Resolve "Support Spack and others"

- `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.

- :code:`PARALLAX` There are two different metadata backends in GekkoFS. The default one uses :code:`rocksdb`, however

an alternative based on :code:`PARALLAX` from :code:`FORTH` is available. To enable it, use the

:code:`-DGKFS_ENABLE_PARALLAX:BOOL=ON` option, you can also disable :code:`rocksdb` with

:code:`-DGKFS_ENABLE_ROCKSDB:BOOL=OFF`. Once it is enabled, :code:`--dbbackend` option will be functional.

.. _step_by_step_installation:

- GekkoFS daemon (server): :code:`${GKFS_INSTALL_PATH}/bin/gkfs_daemon`

- GekkoFS client interception library: :code:`${GKFS_INSTALL_PATH}/lib/libgkfs_intercept.so`

Install GekkoFS via Spack (alternative)

---------------------

Spack is a package manager for supercomputers and Linux. It makes it easy to install scientific software for regular

users. Spack is another method to install GekkoFS where Spack handles all the dependencies and setting up the environment.

Install Spack

=========================

First, install Spack. You can find the instructions here: https://spack.readthedocs.io/en/latest/getting_started.html

    .. code-block:: console

        git clone https://github.com/spack/spack.git

        . spack/share/spack/setup-env.sh

.. attention::

    Note that the second line needs to be executed every time you open a new terminal. It sets up the environment for Spack

and the corresponding environment variables, e.g., $PATH.

Install GekkoFS with Spack

=========================

To install GekkoFS with Spack, the GekkoFS repository needs to be added to Spack as it is not part of the official Spack

repository.

    .. code-block:: console

        spack repo add gekkofs/scripts/spack

When added, the GekkoFS package is available. Its installation variants and options can be checked via:

    .. code-block:: console

        spack info gekkofs

Then install GekkoFS with Spack:

    .. code-block:: console

        spack install gekkofs

        # for installing tests dependencies and running tests

        spack install -v --test=root gekkofs

Finally, GekkoFS is loaded into the currently used environment:

    .. code-block:: console

        spack load gekkofs

This installs the latest release version including its required Git submodules. The installation directory is

:code:`$SPACK_ROOT/opt/spack/linux-<arch>/<compiler>/<version>/gekkofs-<version>`. The GekkoFS daemon (:code:`gkfs_daemon`) is

located in the :code:`bin` directory and the GekkoFS client (:code:`libgkfs_intercept.so`) is located in the :code:`lib` directory.

Note that loading the environment adds the GekkoFS daemon to the `$PATH` environment variable. Therefore, the GekkoFS

daemon is started by running :code:`gkfs_daemon`. Loading GekkoFS in Spack further provides the :code:`$GKFS_CLIENT` environment

variable pointing to the interception library.

Therefore, the following commands can be run to use GekkoFS:

        .. code-block:: console

            # Consult `-h` or the Readme for further options

            gkfs_daemon -r /tmp/gkfs_rootdir -m /tmp/gkfs_mountdir &

            LD_PRELOAD=$GKFS_CLIENT ls -l /tmp/gkfs_mountdir

            LD_PRELOAD=$GKFS_CLIENT touch /tmp/gkfs_mountdir/foo

            LD_PRELOAD=$GKFS_CLIENT ls -l /tmp/gkfs_mountdir

When done using GekkoFS, unload it from the environment:

    .. code-block:: console

        spack unload gekkofs

Miscellaneous

=========================

Use GekkoFS's latest version (master branch) with Spack:

        .. code-block:: console

            spack install gekkofs@latest

Use a specific compiler on your system, e.g., gcc-11.2.0:

        .. code-block:: console

            spack install gekkofs@latest%gcc@11.2.0

 No newline at end of file

# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other

# Spack Project Developers. See the top-level COPYRIGHT file for details.

#

# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack import *

class Agios(CMakePackage):

    """AGIOS: an I/O request scheduling library at file level."""

    homepage = "https://github.com/francielizanon/agios"

    url      = "https://github.com/jeanbez/agios/archive/refs/tags/v1.0.tar.gz"

    git      = "https://github.com/francielizanon/agios.git"

    version('latest', branch='development')

    version('1.0', sha256='e8383a6ab0180ae8ba9bb2deb1c65d90c00583c3d6e77c70c415de8a98534efd')

    depends_on('libconfig')

# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other

# Spack Project Developers. See the top-level COPYRIGHT file for details.

#

# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack import *

class Bmi(AutotoolsPackage):

    """FIXME: Put a proper description of your package here."""

    homepage = 'https://github.com/radix-io/bmi/'

    git = 'https://github.com/radix-io/bmi.git'

    maintainers = ['carns', 'jeanbez']

    version('main', branch='main')

    depends_on('autoconf', type='build')

    depends_on('automake', type='build')

    # need to override 'autoreconf' so we can run BMI's 'prepare' script

    def autoreconf(self, spec, prefix):

        Executable('./prepare')()

    def configure_args(self):

        args = [

            '--enable-shared',

            '--enable-bmi-only',

            '--disable-static',

            '--disable-karma',

            '--enable-fast',

            '--disable-strict'

        ]

        return args

--- a/CMake/FindDate.cmake	2021-07-04 23:47:33.784047611 -0700

+++ b/CMake/FindDate.cmake	2021-07-04 23:54:14.063139808 -0700

@@ -35,7 +35,7 @@

 )

 find_library(TZ_LIBRARY

-    NAMES tz

+    NAMES date-tz

 )

 include(FindPackageHandleStandardArgs)

# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other

# Spack Project Developers. See the top-level COPYRIGHT file for details.

#

# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack import *

# for Clion. Comment out when using spack

# from spack.build_systems.cmake import *

# from spack.directives import *

# from spack.multimethod import when

# from spack.util.executable import which

# from spack.package import PackageBase

class Gekkofs(CMakePackage):

    """GekkoFS is a distributed burst buffer file system in user space. It is capable of aggregating the local I/O

    capacity and performance of each compute node in a HPC cluster to produce a high-performance storage space that

    can be accessed in a distributed manner. This storage space allows HPC applications and simulations to run in

    isolation from each other with regards to I/O, which reduces interferences and improves performance."""

    homepage = "https://storage.bsc.es/gitlab/hpc/gekkofs"

    git = "https://storage.bsc.es/gitlab/hpc/gekkofs.git"

    url = "https://storage.bsc.es/projects/gekkofs/releases/gekkofs-v0.9.1.tar.gz"

    maintainers = ['marc_vef', 'ramon_nou']

    # set various versions

    version('latest', branch='master', submodules=True)

    version('0.9.0', sha256='f6f7ec9735417d71d68553b6a4832e2c23f3e406d8d14ffb293855b8aeec4c3a', deprecated=True)

    version('0.9.1', sha256='1772b8a9d4777eca895f88cea6a1b4db2fda62e382ec9f73508e38e9d205d5f7')

    # apply patches

    patch('date-tz.patch')

    # set arguments

    variant('build_type',

            default='Release',

            description='CMake build type',

            values=('Debug', 'Release', 'RelWithDebInfo')

            )

    variant('forwarding', default=False, description='Enables the GekkoFS I/O forwarding mode.')

    variant('agios', default=False, description='Enables the AGIOS scheduler for the forwarding mode.')

    variant('guided_distributor', default=False, description='Enables the guided distributor.')

    variant('prometheus', default=False, description='Enables Prometheus support for statistics.')

    variant('parallax', default=False, description='Enables Parallax key-value database.', when='latest')

    variant('rename', default=False, description='Enables experimental rename support.', when='latest')

    variant('dedicated_psm2', default=False, description='Use dedicated _non-system_ opa-psm2 version 11.2.185.')

    variant('compile', default='x86', multi=False, values=('x86', 'powerpc', 'arm'),

            description='Architecture to compile syscall intercept.')

    # general dependencies

    depends_on('cmake@3.6.0:', type='build')

    depends_on('lz4')

    depends_on('argobots')

    depends_on('syscall-intercept@arm', when='compile=arm')

    depends_on('syscall-intercept@powerpc', when='compile=powerpc')

    depends_on('syscall-intercept@x86', when='compile=x86')

    depends_on('date cxxstd=14 +shared +tz tzdb=system')

    depends_on('opa-psm2@11.2.185', when='+dedicated_psm2')

    # 0.9.0 specific

    depends_on('libfabric@1.13.2', when='@0.9:,latest')

    depends_on('mercury@2.1.0 -debug +ofi -mpi -bmi +sm +shared +boostsys -checksum', when='@0.9:,latest')

    depends_on('mochi-margo@0.9.6', when='@0.9:,latest')

    depends_on('rocksdb@6.20.3 -shared +static +lz4 -snappy -zlib -zstd -bz2 +rtti', when='@0.9.0')

    # 0.9.1 specific

    depends_on('rocksdb@6.26.1 -shared +static +lz4 -snappy -zlib -zstd -bz2 +rtti', when='@0.9.1:,latest')

    # Additional features

    # Agios I/O forwarding

    depends_on('agios@1.0', when='@0.8: +agios')

    depends_on('agios@latest', when='@master +agios')

    # Prometheus CPP

    depends_on('prometheus-cpp', when='@0.9:,latest +prometheus')

    depends_on('parallax', when='@0.9:,latest +parallax')

    # known incompatbilities

    conflicts('%gcc@11:', when='@:0.9.1')

    def cmake_args(self):

        """Set up GekkoFS CMake arguments"""

        args = [

            self.define('CMAKE_INSTALL_LIBDIR', self.prefix.lib),

            self.define('GKFS_BUILD_TESTS', self.run_tests),

            self.define_from_variant('GKFS_ENABLE_FORWARDING', 'forwarding'),

            self.define_from_variant('GKFS_ENABLE_AGIOS', 'agios'),

            self.define_from_variant('GKFS_USE_GUIDED_DISTRIBUTION', 'guided_distributor'),

            self.define_from_variant('GKFS_ENABLE_PROMETHEUS', 'prometheus'),

            self.define_from_variant('GKFS_USE_PARALLAX', 'parallax'),

            self.define_from_variant('GKFS_RENAME_SUPPORT', 'rename'),

        ]

        return args

    def check(self):

        """Run tests"""

        with working_dir(self.build_directory):

            make('test', parallel=False)

    def setup_run_environment(self, env):

        env.set('GKFS_CLIENT', join_path(self.prefix.lib, 'libgkfs_intercept.so'))