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.
- >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
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
GekkoFS base dependencies: yum install gcc-c++ git curl cmake autoconf automake libtool libconfig
GekkoFS testing support: python38-devel
(>Python-3.6 required)
- Make sure the above listed dependencies are available on your machine
- 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
- 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
- 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:
- 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
- add
- Build and install GekkoFS:
make -j8 install
- Run tests:
make test
- Create build directory:
GekkoFS is now available at:
- GekkoFS daemon (server):
<install_path>/bin/gkfs_daemon
- GekkoFS client interception library:
<install_path>/lib64/libgkfs_intercept.so
On each node a daemon (gkfs_daemon
binary) has to be started. Other tools can be used to execute
the binary on many nodes, e.g., srun
, mpiexec/mpirun
, pdsh
, or pssh
.
You need to decide what Mercury NA plugin you want to use for network communication. ofi+sockets
is the default.
The -P
argument is used for setting another RPC protocol. See below.
ofi+sockets
for using the libfabric plugin with TCP (stable)ofi+tcp
for using the libfabric plugin with TCP (slower than sockets)ofi+verbs
for using the libfabric plugin with Infiniband verbs (reasonably stable) and requires the rdma-core (formerly libibverbs) libraryofi+psm2
for using the libfabric plugin with Intel Omni-Path (unstable) and requires the opa-psm2 library
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.
Note: NFS is not strongly consistent and cannot be used for the hosts file!
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;
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>
).
Further options are available:
Allowed options
Usage: src/daemon/gkfs_daemon [OPTIONS]
Options:
-h,--help Print this help message and exit
-m,--mountdir TEXT REQUIRED Virtual mounting directory where GekkoFS is available.
-r,--rootdir TEXT REQUIRED Local data directory where GekkoFS data for this daemon is stored.
-s,--rootdir-suffix TEXT Creates an additional directory within the rootdir, allowing multiple daemons on one node.
-i,--metadir TEXT Metadata directory where GekkoFS RocksDB data directory is located. If not set, rootdir is used.
-l,--listen TEXT Address or interface to bind the daemon to. Default: local hostname.
When used with ofi+verbs the FI_VERBS_IFACE environment variable is set accordingly which associates the verbs device with the network interface. In case FI_VERBS_IFACE is already defined, the argument is ignored. Default 'ib'.
-H,--hosts-file TEXT Shared file used by deamons to register their endpoints. (default './gkfs_hosts.txt')
-P,--rpc-protocol TEXT Used RPC protocol for inter-node communication.
Available: {ofi+sockets, ofi+verbs, ofi+psm2} for TCP, Infiniband, and Omni-Path, respectively. (Default ofi+sockets)
Libfabric must have enabled support verbs or psm2.
--auto-sm Enables intra-node communication (IPCs) via the `na+sm` (shared memory) protocol, instead of using the RPC protocol. (Default off)
--clean-rootdir Cleans Rootdir >before< launching the deamon
-c,--clean-rootdir-finish Cleans Rootdir >after< the deamon finishes
-d,--dbbackend TEXT Metadata database backend to use. Available: {rocksdb, parallaxdb}
RocksDB is default if not set. Parallax support is experimental.
Note, parallaxdb creates a file called rocksdbx with 8GB created in metadir.
--parallaxsize TEXT parallaxdb - metadata file size in GB (default 8GB), used only with new files
--enable-collection Enables collection of general statistics. Output requires either the --output-stats or --enable-prometheus argument.
--enable-chunkstats Enables collection of data chunk statistics in I/O operations.Output requires either the --output-stats or --enable-prometheus argument.
--output-stats TEXT Creates a thread that outputs the server stats each 10s to the specified file.
--enable-prometheus Enables prometheus output and a corresponding thread.
--prometheus-gateway TEXT Defines the prometheus gateway <ip:port> (Default 127.0.0.1:9091).
--version Print version and exit.
It is possible to run multiple independent GekkoFS instances on the same node. Note, that when these GekkoFS instances
are part of the same file system, use the same rootdir
with different rootdir-suffixe
s.
Shut it down by gracefully killing the process (SIGTERM).
tl;dr example:
export LIBGKFS_ HOSTS_FILE=<hostfile_path>
LD_PRELOAD=<install_path>/lib64/libgkfs_intercept.so cp ~/some_input_data <pseudo_gkfs_mount_dir_path>/some_input_data
LD_PRELOAD=<install_path>/lib64/libgkfs_intercept.so md5sum ~/some_input_data <pseudo_gkfs_mount_dir_path>/some_input_data
Clients read the hostsfile to determine which daemons are part of the GekkoFS instance. Because the client is an
interposition library that is loaded within the context of the application, this information is passed via the
environment variable LIBGKFS_HOSTS_FILE
pointing to the hostsfile path. The client library itself is loaded for each
application process via the LD_PRELOAD
environment variable intercepting file system related calls. If they are
within (or hierarchically under) the GekkoFS mount directory they are processed in the library, otherwise they are
passed to the kernel.
Note, if LD_PRELOAD
is not pointing to the library and, hence the client is not loaded, the mounting directory appears
to be empty.
For MPI application, the LD_PRELOAD
variable can be passed with the -x
argument for mpirun/mpiexec
.
The scripts/run/gkfs
script can be used to simplify starting the GekkoFS daemon on one or multiple nodes. To start
GekkoFS on multiple nodes, a Slurm environment that can execute srun
is required. Users can further
modify scripts/run/gkfs.conf
to mold default configurations to their environment.
The following options are available for scripts/run/gkfs
:
usage: gkfs [-h/--help] [-r/--rootdir <path>] [-m/--mountdir <path>] [-a/--args <daemon_args>] [-f/--foreground <false>]
[--srun <false>] [-n/--numnodes <jobsize>] [--cpuspertask <64>] [--numactl <false>] [-v/--verbose <false>]
{start,stop}
This script simplifies the starting and stopping GekkoFS daemons. If daemons are started on multiple nodes,
a Slurm environment is required. The script looks for the 'gkfs.conf' file in the same directory where
additional permanent configurations can be set.
positional arguments:
command Command to execute: 'start' and 'stop'
optional arguments:
-h, --help Shows this help message and exits
-r, --rootdir <path> Providing the rootdir path for GekkoFS daemons.
-m, --mountdir <path> Providing the mountdir path for GekkoFS daemons.
-a, --args <daemon_arguments>
Add various additional daemon arguments, e.g., "-l ib0 -P ofi+psm2".
-f, --foreground Starts the script in the foreground. Daemons are stopped by pressing 'q'.
--srun Use srun to start daemons on multiple nodes.
-n, --numnodes <n> GekkoFS daemons are started on n nodes.
Nodelist is extracted from Slurm via the SLURM_JOB_ID env variable.
--cpuspertask <#cores> Set the number of cores the daemons can use. Must use '--srun'.
--numactl Use numactl for the daemon. Modify gkfs.conf for further numactl configurations.
-c, --config Path to configuration file. By defaults looks for a 'gkfs.conf' in this directory.
-v, --verbose Increase verbosity
The following environment variables can be used to enable logging in the client library: LIBGKFS_LOG=<module>
and LIBGKFS_LOG_OUTPUT=<path/to/file>
to configure the output module and set the path to the log file of the client
library. If not path is specified in LIBGKFS_LOG_OUTPUT
, the client library will send log messages
to /tmp/gkfs_client.log
.
The following modules are available:
none
: don't print any messagessyscalls
: 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 asexecve()
,execve_at()
,exit()
, andexit_group()
. This module will only be available if the client library is built inDebug
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 inDebug
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 inDebug
mode.most
: All previous options combined exceptsyscalls_at_entry
. This module will only be available if the client library is built inDebug
mode.all
: All previous options combined.trace_reads
: Generate log line with extra information in read operations for guided distributorhelp
: 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,
setting it to LIBGKFS_LOG_SYSCALL_FILTER=epoll_wait,epoll_create
will filter
out any log entries from the epoll_wait()
and epoll_create()
system calls.
Additionally, setting the LIBGKFS_LOG_OUTPUT_TRUNC
environment variable with a value different from 0
will instruct
the logging subsystem to truncate the file used for logging, rather than append to it.
For the daemon, the GKFS_DAEMON_LOG_PATH=<path/to/file>
environment variable can be provided to set the path to the
log file, and the log module can be selected with the GKFS_DAEMON_LOG_LEVEL={off,critical,err,warn,info,debug,trace}
environment variable.
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
The data distribution can be selected at compilation time, we have 2 distributors available:
Chunks are distributed randomly to the different GekkoFS servers.
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
ONGKFS_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.
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.
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.
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:
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.
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.
GekkoFS daemons are able to output general operations (--enable-collection
) and data chunk
statistics (--enable-chunkstats
) to a specified output file via --output-stats <FILE>
. Prometheus can also be used
instead or in addition to the output file. It must be enabled at compile time via the CMake
argument -DGKFS_ENABLE_PROMETHEUS
and the daemon argument --enable-prometheus
. The corresponding statistics are then
pushed to the Prometheus instance.
This software was partially supported by the EC H2020 funded NEXTGenIO project (Project ID: 671951, www.nextgenio.eu).
This software was partially supported by the ADA-FS project under the SPPEXA project (http://www.sppexa.de/) funded by the DFG.
This software is partially supported by the FIDIUM project funded by the DFG.
This software is partially supported by the ADMIRE project (https://www.admire-eurohpc.eu/) funded by the European Union’s Horizon 2020 JTI-EuroHPC Research and Innovation Programme (Grant 956748).