From fd5d2a19e9238aa10b6d2019f963be6e506c79da Mon Sep 17 00:00:00 2001
From: Marc Vef <vef@uni-mainz.de>
Date: Tue, 10 May 2022 19:55:14 +0200
Subject: [PATCH 01/10] Adding first version for spack

---
 scripts/spack/README.md                       |  55 +++++++
 scripts/spack/packages/agios/package.py       |  20 +++
 scripts/spack/packages/bmi/package.py         |  36 +++++
 scripts/spack/packages/gekkofs/daemon.patch   |  42 ++++++
 scripts/spack/packages/gekkofs/date-tz.patch  |  11 ++
 scripts/spack/packages/gekkofs/package.py     |  84 +++++++++++
 scripts/spack/packages/rocksdb/package.py     | 139 ++++++++++++++++++
 .../spack/packages/rocksdb/pkg-config.patch   |  14 ++
 .../packages/syscall-intercept/package.py     |  21 +++
 .../syscall-intercept/syscall-intercept.patch | 131 +++++++++++++++++
 scripts/spack/repo.yaml                       |   2 +
 11 files changed, 555 insertions(+)
 create mode 100644 scripts/spack/README.md
 create mode 100644 scripts/spack/packages/agios/package.py
 create mode 100644 scripts/spack/packages/bmi/package.py
 create mode 100644 scripts/spack/packages/gekkofs/daemon.patch
 create mode 100644 scripts/spack/packages/gekkofs/date-tz.patch
 create mode 100755 scripts/spack/packages/gekkofs/package.py
 create mode 100644 scripts/spack/packages/rocksdb/package.py
 create mode 100644 scripts/spack/packages/rocksdb/pkg-config.patch
 create mode 100644 scripts/spack/packages/syscall-intercept/package.py
 create mode 100644 scripts/spack/packages/syscall-intercept/syscall-intercept.patch
 create mode 100755 scripts/spack/repo.yaml

diff --git a/scripts/spack/README.md b/scripts/spack/README.md
new file mode 100644
index 000000000..1e1657901
--- /dev/null
+++ b/scripts/spack/README.md
@@ -0,0 +1,55 @@
+
+### Spack
+
+You can use Spack to install GekkoFS and let it handle all the dependencies. First, you will need to install Spack:
+
+```
+git clone https://github.com/spack/spack.git
+. spack/share/spack/setup-env.sh
+```
+
+Once Spack is installed and available in your path, add gekkofs to the Spack namespace.
+
+```
+spack repo add gekkofs/scripts/spack
+```
+
+You can then check that Spack can find GekkoFS by typing:
+
+```
+spack info gekkofs
+```
+
+Finally, just install GekkoFS. You can also install variants (tests, forwarding mode, AGIOS scheduling).
+
+```bash
+spack install gekkofs
+# for installing tests dependencies and running tests
+spack install -v --test=root gekkofs +tests
+```
+
+Remember to load GekkoFS to run:
+
+```
+spack load gekkofs
+```
+
+If you want to enable the forwarding mode:
+
+```
+spack install gekkofs +forwarding
+```
+
+If you want to enable the AGIOS scheduling library for the forwarding mode:
+
+```
+spack install gekkofs +forwarding +agios
+```
+
+If you want to use the latest developer branch of GekkoFS:
+
+```
+spack install gekkofs@latest
+```
+
+The default is using version 0.9.1 the last stable release.
diff --git a/scripts/spack/packages/agios/package.py b/scripts/spack/packages/agios/package.py
new file mode 100644
index 000000000..c15787fa8
--- /dev/null
+++ b/scripts/spack/packages/agios/package.py
@@ -0,0 +1,20 @@
+# 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')
+
diff --git a/scripts/spack/packages/bmi/package.py b/scripts/spack/packages/bmi/package.py
new file mode 100644
index 000000000..a5049ba4c
--- /dev/null
+++ b/scripts/spack/packages/bmi/package.py
@@ -0,0 +1,36 @@
+# 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
diff --git a/scripts/spack/packages/gekkofs/daemon.patch b/scripts/spack/packages/gekkofs/daemon.patch
new file mode 100644
index 000000000..157a92aaa
--- /dev/null
+++ b/scripts/spack/packages/gekkofs/daemon.patch
@@ -0,0 +1,42 @@
+--- a/src/daemon/CMakeLists.txt	2021-07-08 16:40:56.952476529 -0700
++++ b/src/daemon/CMakeLists.txt	2021-07-08 16:49:09.257352458 -0700
+@@ -66,31 +66,23 @@
+     )
+ ################### Forwarding daemon ###################
+ if (GKFS_ENABLE_FORWARDING)
+-    if (GKFS_ENABLE_AGIOS)
+-        set(FWD_DAEMON_SRC
+-            ${DAEMON_SRC}
+-            scheduler/agios.cpp
++    set(FWD_DAEMON_SRC
++        ${DAEMON_SRC}
++        scheduler/agios.cpp
+         )
+-        set(FWD_DAEMON_HEADERS
+-            ${DAEMON_HEADERS}
+-            ../../include/daemon/scheduler/agios.hpp
++    set(FWD_DAEMON_HEADERS
++        ${DAEMON_HEADERS}
++        ../../include/daemon/scheduler/agios.hpp
+         )
+-        add_executable(gkfwd_daemon ${FWD_DAEMON_SRC} ${FWD_DAEMON_HEADERS})
++    add_executable(gkfwd_daemon ${FWD_DAEMON_SRC} ${FWD_DAEMON_HEADERS})
+ 
++    if (GKFS_ENABLE_AGIOS)
+         target_compile_definitions(gkfwd_daemon
+             PUBLIC
+             GKFS_ENABLE_FORWARDING
+             DGKFS_ENABLE_AGIOS
+             )
+     else ()
+-        set(FWD_DAEMON_SRC
+-            ${DAEMON_SRC}
+-        )
+-        set(FWD_DAEMON_HEADERS
+-            ${DAEMON_HEADERS}
+-        )
+-        add_executable(gkfwd_daemon ${FWD_DAEMON_SRC} ${FWD_DAEMON_HEADERS})
+-
+         target_compile_definitions(gkfwd_daemon
+             PUBLIC
+             GKFS_ENABLE_FORWARDING
diff --git a/scripts/spack/packages/gekkofs/date-tz.patch b/scripts/spack/packages/gekkofs/date-tz.patch
new file mode 100644
index 000000000..56be63d19
--- /dev/null
+++ b/scripts/spack/packages/gekkofs/date-tz.patch
@@ -0,0 +1,11 @@
+--- 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)
diff --git a/scripts/spack/packages/gekkofs/package.py b/scripts/spack/packages/gekkofs/package.py
new file mode 100755
index 000000000..dd7cd4797
--- /dev/null
+++ b/scripts/spack/packages/gekkofs/package.py
@@ -0,0 +1,84 @@
+# 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 *
+from spack.build_systems.cmake import *
+from spack.directives import *
+from spack.multimethod import when
+from spack.util.executable import which
+
+class Gekkofs(CMakePackage):
+    """GekkoFS is a file system 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 = ['jeanbez', 'marcvef']
+    # set various versions
+    version('latest', branch='master', submodules=True)
+    version('0.8.0', sha256='106c032d8cdab88173ab116c213201aa5aaad8d7dfc7b5087c94db329e7090e3')
+    version('0.9.0', sha256='f6f7ec9735417d71d68553b6a4832e2c23f3e406d8d14ffb293855b8aeec4c3a')
+    version('0.9.1', sha256='1772b8a9d4777eca895f88cea6a1b4db2fda62e382ec9f73508e38e9d205d5f7')
+    # apply patches
+    patch('date-tz.patch')
+    patch('daemon.patch', when='@0.8')
+    # set arguments
+    variant('build_type',
+            default='Release',
+            description='CMake build type',
+            values=('Debug', 'Release', 'RelWithDebInfo')
+            )
+
+    variant('tests', default=False, description='Build and runs GekkoFS tests.')
+    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('dedicated_psm2', default=False, description='Use dedicated _non-system_ opa-psm2 version 11.2.185.')
+
+    # general dependencies
+    depends_on('cmake@3.6.0:', type='build')
+    depends_on('lz4', when='@0.8:')
+    depends_on('argobots')
+    depends_on('syscall-intercept')
+    depends_on('date cxxstd=14 +shared +tz tzdb=system')
+    depends_on('opa-psm2@11.2.185', when='+dedicated_psm2')
+    # 0.8.0 specific
+    depends_on('libfabric@1.8.1', when='@0.8')
+    depends_on('bzip2', when='@0.8')
+    depends_on('zstd', when='@0.8')
+    depends_on('uuid', when='@0.8')
+    depends_on('bmi', when='@0.8')
+    depends_on('mercury@2.0.0 +debug +ofi +mpi +sm +shared +boostsys -checksum', when='@0.8')
+    depends_on('margo', when='@0.8')
+    depends_on('rocksdb@6.11.4 -shared +static +lz4 +snappy +zlib +rtti', when='@0.8')
+    # 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:,latest')
+    # Agios I/O forwarding
+    depends_on('agios@1.0', when='@0.8: +agios')
+    depends_on('agios@latest', when='@master +agios')
+
+    def cmake_args(self):
+        """Set up GekkoFS CMake arguments"""
+        args = [
+            self.define_from_variant('GKFS_BUILD_TESTS', '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'),
+        ]
+        return args
+
+    def check(self):
+        """Run tests"""
+        with working_dir(self.build_directory):
+            make('test', parallel=False)
diff --git a/scripts/spack/packages/rocksdb/package.py b/scripts/spack/packages/rocksdb/package.py
new file mode 100644
index 000000000..d9293d332
--- /dev/null
+++ b/scripts/spack/packages/rocksdb/package.py
@@ -0,0 +1,139 @@
+# 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 Rocksdb(MakefilePackage):
+    """RocksDB: A Persistent Key-Value Store for Flash and RAM Storage"""
+
+    homepage = "https://github.com/facebook/rocksdb"
+    url      = 'https://github.com/facebook/rocksdb/archive/v6.5.3.tar.gz'
+    git      = 'https://github.com/facebook/rocksdb.git'
+
+    version('master',  git=git, branch='master', submodules=True)
+    version('6.20.3',  sha256='c6502c7aae641b7e20fafa6c2b92273d935d2b7b2707135ebd9a67b092169dca')
+    version('6.19.3',  sha256='5c19ffefea2bbe4c275d0c60194220865f508f371c64f42e802b4a85f065af5b')
+    version('6.11.4',  sha256='6793ef000a933af4a834b59b0cd45d3a03a3aac452a68ae669fb916ddd270532')
+    version('6.7.3',   sha256='c4d1397b58e4801b5fd7c3dd9175e6ae84541119cbebb739fe17d998f1829e81')
+    version('6.5.3',   sha256='6dc023a11d61d00c8391bd44f26ba7db06c44be228c10b552edc84e02d7fbde2')
+    version('5.18.3',  sha256='7fb6738263d3f2b360d7468cf2ebe333f3109f3ba1ff80115abd145d75287254')
+    version('5.17.2',  sha256='101f05858650a810c90e4872338222a1a3bf3b24de7b7d74466814e6a95c2d28')
+    version('5.16.6',  sha256='f0739edce1707568bdfb36a77638fd5bae287ca21763ce3e56cf0bfae8fff033')
+    version('5.15.10', sha256='26d5d4259fa352ae1604b5b4d275f947cacc006f4f7d2ef0b815056601b807c0')
+
+    variant('bz2', default=False, description='Enable bz2 compression support')
+    variant('lz4', default=True, description='Enable lz4 compression support')
+    variant('shared', default=True, description='Build shared library')
+    variant('snappy', default=False, description='Enable snappy compression support')
+    variant('static', default=True, description='Build static library')
+    variant('zlib', default=True, description='Enable zlib compression support')
+    variant('zstd', default=False, description='Enable zstandard compression support')
+    variant('tbb', default=False, description='Enable Intel TBB support')
+    variant('rtti', default=False, description='Enable RTTI support')
+
+    depends_on('bzip2', when='+bz2')
+    depends_on('gflags')
+    depends_on('lz4', when='+lz4')
+    depends_on('snappy', when='+snappy')
+    depends_on('zlib', when='+zlib')
+    depends_on('zstd', when='+zstd')
+    depends_on('tbb', when='+tbb')
+
+    # https://github.com/facebook/rocksdb/issues/8286
+    patch('pkg-config.patch', when='@6.13.2:')
+
+    conflicts('~shared~static', msg='have to build one type of library')
+
+    phases = ['install']
+
+    def patch(self):
+        filter_file(
+            '-march=native', '',
+            join_path('build_tools', 'build_detect_platform')
+        )
+
+    def install(self, spec, prefix):
+        cflags = []
+        ldflags = []
+
+        if spec.satisfies('%gcc@9:'):
+            cflags.append('-Wno-error=deprecated-copy')
+            cflags.append('-Wno-error=pessimizing-move')
+            cflags.append('-Wno-error=redundant-move')
+
+        if '+rtti' in self.spec:
+            cflags.append('-fPIC')
+
+            env['USE_RTTI'] = '1'
+
+        if '+zlib' in self.spec:
+            cflags.append('-I' + self.spec['zlib'].prefix.include)
+            ldflags.append(self.spec['zlib'].libs.ld_flags)
+        else:
+            env['ROCKSDB_DISABLE_ZLIB'] = 'YES'
+
+        if '+bz2' in self.spec:
+            cflags.append('-I' + self.spec['bz2'].prefix.include)
+            ldflags.append(self.spec['bz2'].libs.ld_flags)
+        else:
+            env['ROCKSDB_DISABLE_BZIP'] = 'YES'
+
+        if '+tbb' in self.spec:
+            cflags.append(spec['tbb'].headers.cpp_flags)
+            ldflags.append('-L' + spec['tbb'].prefix.lib)
+        else:
+            env['ROCKSDB_DISABLE_TBB'] = 'YES'
+
+        for pkg in ['lz4', 'snappy', 'zstd']:
+            if '+' + pkg in self.spec:
+                cflags.append(self.spec[pkg].headers.cpp_flags)
+                ldflags.append(self.spec[pkg].libs.ld_flags)
+            else:
+                env['ROCKSDB_DISABLE_' + pkg.upper()] = 'YES'
+
+        cflags.append(self.spec['gflags'].headers.cpp_flags)
+        ldflags.append(self.spec['gflags'].libs.ld_flags)
+
+        env['CFLAGS'] = ' '.join(cflags)
+        env['PLATFORM_FLAGS'] = ' '.join(ldflags)
+
+        if self.spec.satisfies('@6.13.2:'):
+            env['PREFIX'] = self.spec.prefix
+        else:
+            env['INSTALL_PATH'] = self.spec.prefix
+
+        if '+static' in spec:
+            make('install-static')
+
+        # We need to clean before building the shared library, otherwise
+        # we might end up with errors regarding missing -fPIC.
+        if '+static+shared' in spec:
+            make('clean')
+
+        if '+shared' in spec:
+            make('install-shared')
+
+    @run_after('install')
+    def install_pkgconfig(self):
+        if self.spec.satisfies('@6.13.2:'):
+            return
+
+        libdir = self.spec['rocksdb'].libs.directories[0]
+        pkg_path = join_path(libdir, 'pkgconfig')
+        mkdirp(pkg_path)
+
+        with open(join_path(pkg_path, 'rocksdb.pc'), 'w') as f:
+            f.write('prefix={0}\n'.format(self.prefix))
+            f.write('exec_prefix=${prefix}\n')
+            f.write('libdir={0}\n'.format(libdir))
+            f.write('includedir={0}\n'.format(self.prefix.include))
+            f.write('\n')
+            f.write('Name: rocksdb\n')
+            f.write('Description: RocksDB: A Persistent Key-Value Store for'
+                    ' Flash and RAM Storage\n')
+            f.write('Version: {0}\n'.format(self.spec.version))
+            f.write('Cflags: -I${includedir}\n')
+            f.write('Libs: -L${libdir} -lrocksdb -ldl\n')
diff --git a/scripts/spack/packages/rocksdb/pkg-config.patch b/scripts/spack/packages/rocksdb/pkg-config.patch
new file mode 100644
index 000000000..8266f7306
--- /dev/null
+++ b/scripts/spack/packages/rocksdb/pkg-config.patch
@@ -0,0 +1,14 @@
+--- a/Makefile
++++ b/Makefile
+@@ -1917,9 +1917,9 @@ gen-pc:
+ 	-echo 'Name: rocksdb' >> rocksdb.pc
+ 	-echo 'Description: An embeddable persistent key-value store for fast storage' >> rocksdb.pc
+ 	-echo Version: $(shell ./build_tools/version.sh full) >> rocksdb.pc
+-	-echo 'Libs: -L$${libdir} $(EXEC_LDFLAGS) -lrocksdb' >> rocksdb.pc
++	-echo 'Libs: -L$${libdir} $(subst ','\'',$(EXEC_LDFLAGS)) -lrocksdb' >> rocksdb.pc
+ 	-echo 'Libs.private: $(PLATFORM_LDFLAGS)' >> rocksdb.pc
+-	-echo 'Cflags: -I$${includedir} $(PLATFORM_CXXFLAGS)' >> rocksdb.pc
++	-echo 'Cflags: -I$${includedir}' >> rocksdb.pc
+ 
+ #-------------------------------------------------
+ 
diff --git a/scripts/spack/packages/syscall-intercept/package.py b/scripts/spack/packages/syscall-intercept/package.py
new file mode 100644
index 000000000..6282f4bee
--- /dev/null
+++ b/scripts/spack/packages/syscall-intercept/package.py
@@ -0,0 +1,21 @@
+# 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 SyscallIntercept(CMakePackage):
+    """FIXME: Put a proper description of your package here."""
+
+    homepage = "https://github.com/pmem/syscall_intercept"
+    git      = "https://github.com/pmem/syscall_intercept.git"
+
+    maintainers = ['jeanbez']
+
+    version('304404', commit='304404581c57d43478438d175099d20260bae74e')
+
+    depends_on('capstone@4.0.1')
+
+    patch('syscall-intercept.patch')
diff --git a/scripts/spack/packages/syscall-intercept/syscall-intercept.patch b/scripts/spack/packages/syscall-intercept/syscall-intercept.patch
new file mode 100644
index 000000000..00c7e2674
--- /dev/null
+++ b/scripts/spack/packages/syscall-intercept/syscall-intercept.patch
@@ -0,0 +1,131 @@
+diff --git a/include/libsyscall_intercept_hook_point.h b/include/libsyscall_intercept_hook_point.h
+index 2fe7d57..43a8974 100644
+--- a/include/libsyscall_intercept_hook_point.h
++++ b/include/libsyscall_intercept_hook_point.h
+@@ -56,9 +56,18 @@ extern int (*intercept_hook_point)(long syscall_number,
+ 			long arg2, long arg3,
+ 			long arg4, long arg5,
+ 			long *result);
+-
+-extern void (*intercept_hook_point_clone_child)(void);
+-extern void (*intercept_hook_point_clone_parent)(long pid);
++extern void (*intercept_hook_point_clone_child)(
++			unsigned long flags, void *child_stack,
++			int *ptid, int *ctid, long newtls);
++extern void (*intercept_hook_point_clone_parent)(
++			unsigned long flags, void *child_stack,
++			int *ptid, int *ctid, long newtls,
++			long returned_pid);
++extern void (*intercept_hook_point_post_kernel)(long syscall_number,
++			long arg0, long arg1,
++			long arg2, long arg3,
++			long arg4, long arg5,
++			long result);
+ 
+ /*
+  * syscall_no_intercept - syscall without interception
+diff --git a/src/intercept.c b/src/intercept.c
+index 41fd95d..c0cd865 100644
+--- a/src/intercept.c
++++ b/src/intercept.c
+@@ -67,9 +67,23 @@ int (*intercept_hook_point)(long syscall_number,
+ 			long *result)
+ 	__attribute__((visibility("default")));
+ 
+-void (*intercept_hook_point_clone_child)(void)
++void (*intercept_hook_point_clone_child)(
++		unsigned long flags, void *child_stack,
++		int *ptid, int *ctid,
++		long newtls)
+ 	__attribute__((visibility("default")));
+-void (*intercept_hook_point_clone_parent)(long)
++
++void (*intercept_hook_point_clone_parent)(
++		unsigned long flags, void *child_stack,
++		int *ptid, int *ctid,
++		long newtls, long returned_pid)
++	__attribute__((visibility("default")));
++
++void (*intercept_hook_point_post_kernel)(long syscall_number,
++			long arg0, long arg1,
++			long arg2, long arg3,
++			long arg4, long arg5,
++			long result)
+ 	__attribute__((visibility("default")));
+ 
+ bool debug_dumps_on;
+@@ -655,6 +669,21 @@ intercept_routine(struct context *context)
+ 					desc.args[3],
+ 					desc.args[4],
+ 					desc.args[5]);
++
++		/*
++		 * some users might want to execute code after a syscall has
++		 * been forwarded to the kernel (for example, to check its
++		 * return value).
++		 */
++		if (intercept_hook_point_post_kernel != NULL)
++			intercept_hook_point_post_kernel(desc.nr,
++				desc.args[0],
++				desc.args[1],
++				desc.args[2],
++				desc.args[3],
++				desc.args[4],
++				desc.args[5],
++				result);
+ 	}
+ 
+ 	intercept_log_syscall(patch, &desc, KNOWN, result);
+@@ -670,12 +699,26 @@ intercept_routine(struct context *context)
+ struct wrapper_ret
+ intercept_routine_post_clone(struct context *context)
+ {
++	struct syscall_desc desc;
++	get_syscall_in_context(context, &desc);
++
+ 	if (context->rax == 0) {
+ 		if (intercept_hook_point_clone_child != NULL)
+-			intercept_hook_point_clone_child();
++			intercept_hook_point_clone_child(
++				(unsigned long)desc.args[0],
++				(void *)desc.args[1],
++				(int *)desc.args[2],
++				(int *)desc.args[3],
++				desc.args[4]);
+ 	} else {
+ 		if (intercept_hook_point_clone_parent != NULL)
+-			intercept_hook_point_clone_parent(context->rax);
++			intercept_hook_point_clone_parent(
++				(unsigned long)desc.args[0],
++				(void *)desc.args[1],
++				(int *)desc.args[2],
++				(int *)desc.args[3],
++				desc.args[4],
++				context->rax);
+ 	}
+ 
+ 	return (struct wrapper_ret){.rax = context->rax, .rdx = 1 };
+diff --git a/test/test_clone_thread_preload.c b/test/test_clone_thread_preload.c
+index c7663a2..bff239e 100644
+--- a/test/test_clone_thread_preload.c
++++ b/test/test_clone_thread_preload.c
+@@ -96,8 +96,18 @@ hook(long syscall_number,
+  * of the clone syscall.
+  */
+ static void
+-hook_child(void)
++hook_child(unsigned long clone_flags,
++			void *child_stack,
++			int *ptid,
++			int *ctid,
++			long newtls)
+ {
++	(void) clone_flags;
++	(void) child_stack;
++	(void) ptid;
++	(void) ctid;
++	(void) newtls;
++
+ 	static const char msg[] = "clone_hook_child called\n";
+ 
+ 	assert(flags != -1);
diff --git a/scripts/spack/repo.yaml b/scripts/spack/repo.yaml
new file mode 100755
index 000000000..b149b8751
--- /dev/null
+++ b/scripts/spack/repo.yaml
@@ -0,0 +1,2 @@
+repo:
+  namespace: 'gekkofs'
-- 
GitLab


From a02ce01107ffba1b61411ff2d20f31fd76c9acb7 Mon Sep 17 00:00:00 2001
From: rnou <ramon.nou@bsc.es>
Date: Thu, 9 Feb 2023 13:33:05 +0100
Subject: [PATCH 02/10] architecture compilation for syscall_intercept

---
 scripts/spack/packages/gekkofs/package.py     |   6 +-
 .../packages/syscall-intercept/package.py     |  20 +++-
 .../syscall-intercept-arm.patch               | 107 ++++++++++++++++++
 3 files changed, 128 insertions(+), 5 deletions(-)
 create mode 100644 scripts/spack/packages/syscall-intercept/syscall-intercept-arm.patch

diff --git a/scripts/spack/packages/gekkofs/package.py b/scripts/spack/packages/gekkofs/package.py
index dd7cd4797..208f42f7f 100755
--- a/scripts/spack/packages/gekkofs/package.py
+++ b/scripts/spack/packages/gekkofs/package.py
@@ -41,12 +41,14 @@ to I/O, which reduces interferences and improves performance."""
     variant('guided_distributor', default=False, description='Enables the guided distributor.')
     # variant('prometheus', default=False, description='Enables Prometheus support for statistics.')
     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', when='@0.8:')
     depends_on('argobots')
-    depends_on('syscall-intercept')
+    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')
     # 0.8.0 specific
diff --git a/scripts/spack/packages/syscall-intercept/package.py b/scripts/spack/packages/syscall-intercept/package.py
index 6282f4bee..500a1fb5a 100644
--- a/scripts/spack/packages/syscall-intercept/package.py
+++ b/scripts/spack/packages/syscall-intercept/package.py
@@ -9,13 +9,27 @@ from spack import *
 class SyscallIntercept(CMakePackage):
     """FIXME: Put a proper description of your package here."""
 
-    homepage = "https://github.com/pmem/syscall_intercept"
-    git      = "https://github.com/pmem/syscall_intercept.git"
+    homepage = "https://github.com/GekkoFS/syscall_intercept"
+    git      = "https://github.com/GekkoFS/syscall_intercept.git"
 
     maintainers = ['jeanbez']
 
     version('304404', commit='304404581c57d43478438d175099d20260bae74e')
+    version('x86', branch='master')
+    version('powerpc', branch='powerpc')
+    version('arm', branch='arm')
 
     depends_on('capstone@4.0.1')
 
-    patch('syscall-intercept.patch')
+    with when('@arm'):
+        patch('syscall-intercept-arm.patch')
+
+    with when('@x86'):
+        patch('syscall-intercept.patch')
+
+    @property
+    def root_cmakelists_dir(self):
+        if self.version==Version('arm'):
+            return "arch/aarch64"
+        else:
+            return self.stage.source_path
diff --git a/scripts/spack/packages/syscall-intercept/syscall-intercept-arm.patch b/scripts/spack/packages/syscall-intercept/syscall-intercept-arm.patch
new file mode 100644
index 000000000..04b163de8
--- /dev/null
+++ b/scripts/spack/packages/syscall-intercept/syscall-intercept-arm.patch
@@ -0,0 +1,107 @@
+diff --git a/arch/aarch64/include/libsyscall_intercept_hook_point.h b/arch/aarch64/include/libsyscall_intercept_hook_point.h
+index 2fe7d57..46f7eff 100644
+--- a/arch/aarch64/include/libsyscall_intercept_hook_point.h
++++ b/arch/aarch64/include/libsyscall_intercept_hook_point.h
+@@ -57,8 +57,21 @@ extern int (*intercept_hook_point)(long syscall_number,
+ 			long arg4, long arg5,
+ 			long *result);
+ 
+-extern void (*intercept_hook_point_clone_child)(void);
+-extern void (*intercept_hook_point_clone_parent)(long pid);
++
++extern void (*intercept_hook_point_clone_child)(
++			unsigned long flags, void *child_stack,
++			int *ptid, int *ctid, long newtls);
++
++extern void (*intercept_hook_point_clone_parent)(
++			unsigned long flags, void *child_stack,
++			int *ptid, int *ctid, long newtls,
++			long returned_pid);
++
++extern void (*intercept_hook_point_post_kernel)(long syscall_number,
++			long arg0, long arg1,
++			long arg2, long arg3,
++			long arg4, long arg5,
++			long result);
+ 
+ /*
+  * syscall_no_intercept - syscall without interception
+diff --git a/arch/aarch64/src/intercept.c b/arch/aarch64/src/intercept.c
+index a15aa97..72e4b7a 100644
+--- a/arch/aarch64/src/intercept.c
++++ b/arch/aarch64/src/intercept.c
+@@ -68,11 +68,24 @@ int (*intercept_hook_point)(long syscall_number,
+ 			long *result)
+ 	__attribute__((visibility("default")));
+ 
+-void (*intercept_hook_point_clone_child)(void)
+-	__attribute__((visibility("default")));
+-void (*intercept_hook_point_clone_parent)(long)
+-	__attribute__((visibility("default")));
+-
++void (*intercept_hook_point_clone_child)(
++		unsigned long flags, void *child_stack,
++		int *ptid, int *ctid,
++		long newtls)
++__attribute__((visibility("default")));
++
++void (*intercept_hook_point_clone_parent)(
++		unsigned long flags, void *child_stack,
++		int *ptid, int *ctid,
++		long newtls, long returned_pid)
++__attribute__((visibility("default")));
++
++void (*intercept_hook_point_post_kernel)(long syscall_number,
++		long arg0, long arg1,
++		long arg2, long arg3,
++		long arg4, long arg5,
++		long result)
++__attribute__((visibility("default")));
+ bool debug_dumps_on;
+ 
+ void
+@@ -630,7 +643,15 @@ intercept_routine(struct context *context)
+ 
+ 	if (handle_magic_syscalls(&desc, &result) == 0)
+ 		return (struct wrapper_ret){.x0 = result, .x1 = 1 };
+-
++	if (intercept_hook_point_post_kernel != NULL)
++		intercept_hook_point_post_kernel(desc.nr,
++				desc.args[0],
++				desc.args[1],
++				desc.args[2],
++				desc.args[3],
++				desc.args[4],
++				desc.args[5],
++				result);
+ 	intercept_log_syscall(patch, &desc, UNKNOWN, 0);
+ 
+ 	if (intercept_hook_point != NULL)
+@@ -693,12 +714,25 @@ intercept_routine(struct context *context)
+ struct wrapper_ret
+ intercept_routine_post_clone(struct context *context)
+ {
++	struct syscall_desc desc;
++	get_syscall_in_context(context, &desc);
+ 	if (context->x0 == 0) {
+ 		if (intercept_hook_point_clone_child != NULL)
+-			intercept_hook_point_clone_child();
++			intercept_hook_point_clone_child(
++				(unsigned long)desc.args[0],
++				(void *)desc.args[1],
++				(int *)desc.args[2],
++				(int *)desc.args[3],
++				desc.args[4]);
+ 	} else {
+ 		if (intercept_hook_point_clone_parent != NULL)
+-			intercept_hook_point_clone_parent(context->x0);
++			intercept_hook_point_clone_parent(
++					(unsigned long)desc.args[0],
++					(void *)desc.args[1],
++					(int *)desc.args[2],
++					(int *)desc.args[3],
++					desc.args[4],
++					context->x0);
+ 	}
+ 
+ 	return (struct wrapper_ret){.x0 = context->x0, .x1 = 1 };
-- 
GitLab


From 50f78f56e16faf88df48ae0d9aa3a20130190a91 Mon Sep 17 00:00:00 2001
From: Ramon Nou <ramon.nou@bsc.es>
Date: Tue, 14 Feb 2023 11:44:04 +0100
Subject: [PATCH 03/10] Adding $GKFS_PRLD env, and clone pathc

---
 scripts/spack/packages/gekkofs/package.py       |  3 +++
 .../spack/packages/syscall-intercept/package.py |  1 +
 .../syscall-intercept-clone.patch               | 17 +++++++++++++++++
 3 files changed, 21 insertions(+)
 create mode 100644 scripts/spack/packages/syscall-intercept/syscall-intercept-clone.patch

diff --git a/scripts/spack/packages/gekkofs/package.py b/scripts/spack/packages/gekkofs/package.py
index 208f42f7f..30e0f8c0d 100755
--- a/scripts/spack/packages/gekkofs/package.py
+++ b/scripts/spack/packages/gekkofs/package.py
@@ -84,3 +84,6 @@ to I/O, which reduces interferences and improves performance."""
         """Run tests"""
         with working_dir(self.build_directory):
             make('test', parallel=False)
+
+    def setup_run_environment(self, env): 
+        env.set('GKFS_PRLD', join_path(self.prefix.lib, 'libgkfs_intercept.so'))
diff --git a/scripts/spack/packages/syscall-intercept/package.py b/scripts/spack/packages/syscall-intercept/package.py
index 500a1fb5a..0243adc7d 100644
--- a/scripts/spack/packages/syscall-intercept/package.py
+++ b/scripts/spack/packages/syscall-intercept/package.py
@@ -26,6 +26,7 @@ class SyscallIntercept(CMakePackage):
 
     with when('@x86'):
         patch('syscall-intercept.patch')
+        patch('syscall-intercept-clone.patch')
 
     @property
     def root_cmakelists_dir(self):
diff --git a/scripts/spack/packages/syscall-intercept/syscall-intercept-clone.patch b/scripts/spack/packages/syscall-intercept/syscall-intercept-clone.patch
new file mode 100644
index 000000000..db2d622e7
--- /dev/null
+++ b/scripts/spack/packages/syscall-intercept/syscall-intercept-clone.patch
@@ -0,0 +1,17 @@
+diff --git a/src/intercept.c b/src/intercept.c
+index 41fd95d..c0cd865 100644
+--- a/src/intercept.c
++++ b/src/intercept.c
+@@ -689,7 +689,12 @@ intercept_routine(struct context *context)
+ 		 * the clone_child_intercept_routine instead, executing
+ 		 * it on the new child threads stack, then returns to libc.
+ 		 */
++#ifdef SYS_clone3
++		if ((desc.nr == SYS_clone || desc.nr == SYS_clone3) &&
++				desc.args[1] != 0)
++#else
+ 		if (desc.nr == SYS_clone && desc.args[1] != 0)
++#endif
+ 			return (struct wrapper_ret){
+ 				.rax = context->rax, .rdx = 2 };
+ 		else
-- 
GitLab


From 43149fc09c569e1ae4a2f77bc7479f2a6814fb1f Mon Sep 17 00:00:00 2001
From: Ramon Nou <ramon.nou@bsc.es>
Date: Tue, 14 Feb 2023 14:11:46 +0100
Subject: [PATCH 04/10] Add prometheus package

---
 scripts/spack/packages/gekkofs/package.py     |  6 ++-
 .../spack/packages/prometheus-cpp/package.py  | 41 +++++++++++++++++++
 2 files changed, 45 insertions(+), 2 deletions(-)
 create mode 100644 scripts/spack/packages/prometheus-cpp/package.py

diff --git a/scripts/spack/packages/gekkofs/package.py b/scripts/spack/packages/gekkofs/package.py
index 30e0f8c0d..3e4829c14 100755
--- a/scripts/spack/packages/gekkofs/package.py
+++ b/scripts/spack/packages/gekkofs/package.py
@@ -39,7 +39,7 @@ to I/O, which reduces interferences and improves performance."""
     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('prometheus', default=False, description='Enables Prometheus support for statistics.')
     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
@@ -68,6 +68,8 @@ to I/O, which reduces interferences and improves performance."""
     # 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')
 
     def cmake_args(self):
         """Set up GekkoFS CMake arguments"""
@@ -76,7 +78,7 @@ to I/O, which reduces interferences and improves performance."""
             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_ENABLE_PROMETHEUS', 'prometheus'),
         ]
         return args
 
diff --git a/scripts/spack/packages/prometheus-cpp/package.py b/scripts/spack/packages/prometheus-cpp/package.py
new file mode 100644
index 000000000..9d0db7fb0
--- /dev/null
+++ b/scripts/spack/packages/prometheus-cpp/package.py
@@ -0,0 +1,41 @@
+# 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)
+
+# ----------------------------------------------------------------------------
+# If you submit this package back to Spack as a pull request,
+# please first remove this boilerplate and all FIXME comments.
+#
+# This is a template package file for Spack.  We've put "FIXME"
+# next to all the things you'll want to change. Once you've handled
+# them, you can save this file and test your package like this:
+#
+#     spack install prometheus-cpp
+#
+# You can edit this file again by typing:
+#
+#     spack edit prometheus-cpp
+#
+# See the Spack documentation for more information on packaging.
+# ----------------------------------------------------------------------------
+
+from spack.package import *
+
+
+class PrometheusCpp(CMakePackage):
+    """Prometheus CPP bindings."""
+
+    # FIXME: Add a proper url for your package's homepage here.
+    homepage = "https://gitgub.com/jupp0r/prometheus-cpp"
+    url = "https://github.com/jupp0r/prometheus-cpp/releases/download/v1.0.0/prometheus-cpp-with-submodules.tar.gz"
+
+    # FIXME: Add a list of GitHub accounts to
+    # notify when the package is updated.
+    # maintainers("github_user1", "github_user2")
+
+    version("1.0.0", sha256="593ea4e2b6f4ecf9bd73136e35f5ec66a69249f8cbbb90963e9e04517fb471c0")
+
+    # FIXME: Add dependencies if required.
+    # depends_on("foo")
+
-- 
GitLab


From fda0bf30c90b6fd61fa7415e83fcc99ce59f97af Mon Sep 17 00:00:00 2001
From: Ramon Nou <ramon.nou@bsc.es>
Date: Wed, 15 Feb 2023 12:59:23 +0100
Subject: [PATCH 05/10] Add Parallax spack

---
 scripts/spack/packages/gekkofs/package.py  |  3 ++
 scripts/spack/packages/parallax/package.py | 42 ++++++++++++++++++++++
 2 files changed, 45 insertions(+)
 create mode 100644 scripts/spack/packages/parallax/package.py

diff --git a/scripts/spack/packages/gekkofs/package.py b/scripts/spack/packages/gekkofs/package.py
index 3e4829c14..934eb2bd2 100755
--- a/scripts/spack/packages/gekkofs/package.py
+++ b/scripts/spack/packages/gekkofs/package.py
@@ -40,6 +40,7 @@ to I/O, which reduces interferences and improves performance."""
     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.')
     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
@@ -70,6 +71,7 @@ to I/O, which reduces interferences and improves performance."""
     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')
 
     def cmake_args(self):
         """Set up GekkoFS CMake arguments"""
@@ -79,6 +81,7 @@ to I/O, which reduces interferences and improves performance."""
             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'),
         ]
         return args
 
diff --git a/scripts/spack/packages/parallax/package.py b/scripts/spack/packages/parallax/package.py
new file mode 100644
index 000000000..0cc86af7a
--- /dev/null
+++ b/scripts/spack/packages/parallax/package.py
@@ -0,0 +1,42 @@
+# 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)
+
+# ----------------------------------------------------------------------------
+# If you submit this package back to Spack as a pull request,
+# please first remove this boilerplate and all FIXME comments.
+#
+# This is a template package file for Spack.  We've put "FIXME"
+# next to all the things you'll want to change. Once you've handled
+# them, you can save this file and test your package like this:
+#
+#     spack install parallax
+#
+# You can edit this file again by typing:
+#
+#     spack edit parallax
+#
+# See the Spack documentation for more information on packaging.
+# ----------------------------------------------------------------------------
+
+from spack.package import *
+
+
+class Parallax(CMakePackage):
+    """Parallax Key-vale database."""
+
+    # FIXME: Add a proper url for your package's homepage here.
+    homepage = "https://github.com/CARV-ICS-FORTH/paralla"
+    git = "https://github.com/CARV-ICS-FORTH/parallax.git"
+
+    # FIXME: Add a list of GitHub accounts to
+    # notify when the package is updated.
+    # maintainers("github_user1", "github_user2")
+
+    # FIXME: Add proper versions and checksums here.
+    version('1.0.0', commit='ffdea6e820f5c4c2d33e60d9a4b15ef9e6bbcfdd')
+
+    # FIXME: Add dependencies if required.
+    #depends_on("foo")
+
-- 
GitLab


From dfa057c26f7e589b860818c49fc018939118efdf Mon Sep 17 00:00:00 2001
From: Ramon Nou <ramon.nou@bsc.es>
Date: Thu, 23 Feb 2023 13:11:56 +0100
Subject: [PATCH 06/10] Rename support option

---
 scripts/spack/packages/gekkofs/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/scripts/spack/packages/gekkofs/package.py b/scripts/spack/packages/gekkofs/package.py
index 934eb2bd2..0878ac83c 100755
--- a/scripts/spack/packages/gekkofs/package.py
+++ b/scripts/spack/packages/gekkofs/package.py
@@ -41,6 +41,7 @@ to I/O, which reduces interferences and improves performance."""
     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.')
+    variant('rename', default=False, description='Enables experimental rename support.')
     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
@@ -82,6 +83,7 @@ to I/O, which reduces interferences and improves performance."""
             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('RENAME_SUPPORT', 'rename'),
         ]
         return args
 
-- 
GitLab


From c58da6a6225655db9bc26a9099e2b97697cb1bf6 Mon Sep 17 00:00:00 2001
From: Marc Vef <vef@uni-mainz.de>
Date: Thu, 9 Mar 2023 20:21:58 +0100
Subject: [PATCH 07/10] Finalizing Spack support and documentation

---
 README.md                                 | 114 +++++++++++++---------
 scripts/spack/README.md                   |  72 ++++++++++----
 scripts/spack/packages/gekkofs/package.py |  68 ++++++-------
 scripts/spack/packages/rocksdb/package.py |   5 +-
 4 files changed, 158 insertions(+), 101 deletions(-)

diff --git a/README.md b/README.md
index b712ce043..6f571eff6 100644
--- a/README.md
+++ b/README.md
@@ -13,15 +13,18 @@ to I/O, which reduces interferences and improves performance.
 
 - \>gcc-8 (including g++) for C++11 support
 - General build tools: Git, Curl, CMake >3.6 (>3.11 for GekkoFS testing), Autoconf, Automake
-- Miscellaneous: Libtool, Libconfig 
+- Miscellaneous: Libtool, Libconfig
 
 ### Debian/Ubuntu
+
 GekkoFS base dependencies: `apt install git curl cmake autoconf automake libtool libconfig-dev`
 
 GekkoFS testing support: `apt install python3-dev python3 python3-venv`
 
 With testing
+
 ### CentOS/Red Hat
+
 GekkoFS base dependencies: `yum install gcc-c++ git curl cmake autoconf automake libtool libconfig`
 
 GekkoFS testing support: `python38-devel` (**>Python-3.6 required**)
@@ -30,27 +33,34 @@ GekkoFS testing support: `python38-devel` (**>Python-3.6 required**)
 
 1. Make sure the above listed dependencies are available on your machine
 2. Clone GekkoFS: `git clone --recurse-submodules https://storage.bsc.es/gitlab/hpc/gekkofs.git`
-   - (Optional) (Optional) If you checked out the sources using `git` without the `--recursive` option, you need to
-     execute the following command from the root of the source directory: `git submodule update --init`
+    - (Optional) (Optional) If you checked out the sources using `git` without the `--recursive` option, you need to
+      execute the following command from the root of the source directory: `git submodule update --init`
 3. Set up the necessary environment variables where the compiled direct GekkoFS dependencies will be installed at (we
    assume the path `/home/foo/gekkofs_deps/install` in the following)
-   - `export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/foo/gekkofs_deps/install/lib:/home/foo/gekkofs_deps/install/lib64`
+    - `export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/foo/gekkofs_deps/install/lib:/home/foo/gekkofs_deps/install/lib64`
 4. Download and compile the direct dependencies, e.g.,
-   - Download example: `gekkofs/scripts/dl_dep.sh /home/foo/gekkofs_deps/git`
-   - Compilation example: `gekkofs/scripts/compile_dep.sh /home/foo/gekkofs_deps/git /home/foo/gekkofs_deps/install`
-   - Consult `-h` for additional arguments for each script
+    - Download example: `gekkofs/scripts/dl_dep.sh /home/foo/gekkofs_deps/git`
+    - Compilation example: `gekkofs/scripts/compile_dep.sh /home/foo/gekkofs_deps/git /home/foo/gekkofs_deps/install`
+    - Consult `-h` for additional arguments for each script
 5. Compile GekkoFS and run optional tests
-   - Create build directory: `mkdir gekkofs/build && cd gekkofs/build`
-   - Configure GekkoFS: `cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=/home/foo/gekkofs_deps/install ..`
-       - add `-DCMAKE_INSTALL_PREFIX=<install_path>` where the GekkoFS client library and server executable should be available 
-       - add `-DGKFS_BUILD_TESTS=ON` if tests should be build
-   - Build and install GekkoFS: `make -j8 install`
-   - Run tests: `make test`
+    - Create build directory: `mkdir gekkofs/build && cd gekkofs/build`
+    - Configure GekkoFS: `cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=/home/foo/gekkofs_deps/install ..`
+        - add `-DCMAKE_INSTALL_PREFIX=<install_path>` where the GekkoFS client library and server executable should be
+          available
+        - add `-DGKFS_BUILD_TESTS=ON` if tests should be build
+    - Build and install GekkoFS: `make -j8 install`
+    - Run tests: `make test`
 
 GekkoFS is now available at:
+
 - GekkoFS daemon (server): `<install_path>/bin/gkfs_daemon`
 - GekkoFS client interception library: `<install_path>/lib64/libgkfs_intercept.so`
 
+## Use Spack to install GekkoFS (alternative)
+
+The Spack tool can be used to easily install GekkoFS and its dependencies. Refer to the
+following [README](scripts/spack/README.md) for details.
+
 # Run GekkoFS
 
 ## General
@@ -70,9 +80,11 @@ The `-P` argument is used for setting another RPC protocol. See below.
 
 ## The GekkoFS hostsfile
 
-Each GekkoFS daemon needs to register itself in a shared file (*hostsfile*) which needs to be accessible to _all_ GekkoFS clients and daemons.
+Each GekkoFS daemon needs to register itself in a shared file (*hostsfile*) which needs to be accessible to _all_
+GekkoFS clients and daemons.
 Therefore, the hostsfile describes a file system and which node is part of that specific GekkoFS file system instance.
-In a typical cluster environment this hostsfile should be placed within a POSIX-compliant parallel file system, such as GPFS or Lustre.
+In a typical cluster environment this hostsfile should be placed within a POSIX-compliant parallel file system, such as
+GPFS or Lustre.
 
 *Note: NFS is not strongly consistent and cannot be used for the hosts file!*
 
@@ -80,7 +92,9 @@ In a typical cluster environment this hostsfile should be placed within a POSIX-
 
 tl;dr example: `<install_path>/bin/gkfs_daemon -r <fs_data_path> -m <pseudo_gkfs_mount_dir_path> -H <hostsfile_path>`
 
-Run the GekkoFS daemon on each node specifying its locally used directory where the file system data and metadata is stored (`-r/--rootdir <fs_data_path>`), e.g., the node-local SSD;
+Run the GekkoFS daemon on each node specifying its locally used directory where the file system data and metadata is
+stored (`-r/--rootdir <fs_data_path>`), e.g., the node-local SSD;
+
 2. the pseudo mount directory used by clients to access GekkoFS (`-m/--mountdir <pseudo_gkfs_mount_dir_path>`); and
 3. the hostsfile path (`-H/--hostsfile <hostfile_path>`).
 
@@ -191,28 +205,28 @@ to `/tmp/gkfs_client.log`.
 The following modules are available:
 
 - `none`: don't print any messages
- - `syscalls`: Trace system calls: print the name of each system call, its
-   arguments, and its return value. All system calls are printed after being
-   executed save for those that may not return, such as `execve()`,
-   `execve_at()`, `exit()`, and `exit_group()`. This module will only be
-   available if the client library is built in `Debug` mode.
- - `syscalls_at_entry`: Trace system calls: print the name of each system call
-   and its arguments. All system calls are printed before being executed and
-   therefore their return values are not available in the log. This module will
-   only be available if the client library is built in `Debug` mode.
- - `info`: Print information messages.
- - `critical`: Print critical errors.
- - `errors`: Print errors.
- - `warnings`: Print warnings.
- - `mercury`: Print Mercury messages.
- - `debug`: Print debug messages.  This module will only be available if the
-   client library is built in `Debug` mode.
- - `most`: All previous options combined except `syscalls_at_entry`. This
-   module will only be available if the client library is built in `Debug`
-   mode.
- - `all`: All previous options combined.
- - `trace_reads`: Generate log line with extra information in read operations for guided distributor
- - `help`: Print a help message and exit.
+- `syscalls`: Trace system calls: print the name of each system call, its
+  arguments, and its return value. All system calls are printed after being
+  executed save for those that may not return, such as `execve()`,
+  `execve_at()`, `exit()`, and `exit_group()`. This module will only be
+  available if the client library is built in `Debug` mode.
+- `syscalls_at_entry`: Trace system calls: print the name of each system call
+  and its arguments. All system calls are printed before being executed and
+  therefore their return values are not available in the log. This module will
+  only be available if the client library is built in `Debug` mode.
+- `info`: Print information messages.
+- `critical`: Print critical errors.
+- `errors`: Print errors.
+- `warnings`: Print warnings.
+- `mercury`: Print Mercury messages.
+- `debug`: Print debug messages. This module will only be available if the
+  client library is built in `Debug` mode.
+- `most`: All previous options combined except `syscalls_at_entry`. This
+  module will only be available if the client library is built in `Debug`
+  mode.
+- `all`: All previous options combined.
+- `trace_reads`: Generate log line with extra information in read operations for guided distributor
+- `help`: Print a help message and exit.
 
 When tracing sytem calls, specific syscalls can be removed from log messages by
 setting the `LIBGKFS_LOG_SYSCALL_FILTER` environment variable. For instance,
@@ -230,28 +244,33 @@ environment variable.
 
 ## External functions
 
-GekkoFS allows to use external functions on your client code, via LD_PRELOAD. 
+GekkoFS allows to use external functions on your client code, via LD_PRELOAD.
 Source code needs to be compiled with -fPIC. We include a pfind io500 substitution,
- `examples/gfind/gfind.cpp` and a non-mpi version `examples/gfind/sfind.cpp`
+`examples/gfind/gfind.cpp` and a non-mpi version `examples/gfind/sfind.cpp`
 
 ## Data distributors
+
 The data distribution can be selected at compilation time, we have 2 distributors available:
 
 ### Simple Hash (Default)
+
 Chunks are distributed randomly to the different GekkoFS servers.
 
 ### Guided Distributor
 
-The guided distributor allows defining a specific distribution of data on a per directory or file basis. 
-The distribution configurations are defined within a shared file (called `guided_config.txt` henceforth) with the following format:
+The guided distributor allows defining a specific distribution of data on a per directory or file basis.
+The distribution configurations are defined within a shared file (called `guided_config.txt` henceforth) with the
+following format:
 `<path> <chunk_number> <host>`
 
 To enable the distributor, the following CMake compilation flags are required:
+
 * `GKFS_USE_GUIDED_DISTRIBUTION` ON
 * `GKFS_USE_GUIDED_DISTRIBUTION_PATH` `<path_guided_config.txt>`
 
-To use a custom distribution, a path needs to have the prefix `#` (e.g., `#/mdt-hard 0 0`), in which all the data of all files in that directory goes to the same place as the metadata.
-Note, that a chunk/host configuration is inherited to all children files automatically even if not using the prefix. 
+To use a custom distribution, a path needs to have the prefix `#` (e.g., `#/mdt-hard 0 0`), in which all the data of all
+files in that directory goes to the same place as the metadata.
+Note, that a chunk/host configuration is inherited to all children files automatically even if not using the prefix.
 In this example, `/mdt-hard/file1` is therefore also using the same distribution as the `/mdt-hard` directory.
 If no prefix is used, the Simple Hash distributor is used.
 
@@ -260,12 +279,15 @@ If no prefix is used, the Simple Hash distributor is used.
 Creating a guided configuration file is based on an I/O trace file of a previous execution of the application.
 For this the `trace_reads` tracing module is used (see above).
 
-The `trace_reads` module enables a `TRACE_READS` level log at the clients writing the I/O information of the client which is used as the input for a script that creates the guided distributor setting.
+The `trace_reads` module enables a `TRACE_READS` level log at the clients writing the I/O information of the client
+which is used as the input for a script that creates the guided distributor setting.
 Note that capturing the necessary trace records can involve performance degradation.
-To capture the I/O of each client within a SLURM environment, i.e., enabling the `trace_reads` module and print its output to a user-defined path, the following example can be used:
+To capture the I/O of each client within a SLURM environment, i.e., enabling the `trace_reads` module and print its
+output to a user-defined path, the following example can be used:
 `srun -N 10 -n 320 --export="ALL" /bin/bash -c "export LIBGKFS_LOG=trace_reads;LIBGKFS_LOG_OUTPUT=${HOME}/test/GLOBAL.txt;LD_PRELOAD=${GKFS_PRLD} <app>"`
 
 Then, the `examples/distributors/guided/generate.py` scrpt is used to create the guided distributor configuration file:
+
 * `python examples/distributors/guided/generate.py ~/test/GLOBAL.txt >> guided_config.txt`
 
 Finally, modify `guided_config.txt` to your distribution requirements.
diff --git a/scripts/spack/README.md b/scripts/spack/README.md
index 1e1657901..7f2a581d0 100644
--- a/scripts/spack/README.md
+++ b/scripts/spack/README.md
@@ -1,55 +1,89 @@
+## Spack
 
-### Spack
+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.
 
-You can use Spack to install GekkoFS and let it handle all the dependencies. First, you will need to install Spack:
+### Install Spack
 
-```
+First, install Spack. You can find the instructions here: https://spack.readthedocs.io/en/latest/getting_started.html
+
+```bash
 git clone https://github.com/spack/spack.git
 . spack/share/spack/setup-env.sh
 ```
 
-Once Spack is installed and available in your path, add gekkofs to the Spack namespace.
+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.
+
+```bash
 spack repo add gekkofs/scripts/spack
 ```
 
-You can then check that Spack can find GekkoFS by typing:
+When added, the GekkoFS package is available. Its installation variants and options can be checked via:
 
-```
+```bash
 spack info gekkofs
 ```
 
-Finally, just install GekkoFS. You can also install variants (tests, forwarding mode, AGIOS scheduling).
+Then install GekkoFS with Spack:
 
 ```bash
 spack install gekkofs
 # for installing tests dependencies and running tests
-spack install -v --test=root gekkofs +tests
+spack install -v --test=root gekkofs
 ```
 
-Remember to load GekkoFS to run:
+Finally, GekkoFS is loaded into the currently used environment:
 
-```
+```bash
 spack load gekkofs
 ```
 
-If you want to enable the forwarding mode:
+This installs the latest release version including its required Git submodules. The installation directory is
+`$SPACK_ROOT/opt/spack/linux-<arch>/<compiler>/<version>/gekkofs-<version>`. The GekkoFS daemon (`gkfs_daemon`) is
+located in the `bin` directory and the GekkoFS client (`libgkfs_intercept.so`) is located in the `lib` directory.
 
-```
-spack install gekkofs +forwarding
-```
+Note that loading the environment adds the GekkoFS daemon to the `$PATH` environment variable. Therefore, the GekkoFS
+daemon is started by running `gkfs_daemon`. Loading GekkoFS in Spack further provides the `$GKFS_CLIENT` environment
+variable pointing to the interception library.
 
-If you want to enable the AGIOS scheduling library for the forwarding mode:
+Therefore, the following commands can be run to use GekkoFS:
 
+```bash
+# 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
 ```
-spack install gekkofs +forwarding +agios
+
+When done using GekkoFS, unload it from the environment:
+
+```bash
+spack unload gekkofs
 ```
 
-If you want to use the latest developer branch of GekkoFS:
+### Alternative deployment (on many nodes)
+
+`gekkofs/scripts/run/gkfs` provides a script to deploy GekkoFS in a single command on several nodes by using `srun`.
+Consult the main [README](../../README.md) or GekkoFS documentation for details.
+
+### Miscellaneous
+
+Use GekkoFS's latest version (master branch) with Spack:
 
 ```
 spack install gekkofs@latest
 ```
 
-The default is using version 0.9.1 the last stable release.
+Use a specific compiler on your system, e.g., gcc-11.2.0:
+
+```bash
+spack install gekkofs@latest%gcc@11.2.0
+```
\ No newline at end of file
diff --git a/scripts/spack/packages/gekkofs/package.py b/scripts/spack/packages/gekkofs/package.py
index 0878ac83c..f23dd6f54 100755
--- a/scripts/spack/packages/gekkofs/package.py
+++ b/scripts/spack/packages/gekkofs/package.py
@@ -1,33 +1,34 @@
-# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
+# 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 *
-from spack.build_systems.cmake import *
-from spack.directives import *
-from spack.multimethod import when
-from spack.util.executable import which
+from spack import *
 
-class Gekkofs(CMakePackage):
-    """GekkoFS is a file system 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."""
 
+# 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 = ['jeanbez', 'marcvef']
+    maintainers = ['marc_vef', 'ramon_nou']
     # set various versions
     version('latest', branch='master', submodules=True)
-    version('0.8.0', sha256='106c032d8cdab88173ab116c213201aa5aaad8d7dfc7b5087c94db329e7090e3')
-    version('0.9.0', sha256='f6f7ec9735417d71d68553b6a4832e2c23f3e406d8d14ffb293855b8aeec4c3a')
+    version('0.9.0', sha256='f6f7ec9735417d71d68553b6a4832e2c23f3e406d8d14ffb293855b8aeec4c3a', deprecated=True)
     version('0.9.1', sha256='1772b8a9d4777eca895f88cea6a1b4db2fda62e382ec9f73508e38e9d205d5f7')
     # apply patches
     patch('date-tz.patch')
-    patch('daemon.patch', when='@0.8')
     # set arguments
     variant('build_type',
             default='Release',
@@ -35,38 +36,33 @@ to I/O, which reduces interferences and improves performance."""
             values=('Debug', 'Release', 'RelWithDebInfo')
             )
 
-    variant('tests', default=False, description='Build and runs GekkoFS tests.')
     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.')
-    variant('rename', default=False, description='Enables experimental rename support.')
+    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.')
+    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', when='@0.8:')
+    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')
-    # 0.8.0 specific
-    depends_on('libfabric@1.8.1', when='@0.8')
-    depends_on('bzip2', when='@0.8')
-    depends_on('zstd', when='@0.8')
-    depends_on('uuid', when='@0.8')
-    depends_on('bmi', when='@0.8')
-    depends_on('mercury@2.0.0 +debug +ofi +mpi +sm +shared +boostsys -checksum', when='@0.8')
-    depends_on('margo', when='@0.8')
-    depends_on('rocksdb@6.11.4 -shared +static +lz4 +snappy +zlib +rtti', when='@0.8')
     # 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:,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')
@@ -74,16 +70,20 @@ to I/O, which reduces interferences and improves performance."""
     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_from_variant('GKFS_BUILD_TESTS', 'tests'),
+            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('RENAME_SUPPORT', 'rename'),
+            self.define_from_variant('GKFS_RENAME_SUPPORT', 'rename'),
         ]
         return args
 
@@ -92,5 +92,5 @@ to I/O, which reduces interferences and improves performance."""
         with working_dir(self.build_directory):
             make('test', parallel=False)
 
-    def setup_run_environment(self, env): 
-        env.set('GKFS_PRLD', join_path(self.prefix.lib, 'libgkfs_intercept.so'))
+    def setup_run_environment(self, env):
+        env.set('GKFS_CLIENT', join_path(self.prefix.lib, 'libgkfs_intercept.so'))
diff --git a/scripts/spack/packages/rocksdb/package.py b/scripts/spack/packages/rocksdb/package.py
index d9293d332..78586bbfb 100644
--- a/scripts/spack/packages/rocksdb/package.py
+++ b/scripts/spack/packages/rocksdb/package.py
@@ -13,8 +13,9 @@ class Rocksdb(MakefilePackage):
     url      = 'https://github.com/facebook/rocksdb/archive/v6.5.3.tar.gz'
     git      = 'https://github.com/facebook/rocksdb.git'
 
-    version('master',  git=git, branch='master', submodules=True)
-    version('6.20.3',  sha256='c6502c7aae641b7e20fafa6c2b92273d935d2b7b2707135ebd9a67b092169dca')
+    version('master', git=git, branch='master', submodules=True)
+    version('6.26.1', sha256='5aeb94677bdd4ead46eb4cefc3dbb5943141fb3ce0ba627cfd8cbabeed6475e7')
+    version('6.20.3', sha256='c6502c7aae641b7e20fafa6c2b92273d935d2b7b2707135ebd9a67b092169dca')
     version('6.19.3',  sha256='5c19ffefea2bbe4c275d0c60194220865f508f371c64f42e802b4a85f065af5b')
     version('6.11.4',  sha256='6793ef000a933af4a834b59b0cd45d3a03a3aac452a68ae669fb916ddd270532')
     version('6.7.3',   sha256='c4d1397b58e4801b5fd7c3dd9175e6ae84541119cbebb739fe17d998f1829e81')
-- 
GitLab


From e11740489a27194397aa7ca7a7d116330df4d21d Mon Sep 17 00:00:00 2001
From: Marc Vef <vef@uni-mainz.de>
Date: Thu, 9 Mar 2023 20:39:41 +0100
Subject: [PATCH 08/10] Adding Spack documentation to Sphinx and added
 changelog entry

---
 CHANGELOG.md                   |  2 +
 docs/sphinx/users/building.rst | 87 ++++++++++++++++++++++++++++++++--
 scripts/spack/README.md        |  2 +-
 3 files changed, 87 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f1c92536b..f360b69b9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -38,6 +38,8 @@ to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
     when building to precisely see how a GekkoFS instance has been configured.
 - Added (parallel) append support for consecutive writes with file descriptor opened
   with `O_APPEND` ([!164](https://storage.bsc.es/gitlab/hpc/gekkofs/-/merge_requests/164)).
+- Added support for Spack so that it can be used to install
+  GekkoFS ([!137](https://storage.bsc.es/gitlab/hpc/gekkofs/-/merge_requests/137)).
 
 ### Changed
 
diff --git a/docs/sphinx/users/building.rst b/docs/sphinx/users/building.rst
index 259e84d1a..d84800f5c 100644
--- a/docs/sphinx/users/building.rst
+++ b/docs/sphinx/users/building.rst
@@ -108,9 +108,10 @@ dependencies:
 - `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:
@@ -213,3 +214,83 @@ appropriate subdirectories of :code:`GKFS_INSTALL_PATH`:
 
 - 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
diff --git a/scripts/spack/README.md b/scripts/spack/README.md
index 7f2a581d0..b1f3bce9f 100644
--- a/scripts/spack/README.md
+++ b/scripts/spack/README.md
@@ -6,7 +6,7 @@ Spack is another method to install GekkoFS where Spack handles all the dependenc
 
 ### Install Spack
 
-First, install Spack. You can find the instructions here: https://spack.readthedocs.io/en/latest/getting_started.html
+First, install Spack. You can find the instructions [here](https://spack.readthedocs.io/en/latest/getting_started.html)
 
 ```bash
 git clone https://github.com/spack/spack.git
-- 
GitLab


From 8321783bc58923369dac261da1a6f1c169f41403 Mon Sep 17 00:00:00 2001
From: Marc Vef <vef@uni-mainz.de>
Date: Thu, 9 Mar 2023 20:55:12 +0100
Subject: [PATCH 09/10] Added README FAQ

---
 scripts/spack/README.md                     | 30 ++++++++++++++-
 scripts/spack/packages/gekkofs/daemon.patch | 42 ---------------------
 2 files changed, 29 insertions(+), 43 deletions(-)
 delete mode 100644 scripts/spack/packages/gekkofs/daemon.patch

diff --git a/scripts/spack/README.md b/scripts/spack/README.md
index b1f3bce9f..339a0dce3 100644
--- a/scripts/spack/README.md
+++ b/scripts/spack/README.md
@@ -86,4 +86,32 @@ Use a specific compiler on your system, e.g., gcc-11.2.0:
 
 ```bash
 spack install gekkofs@latest%gcc@11.2.0
-```
\ No newline at end of file
+```
+
+#### FAQ
+
+I cannot run the tests because Python is missing? For Spack and GCC, we rely on the system installed versions. If you
+are working on a supercomputer, you may need to load the corresponding Python module first:
+
+```bash
+# GekkoFS tests require at least Python version 3.6.
+module load python/3.9.10
+```
+
+Everything is failing during the compilation process? See question above, either a GCC is not loaded or it is too old
+and does not support C++17 which we require. In any case, when using Spack it is good practice to use the system
+compiler if possible:
+
+```bash
+# GekkoFS requires at least GCC version 8
+module load gcc/11.2.0
+```
+
+This may not be enough for Spack to recognize it (depending on what time Spack is installed). Therefore, you need to add
+the compiler to spack via:
+
+```bash
+spack compiler find
+```
+
+`spack compiler list` should then list the loaded compiler.
\ No newline at end of file
diff --git a/scripts/spack/packages/gekkofs/daemon.patch b/scripts/spack/packages/gekkofs/daemon.patch
deleted file mode 100644
index 157a92aaa..000000000
--- a/scripts/spack/packages/gekkofs/daemon.patch
+++ /dev/null
@@ -1,42 +0,0 @@
---- a/src/daemon/CMakeLists.txt	2021-07-08 16:40:56.952476529 -0700
-+++ b/src/daemon/CMakeLists.txt	2021-07-08 16:49:09.257352458 -0700
-@@ -66,31 +66,23 @@
-     )
- ################### Forwarding daemon ###################
- if (GKFS_ENABLE_FORWARDING)
--    if (GKFS_ENABLE_AGIOS)
--        set(FWD_DAEMON_SRC
--            ${DAEMON_SRC}
--            scheduler/agios.cpp
-+    set(FWD_DAEMON_SRC
-+        ${DAEMON_SRC}
-+        scheduler/agios.cpp
-         )
--        set(FWD_DAEMON_HEADERS
--            ${DAEMON_HEADERS}
--            ../../include/daemon/scheduler/agios.hpp
-+    set(FWD_DAEMON_HEADERS
-+        ${DAEMON_HEADERS}
-+        ../../include/daemon/scheduler/agios.hpp
-         )
--        add_executable(gkfwd_daemon ${FWD_DAEMON_SRC} ${FWD_DAEMON_HEADERS})
-+    add_executable(gkfwd_daemon ${FWD_DAEMON_SRC} ${FWD_DAEMON_HEADERS})
- 
-+    if (GKFS_ENABLE_AGIOS)
-         target_compile_definitions(gkfwd_daemon
-             PUBLIC
-             GKFS_ENABLE_FORWARDING
-             DGKFS_ENABLE_AGIOS
-             )
-     else ()
--        set(FWD_DAEMON_SRC
--            ${DAEMON_SRC}
--        )
--        set(FWD_DAEMON_HEADERS
--            ${DAEMON_HEADERS}
--        )
--        add_executable(gkfwd_daemon ${FWD_DAEMON_SRC} ${FWD_DAEMON_HEADERS})
--
-         target_compile_definitions(gkfwd_daemon
-             PUBLIC
-             GKFS_ENABLE_FORWARDING
-- 
GitLab


From 3f59f7ad255305728cef20afb23f4caae20ae8b7 Mon Sep 17 00:00:00 2001
From: Marc Vef <vef@uni-mainz.de>
Date: Thu, 9 Mar 2023 21:20:19 +0100
Subject: [PATCH 10/10] Fix Sphinx syntax

---
 docs/sphinx/users/building.rst | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/docs/sphinx/users/building.rst b/docs/sphinx/users/building.rst
index d84800f5c..e0a0beee0 100644
--- a/docs/sphinx/users/building.rst
+++ b/docs/sphinx/users/building.rst
@@ -227,6 +227,7 @@ 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
 
@@ -241,16 +242,19 @@ To install GekkoFS with Spack, the GekkoFS repository needs to be added to 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
@@ -258,6 +262,7 @@ Then install GekkoFS with Spack:
 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
@@ -271,6 +276,7 @@ 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
@@ -280,6 +286,7 @@ Therefore, the following commands can be run to use GekkoFS:
 When done using GekkoFS, unload it from the environment:
 
     .. code-block:: console
+
         spack unload gekkofs
 
 Miscellaneous
@@ -288,9 +295,11 @@ 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
-- 
GitLab