.gitmodules

@@ -28,3 +28,6 @@
 [submodule "external/GSL"]
 	path = external/GSL
 	url = https://github.com/microsoft/GSL
+[submodule "external/pybind11"]
+	path = external/pybind11
+	url = https://github.com/pybind/pybind11.git

CHANGELOG.md

@@ -37,6 +37,7 @@ to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
   - Logging uses a higher FD limit ([!259](https://storage.bsc.es/gitlab/hpc/gekkofs/-/merge_requests/259))
     - Avoid throwing runtime error if the fd is invalid (may happen on destruction)
   - Updated spack for 0.9.4 ([!260](https://storage.bsc.es/gitlab/hpc/gekkofs/-/merge_requests/260))
+  - Updated deps to support GCC-15 ([!262](https://storage.bsc.es/gitlab/hpc/gekkofs/-/merge_requests/262))
   
 ### Fixed
   - Dup3 is supported if O_CLOEXEC is not used (i.e. hexdump) ([!228](https://storage.bsc.es/gitlab/hpc/gekkofs/-/merge_requests/228))

CMake/gkfs-options.cmake

@@ -248,6 +248,13 @@ gkfs_define_option(
     DEFAULT_VALUE ON
 )
 
+#build python bindings
+gkfs_define_option(
+    GKFS_BUILD_PYTHON_BINDINGS
+    HELP_TEXT "Build Python bindings package with pybind11"
+    DEFAULT_VALUE OFF
+)
+
 # use old resolve function
 gkfs_define_option(
     GKFS_USE_LEGACY_PATH_RESOLVE

CMakeLists.txt

@@ -261,6 +261,16 @@ if (GKFS_ENABLE_CLIENT_METRICS)
     )
 endif ()
 
+if (GKFS_BUILD_PYTHON_BINDINGS)
+    ### pybind11: for Python bindings
+    include_from_source(pybind11
+        MESSAGE "[${PROJECT_NAME}] Searching for pybind11"
+        SOURCE_DIR ${GKFS_DEPENDENCIES_PATH}/pybind11
+        GIT_REPOSITORY https://github.com/pybind/pybind11.git
+        GIT_TAG v2.12.0
+    )
+endif ()
+
 ### GSL: Guidelines Support Library
 include_from_source(gsl
 	MESSAGE "[${PROJECT_NAME}] Searching for GSL"

docker/0.9.5/apps/Dockerfile

@@ -58,7 +58,7 @@ COPY --from=builder /usr/local/lib/external /root/wacommplusplus/build/external/
 WORKDIR /root/wacommplusplus/build/example
 RUN mkdir -p input processed output restarts && \
     cd input && \
-    wget -q https://api.meteo.uniparthenope.it/files/rms3/d03/history/2025/01/01/rms3_d03_20250101Z0000.nc && \
+    wget --no-check-certificate -q https://api.meteo.uniparthenope.it/files/rms3/d03/history/2025/01/01/rms3_d03_20250101Z0000.nc && \
     mv rms3_d03_20250101Z0000.nc input.nc && \
     ncks -7 -L 9 --qnt default=1 --ppc default=1 input.nc rms3_d03_20250101Z0000.nc && \
     tar cvzf rms.tar.gz rms3_d03_20250101Z0000.nc && \

docs/sphinx/users/scripts.rst

@@ -24,25 +24,25 @@ on the specifics of the particular GekkoFS build, both scripts rely on
 :code:`configuration profiles` which define a set of related software
 packages which should be downloaded and installed for a specific GekkoFS
 version and/or configuration. To illustrate this, let's take a look at the
-contents of the :code:`default` profile for GekkoFS version :code:`0.9.4`:
+contents of the :code:`default` profile for GekkoFS version :code:`0.9.5`:
 
 .. code-block:: console
 
-    $ dl_dep.sh -l default:0.9.4
-    Configuration profiles for '0.9.4':
+    $ dl_dep.sh -l default:0.9.5
+    Configuration profiles for '0.9.5':
 
-    * default:0.9.4 (/home/user/gekkofs/source/scripts/profiles/0.9.4/default.specs)
+    * default:0.9.5 (/home/user/gekkofs/source/scripts/profiles/0.9.5/default.specs)
 
       All dependencies
 
         lz4: 1.9.3
         capstone: 6.0.0-Alpha1
-        json-c: 0.15-20200726
-        libfabric: HEAD@v1.20.1
-        mercury: v2.4.0
+        json-c: 0.17-20230812
+        libfabric: HEAD@v2.2.0
+        mercury: v2.4.1rc1
         argobots: 1.2
         margo: v0.18.3
-        rocksdb: 8.10.0
+        rocksdb: 10.4.2
         syscall_intercept: d8b2a69961921ed123625c79a609331fc56a8931
 
 
@@ -58,10 +58,10 @@ supercomputer) followed by an optional :code:`VERSION_TAG`.
 
 .. code-block:: console
 
-    $ ./dl_dep.sh -p default:0.9.4 /home/user/gfks/deps
+    $ ./dl_dep.sh -p default:0.9.5 /home/user/gfks/deps
     Destination path is set to  "/tmp/foo"
     Profile name: default
-    Profile version: 0.9.4
+    Profile version: 0.9.5
     ------------------------------------
     Downloaded 'https://github.com/lz4/lz4/archive/v1.9.4.tar.gz' to 'lz4'
     Downloaded 'https://github.com/json-c/json-c/archive/json-c-0.17-20230812.tar.gz' to 'json-c'
@@ -80,10 +80,10 @@ option. In this case, dependency names follow the
 
 .. code-block:: console
 
-   $ ./dl_dep.sh -d mercury@default:0.9.4 /home/user/gfks/deps
+   $ ./dl_dep.sh -d mercury@default:0.9.5 /home/user/gfks/deps
    Destination path is set to  "/tmp/foo"
    Profile name: default
-   Profile version: 0.9.3
+   Profile version: 0.9.5
    ------------------------------------
    Cloned 'https://github.com/mercury-hpc/mercury' to 'mercury' with commit '[v2.4.0]' and flags '--recurse-submodules'
    Done
@@ -105,12 +105,12 @@ certain directory (e.g. :code:`/home/user/gkfs/deps`), the
 
 .. code-block:: console
 
-    $ ./compile_dep.sh -p default:0.9.4 /home/user/gkfs/deps /home/user/gkfs/install -j8
+    $ ./compile_dep.sh -p default:0.9.5 /home/user/gkfs/deps /home/user/gkfs/install -j8
     CORES = 8 (default)
     Sources download path = /tmp/foo
     Installation path = /tmp/bar
     Profile name: default
-    Profile version: 0.9.4
+    Profile version: 0.9.5
     ------------------------------------
     ######## Installing:  lz4 ###############################
     ...

examples/user_library/gkfs_python_lib_example.py

+import gkfs_python as gk
+import os
+import stat as st
+
+def main():
+    gk.init()
+
+    path = "/testfile"
+    path_create_delete = "/testfile2"
+    symlink_path = "/test_symlink"
+    renamed_path = "/testfile_renamed"
+
+    fd = gk.create(path_create_delete, 0o644)
+    print(f"Created file: {path_create_delete}, fd={fd}")
+    gk.remove(path_create_delete)
+    print(f"Deleted file: {path_create_delete}, fd={fd}")
+
+    fd = gk.create(path, 0o644)
+    fd = gk.open(path, os.O_CREAT | os.O_RDWR, st.S_IRUSR | st.S_IWUSR)
+    print(f"Open file: {path}, fd={fd}")
+
+    print(gk.get_file_list("/"))
+
+    gk.write(fd, b"Test GekkoFS!")
+    print(f"write success")
+
+    gk.lseek(fd, 0, os.SEEK_SET)
+    print(f"lseek success")
+
+    data = gk.read(fd, 16)
+    print(f"Read data: {data}")
+
+    gk.pwrite(fd, b"Hello", 0)
+    print(f"pwrite success")
+
+    gk.lseek(fd, 0, os.SEEK_SET)
+    data = gk.read(fd, 16)
+    print(f"Read data: {data}")
+
+    read_data = gk.pread(fd, 5, 5)
+    print(f"Pread data: {read_data}")
+
+    gk.lseek(fd, 0, os.SEEK_SET)
+    # TODO
+    #gk.writev(fd, [b"ABC", b"DEF"])
+
+    data_readv = gk.readv(fd, 2)
+    print(f"Readv data: {data_readv}")
+
+    # TODO
+    #gk.pwritev(fd, [b"ghi", b"jkl"], 3)
+
+    data_preadv = gk.preadv(fd, 2, 0)
+    print(f"Preadv data: {data_preadv}")
+
+    dup_fd = gk.dup(fd)
+    dup2_fd = gk.dup2(fd, dup_fd + 1)
+    print(f"Duplicated fds: {dup_fd}, {dup2_fd}")
+
+    gk.fsync(fd)
+
+    res, stat = gk.stat(path, True, False)
+    print(f"Stat result: {stat}")
+
+    res, statx = gk.statx(-1, path, 0, 0xFFF, True)
+    print(f"Statx result: {statx}")
+
+    accessible = gk.access(path, os.R_OK | os.W_OK)
+    print(f"Access check (R_OK|W_OK): {accessible}")
+
+    file_list = gk.get_file_list("/")
+    print(f"File list: {file_list}")
+
+    gk.close(fd)
+    gk.close(dup_fd)
+    gk.close(dup2_fd)
+
+    gk.truncate(path, 5)
+
+    addr = gk.mmap(0, 4096, 1 | 2, 2, gk.open(path, os.O_RDWR, 0), 0)
+    gk.msync(addr, 4096, 0)
+    gk.munmap(addr, 4096)
+    print("mmap/msync/munmap done")
+
+    # Symlink if available
+    try:
+        gk.mk_symlink(path, symlink_path)
+        target = gk.readlink(symlink_path, 1024)
+        print(f"Symlink points to: {target}")
+    except Exception:
+        print("Symlink not supported or failed.")
+
+    # Rename if available
+    try:
+        gk.rename(path, renamed_path)
+        print(f"Renamed {path} to {renamed_path}")
+    except Exception:
+        print("Rename not supported or failed.")
+
+    file_list = gk.get_file_list("/")
+    print(f"File list: {file_list}")
+
+    gk.remove(renamed_path)
+    print(f"Removed {renamed_path}")
+
+    file_list = gk.get_file_list("/")
+    print(f"File list: {file_list}")
+
+    gk.end()
+
+if __name__ == "__main__":
+    main()
+

pybind11 @ 4dc4aca2

+Subproject commit 4dc4aca2e120180e6bb48c076986feff41b4f5fb

include/client/syscalls/args.hpp

@@ -460,7 +460,7 @@ format_clone_flags_arg_to(FmtBuffer& buffer, const printable_arg& parg) {
 template <typename FmtBuffer>
 inline void
 format_clone3_args_arg_to(FmtBuffer& buffer, const printable_arg& parg) {
-
+#ifdef SYS_clone3
     //  struct clone_args {
     //            u64 flags;        /* Flags bit mask */
     //            u64 pidfd;        /* Where to store PID file descriptor
@@ -529,7 +529,7 @@ format_clone3_args_arg_to(FmtBuffer& buffer, const printable_arg& parg) {
     // set_tid size and cgroup
     fmt::format_to(std::back_inserter(buffer), ",{}={}", "set_tid_size", ca->set_tid_size);
     fmt::format_to(std::back_inserter(buffer), ",{}={}", "cgroup", ca->cgroup);
-    
+#endif
     return;      
 
 

scripts/profiles/0.9.5/agios.specs

@@ -40,14 +40,14 @@ wgetdeps=(
     ["lz4"]="1.9.4"
     ["capstone"]="6.0.0-Alpha1"
     ["argobots"]="1.2"
-    ["rocksdb"]="8.10.0"
+    ["rocksdb"]="10.4.2"
     ["json-c"]="0.17-20230812"
 )
 
 # Dependencies that must be cloned
 clonedeps=(
-    ["libfabric"]="HEAD@v1.20.1"
-    ["mercury"]="v2.4.0"
+    ["libfabric"]="HEAD@v2.2.0"
+    ["mercury"]="v2.4.1rc1"
     ["margo"]="v0.18.3"
     ["syscall_intercept"]="d8b2a69961921ed123625c79a609331fc56a8931"
     ["agios"]="c26a6544200f823ebb8f890dd94e653d148bf226@development"

scripts/profiles/0.9.5/ci.specs

@@ -38,15 +38,15 @@ comment="Dependencies required by the CI"
 # Dependencies that must be downloaded directly
 wgetdeps=(
     ["argobots"]="1.2"
-    ["rocksdb"]="8.10.0"
+    ["rocksdb"]="10.4.2"
     ["prometheus-cpp"]="v1.0.0"
     ["capstone"]="6.0.0-Alpha1"
     )
 
 # Dependencies that must be cloned
 clonedeps=(
-    ["libfabric"]="HEAD@v1.20.1"
-    ["mercury"]="v2.4.0"
+    ["libfabric"]="HEAD@v2.2.0"
+    ["mercury"]="v2.4.1rc1"
     ["margo"]="v0.18.3"
     ["syscall_intercept"]="d8b2a69961921ed123625c79a609331fc56a8931"
     ["agios"]="c26a6544200f823ebb8f890dd94e653d148bf226@development"

scripts/profiles/0.9.5/default.specs

@@ -40,14 +40,14 @@ wgetdeps=(
     ["lz4"]="1.9.4"
     ["capstone"]="6.0.0-Alpha1"
     ["argobots"]="1.2"
-    ["rocksdb"]="8.10.0"
+    ["rocksdb"]="10.4.2"
     ["json-c"]="0.17-20230812"
 )
 
 # Dependencies that must be cloned.
 clonedeps=(
-    ["libfabric"]="HEAD@v1.20.1"
-    ["mercury"]="v2.4.0"
+    ["libfabric"]="HEAD@v2.2.0"
+    ["mercury"]="v2.4.1rc1"
     ["margo"]="v0.18.3"
     ["syscall_intercept"]="d8b2a69961921ed123625c79a609331fc56a8931"
 )

scripts/profiles/0.9.5/default_zmq.specs

@@ -40,7 +40,7 @@ wgetdeps=(
     ["lz4"]="1.9.4"
     ["capstone"]="6.0.0-Alpha1"
     ["argobots"]="1.2"
-    ["rocksdb"]="8.10.0"
+    ["rocksdb"]="10.4.2"
     ["json-c"]="0.17-20230812"
     ["libzmq"]="4.3.5"
     ["cppzmq"]="4.10.0"
@@ -48,8 +48,8 @@ wgetdeps=(
 
 # Dependencies that must be cloned.
 clonedeps=(
-    ["libfabric"]="HEAD@v1.20.1"
-    ["mercury"]="v2.4.0"
+    ["libfabric"]="HEAD@v2.2.0"
+    ["mercury"]="v2.4.1rc1"
     ["margo"]="v0.18.3"
     ["syscall_intercept"]="d8b2a69961921ed123625c79a609331fc56a8931"
 )

scripts/profiles/0.9.5/infiniband_verbs.specs

@@ -40,14 +40,14 @@ wgetdeps=(
     ["lz4"]="1.9.4"
     ["capstone"]="6.0.0-Alpha1"
     ["argobots"]="1.2"
-    ["rocksdb"]="8.10.0"
+    ["rocksdb"]="10.4.2"
     ["json-c"]="0.17-20230812"
 )
 
 # Dependencies that must be cloned
 clonedeps=(
-    ["libfabric%verbs"]="HEAD@v1.20.1"
-    ["mercury"]="v2.4.0"
+    ["libfabric%verbs"]="HEAD@v2.2.0"
+    ["mercury"]="v2.4.1rc1"
     ["margo"]="v0.18.3"
     ["syscall_intercept"]="d8b2a69961921ed123625c79a609331fc56a8931"
 )

scripts/profiles/0.9.5/install/json-c.install

@@ -47,7 +47,7 @@ pkg_install() {
     CURR="${SOURCE_DIR}/json-c"
     prepare_build_dir "${CURR}"
     cd "${CURR}/build"
-    cmake -DCMAKE_INSTALL_PREFIX="${INSTALL_DIR}" -DCMAKE_BUILD_TYPE:STRING=Release ..
+    cmake -DCMAKE_INSTALL_PREFIX="${INSTALL_DIR}" -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ..
     make -j"${CORES}" install
     # Margo doesn't search in both directories, so we make it available in both lib and lib64
     if [[ -f "${INSTALL_DIR}/lib64/pkgconfig/json-c.pc" ]]; then

scripts/profiles/0.9.5/install/mercury.install

@@ -62,7 +62,7 @@ pkg_install() {
     CURR="${SOURCE_DIR}/${ID}"
     prepare_build_dir "${CURR}"
     cd "${CURR}/build"
-    PKG_CONFIG_PATH="${INSTALL_DIR}/lib/pkgconfig" $CMAKE \
+    $CMAKE \
         -DCMAKE_PREFIX_PATH=${INSTALL_DIR} \
         -DCMAKE_BUILD_TYPE:STRING=Release \
         -DBUILD_TESTING:BOOL=ON \

scripts/profiles/0.9.5/install/syscall_intercept.install

@@ -61,7 +61,7 @@ pkg_install() {
     -DCMAKE_BUILD_TYPE:STRING=Debug \
     -DBUILD_EXAMPLES:BOOL=OFF \
     -DSTATIC_CAPSTONE:BOOL=OFF \
-    -DBUILD_TESTS:BOOK=OFF ..
+    -DBUILD_TESTS:BOOK=OFF -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ..
     make -j"${CORES}" install
     if [[ ${EXTRA_INSTALL_ARGS} == "ARM64" ]]; then
         cp "${CURR}"/arch/aarch64/include/libsyscall_intercept_hook_point.h ${INSTALL_DIR}/include

scripts/profiles/0.9.5/mogon2.specs

@@ -39,17 +39,17 @@ comment="Dependencies for Mogon 2 supercomputer"
 wgetdeps=(
     ["lz4"]="1.9.4"
     ["capstone"]="6.0.0-Alpha1"
-    ["argobots"]="1.1"
-    ["rocksdb"]="8.10.0"
+    ["argobots"]="1.2"
+    ["rocksdb"]="10.4.2"
     ["psm2"]="11.2.185"
     ["json-c"]="0.17-20230812"
 )
 
 # Dependencies that must be cloned
 clonedeps=(
-    ["libfabric"]="HEAD@v1.20.1"
-    ["mercury"]="v2.3.1"
-    ["margo"]="v0.15.0"
+    ["libfabric"]="HEAD@v2.2.0"
+    ["mercury"]="v2.4.1rc1"
+    ["margo"]="v0.18.3"
     ["syscall_intercept"]="d8b2a69961921ed123625c79a609331fc56a8931"
     ["date"]="e7e1482087f58913b80a20b04d5c58d9d6d90155"
 )

scripts/profiles/0.9.5/mogon3.specs

@@ -40,7 +40,7 @@ wgetdeps=(
     ["lz4"]="1.9.4"
     ["capstone"]="6.0.0-Alpha1"
     ["argobots"]="1.2"
-    ["rocksdb"]="8.10.0"
+    ["rocksdb"]="10.4.2"
     ["json-c"]="0.17-20230812"
     ["libzmq"]="4.3.5"
     ["cppzmq"]="4.10.0"
@@ -49,7 +49,7 @@ wgetdeps=(
 # Dependencies that must be cloned
 clonedeps=(
 #    ["libfabric"]="HEAD@v1.20.1"
-    ["mercury"]="v2.4.0"
+    ["mercury"]="v2.4.1rc1"
     ["margo"]="v0.18.3"
     ["syscall_intercept"]="d8b2a69961921ed123625c79a609331fc56a8931"
 )

scripts/profiles/0.9.5/ngio.specs

@@ -40,15 +40,15 @@ wgetdeps=(
     ["lz4"]="1.9.4"
     ["capstone"]="6.0.0-Alpha1"
     ["argobots"]="1.2"
-    ["rocksdb"]="8.10.0"
+    ["rocksdb"]="10.4.2"
     ["json-c"]="0.17-20230812"
     ["psm2"]="11.2.185"
 )
 
 # Dependencies that must be cloned
 clonedeps=(
-    ["libfabric"]="HEAD@v1.20.1"
-    ["mercury"]="v2.4.0"
+    ["libfabric"]="HEAD@v2.2.0"
+    ["mercury"]="v2.4.1rc1"
     ["margo"]="v0.18.3"
     ["syscall_intercept"]="d8b2a69961921ed123625c79a609331fc56a8931"
     ["date"]="e7e1482087f58913b80a20b04d5c58d9d6d90155"