Commit c59cc079 authored by Ramon Nou's avatar Ramon Nou
Browse files

Updated to last 32-xxx version

parents 10076d45 006c7d4e

.gitmodules

+3 −0
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[submodule "external/hermes"]

	path = external/hermes

	url = https://github.com/bsc-ssrg/hermes.git

[submodule "external/fmt"]

	path = external/fmt

	url = https://github.com/fmtlib/fmt

CHANGELOG.md

+27 −1
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@@ -6,6 +6,32 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 


## [Unreleased]



## [0.6.2] - 2019-10-07

## Added

 - Paths inside kernel pseudo filesystems (`/sys`, `/proc`) are forwarded directly to the kernel and internal path resolution will be skipped. Be aware that also paths  like  `/sys/../tmp/gkfs_mountpoint/asd` will be forwarded to the kernel

 - Added new Cmake flag `CREATE_CHECK_PARENTS` to controls if the existance of the parent node needs to be checked during the creation of a child node.

## Changed

 - Daemon logs for RPC handlers have been polished

 - Updated Margo, Mercury and Libfabric dependencies

## Fixed

 - mk_node RPC wasn't propagating errors correctly from daemons

 - README has been improoved and got some minor fixes

 - fix wrong path in log call for mk_symlink function



## [0.6.1] - 2019-09-17

## Added

 - Added new Cmake flag `LOG_SYSCALLS` to enable/disable syscall logging.

 - Intercept the 64 bit version of `getdents`.

 - Added debian-based docker image.

## Changed

 - Disable syscalls logging by default

 - Update Mercury, RocksDB and Libfabric dependencies

## Fixed

 - Fix read at the end of file.

 - Don't create log file when using `--version`/`--help` cli flags.

 - On some systems LD_PRELOAD used on /bin/bash binary was not working.

 - Missing definition of `loff_t` on new version of GCC.



## [0.6.0] - 2019-07-26

## Added

- Add compile time option to disable shared memory communication `-DUSE_SHM:BOOL=OFF`

CMakeLists.txt

+31 −27
Original line number Diff line number Diff line
@@ -22,12 +22,12 @@ if (NOT CMAKE_BUILD_TYPE) 
    set(CMAKE_BUILD_TYPE Release

            CACHE STRING "Choose the type of build: Debug Release Memcheck" FORCE)

ENDIF (NOT CMAKE_BUILD_TYPE)

message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")

message(STATUS "[gekkofs] Build type: ${CMAKE_BUILD_TYPE}")



# Compiler flags for various cmake build types

set(WARNINGS_FLAGS "-Wall -Wextra --pedantic -Wno-unused-parameter -Wno-missing-field-initializers")

set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -DNDEBUG -O3")

set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} ${WARNINGS_FLAGS} -g -O0 -DGKFS_DEBUG_BUILD")

set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} ${WARNINGS_FLAGS} -g -O0 -DGKFS_DEBUG_BUILD -DHERMES_DEBUG_BUILD")

set(CMAKE_CXX_FLAGS_MEMCHECK "${WARNINGS_FLAGS} -g -O0 -fsanitize=address -fno-omit-frame-pointer")

set(CMAKE_CXX_FLAGS_MAINTAINER "${WARNINGS_FLAGS} -g -O0 -pg -no-pie")

set(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} -DNDEBUG -O3")
@@ -64,7 +64,7 @@ if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git) 
        endif()

    endif()

endif()

message(STATUS "Project version: ${PROJECT_VERSION}")

message(STATUS "[gekkofs] Project version: ${PROJECT_VERSION}")

set(GKFS_VERSION_MAJOR ${PROJECT_VERSION_MAJOR})

set(GKFS_VERSION_MINOR ${PROJECT_VERSION_MINOR})

set(GKFS_VERSION_PATCH ${PROJECT_VERSION_PATCH})
@@ -100,27 +100,31 @@ find_package(Threads REQUIRED) 


find_package(Date REQUIRED)



set(RPC_PROTOCOL "ofi+tcp" CACHE STRING "Communication plugin used for RPCs")

set(RPC_PROTOCOL "ofi+sockets" CACHE STRING "Communication plugin used for RPCs")

set_property(CACHE RPC_PROTOCOL PROPERTY STRINGS

   "bmi+tcp"

   "ofi+sockets"

   "ofi+tcp"

   "ofi+verbs"

   "ofi+psm2"

)

message(STATUS "RPC protocol: '${RPC_PROTOCOL}'")

message(STATUS "[gekkofs] RPC protocol: '${RPC_PROTOCOL}'")



option(USE_SHM "Use shared memory for intra-node communication" ON)

message(STATUS "Shared-memory communication: ${USE_SHM}")

option(USE_SHM "Use shared memory for intra-node communication" OFF)

message(STATUS "[gekkofs] Shared-memory communication: ${USE_SHM}")



option(CREATE_CHECK_PARENTS "Check parent directory existance before creating child node" ON)

message(STATUS "Create checks parents: ${CREATE_CHECK_PARENTS}")



option(SYMLINK_SUPPORT "Compile with support for symlinks" ON)

if(SYMLINK_SUPPORT)

    add_definitions(-DHAS_SYMLINKS)

endif()

message(STATUS "Symlink support: ${SYMLINK_SUPPORT}")

message(STATUS "[gekkofs] Symlink support: ${SYMLINK_SUPPORT}")



set(MAX_INTERNAL_FDS 256 CACHE STRING "Number of file descriptors reserved for internal use")

add_definitions(-DMAX_INTERNAL_FDS=${MAX_INTERNAL_FDS})

message(STATUS "File descriptors reserved for internal use: ${MAX_INTERNAL_FDS}")

message(STATUS "[gekkofs] File descriptors reserved for internal use: ${MAX_INTERNAL_FDS}")



execute_process(COMMAND getconf OPEN_MAX

                OUTPUT_VARIABLE GETCONF_MAX_FDS
@@ -133,13 +137,14 @@ add_definitions(-DMAX_OPEN_FDS=${GETCONF_MAX_FDS}) 


option(ENABLE_CLIENT_LOG "Enable logging messages" ON)

if(ENABLE_CLIENT_LOG)

    add_definitions(-DGKFS_ENABLE_LOGGING)

endif()

message(STATUS "[gekkofs] Client logging output: ${ENABLE_CLIENT_LOG}")



set(CLIENT_LOG_MESSAGE_SIZE 1024 CACHE STRING "Maximum size of a log message in the client library")

add_definitions(-DLIBGKFS_LOG_MESSAGE_SIZE=${CLIENT_LOG_MESSAGE_SIZE})

    message(STATUS "Maximum log message size in the client library: ${CLIENT_LOG_MESSAGE_SIZE}")

else()

    add_definitions(-DGKFS_DISABLE_LOGGING)

endif()

message(STATUS "Client logging output: ${ENABLE_CLIENT_LOGGING}")

message(STATUS "[gekkofs] Maximum log message size in the client library: ${CLIENT_LOG_MESSAGE_SIZE}")

mark_as_advanced(CLIENT_LOG_MESSAGE_SIZE)



configure_file(include/global/configure.hpp.in include/global/configure.hpp)
@@ -175,19 +180,18 @@ set_target_properties(spdlog 
    INTERFACE_INCLUDE_DIRECTORIES "${CMAKE_SOURCE_DIR}/external"

)



add_library(fmt INTERFACE)

# we cannot use target_include_directories with CMake < 3.11

set_target_properties(fmt

    PROPERTIES

    INTERFACE_INCLUDE_DIRECTORIES "${CMAKE_SOURCE_DIR}/external/spdlog"

)

add_subdirectory(external/fmt)

set_property(TARGET fmt PROPERTY POSITION_INDEPENDENT_CODE ON)



add_library(hermes INTERFACE)

# we cannot use target_include_directories with CMake < 3.11

set_target_properties(hermes

    PROPERTIES

    INTERFACE_INCLUDE_DIRECTORIES "${CMAKE_SOURCE_DIR}/external/hermes/include"

)

if(ENABLE_CLIENT_LOG)

    option(HERMES_LOGGING "" ON)

    option(HERMES_LOGGING_FMT_USE_BUNDLED "" OFF)

    option(HERMES_LOGGING_FMT_HEADER_ONLY "" OFF)

endif()



option(HERMES_MARGO_COMPATIBLE_RPCS "" ON)

add_subdirectory(external/hermes)

target_compile_definitions(hermes INTERFACE)



set(INCLUDE_DIR "${CMAKE_SOURCE_DIR}/include")

README.md

+6 −4
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@@ -102,15 +102,17 @@ optional arguments: 


## Compile GekkoFS

You need to decide what Mercury NA plugin you want to use. The following NA plugins are available, although only BMI is considered stable at the moment.

 - `ofi+tcp` for using the libfabric plugin with TCP

 - `ofi+sockets` for using the libfabric plugin with TCP

 - `ofi+tcp` for using the libfabric plugin with TCP (new version)

 - `ofi+verbs` for using the libfabric plugin with Infiniband verbs (not threadsafe. Do not use.)

 - `ofi+psm2` for using the libfabric plugin with Intel Omni-Path

 - `bmi+tcp` for using the bmi plugin with the tcp protocol 



```bash

mkdir build && cd build

cmake -DCMAKE_BUILD_TYPE=Release ..

cmake -DCMAKE_BUILD_TYPE=Release -DRPC_PROTOCOL='ofi+sockets' ..

make

make install

```



## Run GekkoFS
@@ -121,7 +123,7 @@ parallel-ssh) with python2. 


### Start and shut down daemon directly



`./build/bin/gkfs_daemon -r <fs_data_path> -m <pseudo_mount_dir_path> --hosts <hosts_comma_separated>`

`./build/bin/gkfs_daemon -r <fs_data_path> -m <pseudo_mount_dir_path>`

 

Shut it down by gracefully killing the process.
@@ -134,7 +136,7 @@ The scripts are located in `scripts/{startup_gkfs.py, shutdown_gkfs.py}`. Use th 
Metadata and actual data will be stored at the `<fs_data_path>`. The path where the application works on is set with

`<pseudo_mount_dir_path>`

 

Run the application with the preload library: `LD_PRELOAD=<path>/build/lib/libiointer.so ./application`. In the case of

Run the application with the preload library: `LD_PRELOAD=<path>/build/lib/libgkfs_intercept.so ./application`. In the case of

an MPI application use the `{mpirun, mpiexec} -x` argument.

 

### Logging

docker/debian_build_env.docker

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FROM debian:stable-slim



LABEL Description="This is a debian based environment to build GekkoFS"



ENV GKFS_PATH	/opt/gkfs



ENV SCRIPTS_PATH	${GKFS_PATH}/scripts

ENV DEPS_SRC_PATH	${GKFS_PATH}/deps_src

ENV INSTALL_PATH	${GKFS_PATH}/build_deps



RUN apt-get update && apt-get install -y --no-install-recommends \

		git \

		curl \

		ca-certificates \

		libtool \

		pkg-config \

		make \

		automake \

		cmake \

		gcc \

		g++ \

		# Mercury dependencies

		libltdl-dev \

		lbzip2 \

		# RocksDB

		libsnappy-dev \

		liblz4-dev \

		libzstd-dev \

		libbz2-dev \

		zlib1g-dev \

		# syscall_intercept dependencies

		libcapstone-dev \

		# GekkoFS

		libboost-filesystem-dev \

		libboost-program-options-dev \

		valgrind \

		uuid-dev \

# Clean apt cache to reduce image layer size

&& rm -rf /var/lib/apt/lists/*



# Download dependencies source

COPY scripts/dl_dep.sh		$SCRIPTS_PATH/

RUN /bin/bash $SCRIPTS_PATH/dl_dep.sh $DEPS_SRC_PATH all



# Compile dependencies

COPY scripts/compile_dep.sh $SCRIPTS_PATH/

COPY scripts/patches        $SCRIPTS_PATH/patches

RUN /bin/bash $SCRIPTS_PATH/compile_dep.sh $DEPS_SRC_PATH $INSTALL_PATH