Prepare to merge back into 'dev_toto'

## [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`

## 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

### 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.

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

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

int adafs_open(const std::string& path, mode_t mode, int flags);

int check_parent_dir(const std::string& path);

int adafs_mk_node(const std::string& path, mode_t mode);

int check_parent_dir(const std::string& path);

#include <sys/types.h>

#include <fcntl.h>

int hook_openat(int dirfd, const char *cpath, int flags, mode_t mode);

int hook_close(int fd);

int hook_stat(const char* path, struct stat* buf);