <daemon/backend/metadata/rocksdb_backend.hpp>
+#endif
 #ifdef GKFS_ENABLE_PARALLAX
 #include <daemon/backend/metadata/parallax_backend.hpp>
 #endif
-namespace rdb = rocksdb;
+
 
 namespace gkfs::metadata {
 

include/daemon/classes/fs_data.hpp

@@ -71,9 +71,9 @@ private:
     // Database
     std::shared_ptr<gkfs::metadata::MetadataDB> mdb_;
     std::string dbbackend_;
+    bool keep_rootdir_ = true;
     // Kreon
-    bool reuse_md_ = false;
-    bool keep_md_ = false;
+
     unsigned long long size_md_ = 8589934592ull;
 
     // Storage backend
@@ -206,16 +206,10 @@ public:
     blocks_state(bool blocks_state);
 
     bool
-    kreon_keep_md() const;
-
-    void
-    kreon_keep_md(bool keep_md);
-
-    bool
-    kreon_reuse_md() const;
+    keep_rootdir() const;
 
     void
-    kreon_reuse_md(bool reuse_md);
+    keep_rootdir(bool keep_rootdir_);
 
     unsigned long long
     kreon_size_md() const;

scripts/out

-Destination path is set to  "/home/rnou/depsx"
-Profile name: direct
-Profile version: 0.9.0-experimental
-------------------------------------
-Downloaded 'https://github.com/pmodels/argobots/archive/v1.0rc1.tar.gz' to 'argobots'
-Cloned 'https://github.com/pmem/syscall_intercept.git' to 'syscall_intercept' with commit '[f7cebb7b7e7512a19b78a31ce236ad6ca22636dd]' and flags ''
-Cloned 'https://github.com/CARV-ICS-FORTH/kreon.git' to 'kreon' with commit '[889353d39052f1c4b3bb9f95821e935dc5a5565e]' and flags ''
-Downloaded 'https://github.com/facebook/rocksdb/archive/v6.2.2.tar.gz' to 'rocksdb'
-Cloned 'https://xgitlab.cels.anl.gov/sds/margo.git' to 'margo' with commit '[v0.6.3]' and flags ''
-Cloned 'https://github.com/HowardHinnant/date.git' to 'date' with commit '[e7e1482087f58913b80a20b04d5c58d9d6d90155]' and flags ''
-Cloned 'https://github.com/mercury-hpc/mercury' to 'mercury' with commit '[41caa143a07ed179a3149cac4af0dc7aa3f946fd]' and flags '--recurse-submodules'
-Done

src/daemon/backend/metadata/db.cpp

@@ -58,12 +58,18 @@ struct MetadataDBFactory {
 #else
             GKFS_METADATA_MOD->log()->error("PARALLAX not compiled");
             exit(EXIT_FAILURE);
+#endif
+        } else if(id == "rocksdb") {
+#ifdef GKFS_ENABLE_ROCKSDB
+            return std::make_unique<RocksDBBackend>(path);
+#else
+            GKFS_METADATA_MOD->log()->error("ROCKSDB not compiled");
+            exit(EXIT_FAILURE);
 #endif
         }
 
-
-        // Default rocksdb
-        return std::make_unique<RocksDBBackend>(path);
+        GKFS_METADATA_MOD->log()->error("No valid metadata backend selected");
+        exit(EXIT_FAILURE);
     }
 };
 

src/daemon/backend/metadata/parallax_backend.cpp

@@ -52,8 +52,6 @@ namespace gkfs::metadata {
  */
 ParallaxBackend::~ParallaxBackend() {
     par_close(par_db_);
-    if(GKFS_DATA->kreon_keep_md() == false)
-        unlink(par_path_.c_str());
 }
 
 /**
@@ -85,23 +83,15 @@ ParallaxBackend::ParallaxBackend(const std::string& path) {
     }
 
     // Check size if we want to reuse it
-    if(GKFS_DATA->kreon_reuse_md()) {
-
-        size = lseek(fd, 0, SEEK_END);
-        if(size == -1) {
-            printf("[%s:%s:%d] failed to determine volume size exiting...\n",
-                   __FILE__, __func__, __LINE__);
-            perror("ioctl");
-            exit(EXIT_FAILURE);
-        }
-    }
-    if(GKFS_DATA->kreon_reuse_md() && size == 0) {
-        GKFS_METADATA_MOD->log()->error(
-                "PARALLAX database reused but size is 0");
+    size = lseek(fd, 0, SEEK_END);
+    if(size == -1) {
+        printf("[%s:%s:%d] failed to determine volume size exiting...\n",
+               __FILE__, __func__, __LINE__);
+        perror("ioctl");
         exit(EXIT_FAILURE);
     }
 
-    if(GKFS_DATA->kreon_reuse_md() == false) {
+    if(size == 0) {
         size = GKFS_DATA->kreon_size_md();
 
         lseek(fd, size - 1, SEEK_SET);
@@ -113,12 +103,6 @@ ParallaxBackend::ParallaxBackend(const std::string& path) {
         std::string cmd = "kv_format.parallax --device " + par_path_ +
                           " --max_regions_num 1 ";
         system(cmd.c_str());
-
-        /*
-                fd = open(par_path_.c_str(), O_RDONLY);
-                size = lseek(fd, 0, SEEK_END);
-                close(fd);
-        */
     }
 
     par_options_.create_flag = PAR_CREATE_DB;

src/daemon/classes/fs_data.cpp

@@ -211,23 +211,13 @@ FsData::blocks_state(bool blocks_state) {
 }
 
 bool
-FsData::kreon_keep_md() const {
-    return keep_md_;
+FsData::keep_rootdir() const {
+    return keep_rootdir_;
 }
 
 void
-FsData::kreon_keep_md(bool keep_md) {
-    FsData::keep_md_ = keep_md;
-}
-
-bool
-FsData::kreon_reuse_md() const {
-    return reuse_md_;
-}
-
-void
-FsData::kreon_reuse_md(bool reuse_md) {
-    FsData::reuse_md_ = reuse_md;
+FsData::keep_rootdir(bool keep_rootdir) {
+    FsData::keep_rootdir_ = keep_rootdir;
 }
 
 unsigned long long

src/daemon/daemon.cpp

@@ -409,6 +409,19 @@ destroy_enviroment() {
 
     GKFS_DATA->spdlogger()->info("{}() Closing metadata DB", __func__);
     GKFS_DATA->close_mdb();
+
+
+    // Delete rootdir/metadir if requested
+    if(!GKFS_DATA->keep_rootdir()) {
+        GKFS_DATA->spdlogger()->info("{}() Removing RootDir/MetaDir/MetaFile",
+                                     __func__);
+        fs::remove_all(GKFS_DATA->metadir(), ecode);
+#ifdef GKFS_ENABLE_PARALLAX
+        // some metadata backends uses a file instead of a dir.
+        fs::remove_all(GKFS_DATA->metadir() + "x", ecode);
+#endif
+        fs::remove_all(GKFS_DATA->rootdir(), ecode);
+    }
 }
 
 /**
@@ -558,6 +571,11 @@ parse_input(const cli_options& opts, const CLI::App& desc) {
         fs::remove_all(rootdir_path.native());
         GKFS_DATA->spdlogger()->info("{}() Rootdir cleaned.", __func__);
     }
+
+    if(desc.count("--clean-rootdir-finish")) {
+        GKFS_DATA->keep_rootdir(false);
+    }
+
     GKFS_DATA->spdlogger()->debug("{}() Root directory: '{}'", __func__,
                                   rootdir_path.native());
     fs::create_directories(rootdir_path);
@@ -596,12 +614,6 @@ parse_input(const cli_options& opts, const CLI::App& desc) {
     } else
         GKFS_DATA->dbbackend("rocksdb");
 
-    if(desc.count("--keepmd")) {
-        GKFS_DATA->kreon_keep_md(true);
-    }
-    if(desc.count("--reusemd")) {
-        GKFS_DATA->kreon_reuse_md(true);
-    }
     if(desc.count("--kreonsize")) { // Size in GB
         GKFS_DATA->kreon_size_md(stoi(opts.kreonsize));
     }
@@ -661,16 +673,17 @@ main(int argc, const char* argv[]) {
     desc.add_flag(
                 "--clean-rootdir,-c",
                 "Cleans Rootdir >before< launching the deamon");
+    desc.add_flag(
+                "--clean-rootdir-finish,-f",
+                "Cleans Rootdir >after< the deamon finishes");
     desc.add_option(
                 "--dbbackend,-d", opts.dbbackend,
-                "Database Backend to use. If not set, rocksdb is used. For parallaxdb, a file called rocksdb with 8GB is needed in metadir");
-    desc.add_flag("--keepmd", "Kreondb - Keeps metadir (default off)");
-    desc.add_flag("--reusemd",
-                    "Kreondb - Avoids initializing the metadata file, (default off)");
+                "Database Backend to use. If not set, rocksdb is used. For parallaxdb, a file called rocksdbx with 8GB will be created in metadir");
+   
+   
     desc.add_option("--kreonsize",opts.kreonsize,
-                    "Kreondb - Metatada file size in GB (default 8), "
+                    "parallaxdb - Metatada file size in GB (default 8), "
                     "used only with new files");
-
     desc.add_flag("--version", "Print version and exit.");
     // clang-format on
     try {

tests/integration/harness/gkfs.py

@@ -251,7 +251,9 @@ class Daemon:
                  '--rootdir', self.rootdir,
                  '-l', self._address,
                  '--metadir', self._metadir,
-                 '--dbbackend', self._database ]
+                 '--dbbackend', self._database]
+        if self._database == "parallaxdb" :
+            args.append('--clean-rootdir-finish')
 
         logger.debug(f"spawning daemon")
         logger.debug(f"cmdline: {self._cmd} " + " ".join(map(str, args)))