Updated readme file for current state of our scripts

### Debian/Ubuntu - Dependencies

- Upgrade your gcc to version at least 4.8 to get C++11 support.

- Install gflags. First, try: `sudo apt-get install libgflags-dev` If this doesn't work and you're using Ubuntu, here's a nice tutorial: (http://askubuntu.com/questions/312173/installing-gflags-12-04)

- Install gflags. First, try: `sudo apt-get install libgflags-dev` If this doesn't work and you're using Ubuntu, here's

a nice tutorial: (http://askubuntu.com/questions/312173/installing-gflags-12-04)

- Install snappy. This is usually as easy as: `sudo apt-get install libsnappy-dev`

- Install zlib. Try: `sudo apt-get install zlib1g-dev`

- Install bzip2: `sudo apt-get install libbz2-dev`

    git checkout v2.0

    ./configure && make && sudo make install

```

__Notice:__ Once installed, please add the include path for gflags to your CPATH environment variable and the lib path to LIBRARY_PATH. If installed with default settings, the include path will be /usr/local/include and the lib path will be /usr/local/lib.

__Notice:__ Once installed, please add the include path for gflags to your CPATH environment variable and the lib path

to LIBRARY_PATH. If installed with default settings, the include path will be /usr/local/include and the lib path will

be /usr/local/lib.

- Install snappy:

    `sudo yum install snappy snappy-devel`

- Install zlib:

## Clone and compile direct ADA-FS dependencies

- Go to the subfolder `ifs/scripts` and first clone all dependencies projects. You can choose the according na_plugin (execute the script for help):

- Go to the subfolder `ifs/scripts` and first clone all dependencies projects. You can choose the according na_plugin

(execute the script for help):

```bash

./clone_dep.sh <git_clone_path> <na_layer>

usage: dl_dep.sh [-h] [-n <NAPLUGIN>] [-c <CLUSTER>]

                    source_path

This script gets all ADA-FS dependency sources (excluding the fs itself)

positional arguments:

        source_path              path where the dependency downloads are put

optional arguments:

        -h, --help              shows this help message and exits

        -n <NAPLUGIN>, --na <NAPLUGIN>

                                network layer that is used for communication. Valid: {bmi,cci,ofi,all}

                                defaults to 'all'

        -c <CLUSTER>, --cluster <CLUSTER>

                                additional configurations for specific compute clusters

                                supported clusters: {mogon1,fh2}

```

- Now use the install script to compile them and install them to the desired directory. You can choose the according na_plugin (execute the script for help):

- Now use the install script to compile them and install them to the desired directory. You can choose the according

na_plugin (execute the script for help):

```bash

./compile_dep.sh <git_clone_path> <install_path> <na_layer>

usage: compile_dep.sh [-h] [-n <NAPLUGIN>] [-c <CLUSTER>] [-j <COMPILE_CORES>]

                      source_path install_path

This script compiles all ADA-FS dependencies (excluding the fs itself)

positional arguments:

    source_path 	path to the cloned dependencies path from clone_dep.sh

    install_path    path to the install path of the compiled dependencies

optional arguments:

    -h, --help      shows this help message and exits

    -n <NAPLUGIN>, --na <NAPLUGIN>

                network layer that is used for communication. Valid: {bmi,cci,ofi,all}

                defaults to 'all'

    -c <CLUSTER>, --cluster <CLUSTER>

                additional configurations for specific compute clusters

                supported clusters: {mogon1,mogon2,fh2}

    -j <COMPILE_CORES>, --compilecores <COMPILE_CORES>

                number of cores that are used to compile the depdencies

                defaults to number of available cores

```

## Compile ADA-FS

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.

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.

The following options are available with cmake:

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

- `-DUSE_CCI` for using the cci plugin with Infiniband verbs

- `-DUSE_OFI_VERBS` for using the libfabric plugin with Infiniband verbs

- `-DUSE_OFI_PSM2` for using the libfabric plugin with Intel Omnipath

- `-DUSE_BMI` for using the bmi plugin with the tcp protocol (Stable for TCP/IP)

- `-DUSE_CCI` for using the cci plugin with Infiniband verbs (Stable with Infiniband)

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

- `-DUSE_OFI_PSM2` for using the libfabric plugin with Intel Omni-Path (This plugin is still in development by the

Mercury team but will be used for the Omni-Path fabric.)

In addition you can add a specific directory where all dependencies are located, i.e., headers and libraries. This can

be done by using `-DADAFS_DEPS_INSTALL=<path>`. If the variable is not set this path points to `/usr/local`.

```bash

mkdir build && cd build

cmake -DUSE_{BMI,CCI,OFI_VERBS,OFI_PSM2} ..

cmake -DUSE_{BMI,CCI,OFI_VERBS,OFI_PSM2}:BOOL=ON -DADAFS_DEPS_INSTALL=<path> -DCMAKE_BUILD_TYPE={Release, Debug}} ..

make

```

## Run ADA-FS

First on each node a daemon has to be started: 

First on each node a daemon has to be started. This can be done in two ways using the `adafs_daemon` binary directly or

the corresponding startup and shutdown scripts. The latter is recommended for cluster usage. It requires pssh (or

parallel-ssh) with python2.

### Start and shut down daemon directly

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

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>`

Shut it down by gracefully killing the process.

### Startup and shutdown scripts

The scripts are located in `ifs/scripts/{startup_adafs.py, shutdown_adafs.py}`. Use the -h argument for their usage.

## Miscellaneous

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`

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

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

Please consult `configure.hpp` for log locations and verbosity, etc.

Please consult `configure_public.hpp` for log locations and verbosity, etc. `include/configure.hpp` contains file system

specific configurations normal user should not be needed to modify.