- io500
-
#!/bin/bash
#BSUB -q par-multi
#BSUB -oo /home/users/kunkel/io-500-dev/job.out
#BSUB -eo /home/users/kunkel/io-500-dev/job.err
#BSUB -W 45:00
#BSUB -n 128
#BSUB -R "span[ptile=2]"
#BSUB -m ivybridge128G
#### && (hname != host228)"
cd /home/users/kunkel/io-500-dev
export MODULEPATH=$MODULEPATH:/home/users/kunkel/install/modules
module load kunkel/openmpi/3.1
#
# INSTRUCTIONS:
# Edit this file as needed for your machine.
# This simplified version is just for running on a single node.
# It is a simplified version of the site-configs/sandia/startup.sh which include SLURM directives.
# Most of the variables set in here are needed for io500_fixed.sh which gets sourced at the end of this.
# Please also edit 'extra_description' function.
set -euo pipefail # better error handling
# turn these to True successively while you debug and tune this benchmark.
# for each one that you turn to true, go and edit the appropriate function.
# to find the function name, see the 'main' function.
# These are listed in the order that they run.
io500_run_ior_easy="True" # does the write phase and enables the subsequent read
io500_run_md_easy="True" # does the creat phase and enables the subsequent stat
io500_run_ior_hard="True" # does the write phase and enables the subsequent read
io500_run_md_hard="True" # does the creat phase and enables the subsequent read
io500_run_find="True"
io500_run_ior_easy_read="True"
io500_run_md_easy_stat="True"
io500_run_ior_hard_read="True"
io500_run_md_hard_stat="True"
io500_run_md_hard_read="True"
io500_run_md_easy_delete="True" # turn this off if you want to just run find by itself
io500_run_md_hard_delete="True" # turn this off if you want to just run find by itself
io500_run_mdreal="False" # this one is optional
io500_cleanup_workdir="False" # this flag is currently ignored. You'll need to clean up your data files manually if you want to.
# to run this benchmark, find and edit each of these functions.
# please also edit 'extra_description' function to help us collect the required data.
function main {
setup_directories
setup_paths
setup_ior_easy # required if you want a complete score
setup_ior_hard # required if you want a complete score
setup_mdt_easy # required if you want a complete score
setup_mdt_hard # required if you want a complete score
setup_find # required if you want a complete score
setup_mdreal # optional
run_benchmarks
}
function setup_directories {
# set directories for where the benchmark files are created and where the results will go.
# If you want to set up stripe tuning on your output directories or anything similar, then this is good place to do it.
timestamp=`date +%Y.%m.%d-%H.%M.%S` # create a uniquifier
io500_workdir=$PWD/datafiles/io500.$timestamp # directory where the data will be stored
io500_result_dir=$PWD/results/$timestamp # the directory where the output results will be kept
mkdir -p $io500_workdir $io500_result_dir
}
function setup_paths {
# Set the paths to the binaries. If you ran ./utilities/prepare.sh successfully, then binaries are in ./bin/
io500_ior_cmd=$PWD/bin/ior
io500_mdtest_cmd=$PWD/bin/mdtest
io500_mdreal_cmd=$PWD/bin/md-real-io
io500_mpirun="mpiexec"
io500_mpiargs=""
}
function setup_ior_easy {
io500_ior_easy_params="-t 2048k -b 20g -F" # 2M writes, 2 GB per proc, file per proc
}
function setup_mdt_easy {
io500_mdtest_easy_params="-u -L" # unique dir per thread, files only at leaves
io500_mdtest_easy_files_per_proc=200000
}
function setup_ior_hard {
io500_ior_hard_writes_per_proc=7000
io500_ior_hard_other_options="" #e.g., -E to keep precreated files using lfs setstripe, or -a MPIIO
}
function setup_mdt_hard {
io500_mdtest_hard_files_per_proc=8000
}
function setup_find {
#
# setup the find command. This is an area where innovation is allowed.
# There are three default options provided. One is a serial find, one is python
# parallel version, one is C parallel version. Current default is to use serial.
# But it is very slow. We recommend to either customize or use the C parallel version.
# For GPFS, we recommend to use the provided mmfind wrapper described below.
# Instructions below.
# If a custom approach is used, please provide enough info so others can reproduce.
# the serial version that should run (SLOWLY) without modification
#io500_find_mpi="False"
#io500_find_cmd=$PWD/bin/sfind.sh
#io500_find_cmd_args=""
# a parallel version in C, the -s adds a stonewall
# for a real run, turn -s (stonewall) off or set it at 300 or more
# to prepare this (assuming you've run ./utilities/prepare.sh already):
# > cd build/pfind
# > ./prepare.sh
# > ./compile.sh
# > cp pfind ../../bin/
# If you use io500_find_mpi="True", then this will run with the same
# number of MPI nodes and ranks as the other phases.
# If you prefer another number, and fewer might be better here,
# Then you can set io500_find_mpi to be "False" and write a wrapper
# script for this which sets up MPI as you would like. Then change
# io500_find_cmd to point to your wrapper script.
io500_find_mpi="True"
io500_find_cmd="$PWD/bin/pfind"
io500_find_cmd_args="-r $io500_result_dir/pfind_results -s 100 -v -v -v"
# for GPFS systems, you should probably use the provided mmfind wrapper
# if you used ./utilities/prepare.sh, you'll find this wrapper in ./bin/mmfind.sh
#io500_find_mpi="False"
#io500_find_cmd="$PWD/bin/mmfind.sh"
#io500_find_cmd_args=""
}
function setup_mdreal {
io500_mdreal_params="-P=5000 -I=1000"
}
function run_benchmarks {
# Important: source the io500_fixed.sh script. Do not change it. If you discover
# a need to change it, please email the mailing list to discuss
source ./utilities/io500_fixed.sh 2>&1 | tee $io500_result_dir/io-500-summary.$timestamp.txt
}
# Add key/value pairs defining your system
# Feel free to add extra ones if you'd like
function extra_description {
# top level info
io500_info_system_name='xxx' # e.g. Oakforest-PACS
io500_info_institute_name='xxx' # e.g. JCAHPC
io500_info_storage_age_in_months='xxx' # not install date but age since last refresh
io500_info_storage_install_date='xxx' # MM/YY
io500_info_filesystem='xxx' # e.g. BeeGFS, DataWarp, GPFS, IME, Lustre
io500_info_filesystem_version='xxx'
io500_info_filesystem_vendor='xxx'
# client side info
io500_info_num_client_nodes='xxx'
io500_info_procs_per_node='xxx'
# server side info
io500_info_num_metadata_server_nodes='xxx'
io500_info_num_data_server_nodes='xxx'
io500_info_num_data_storage_devices='xxx' # if you have 5 data servers, and each has 5 drives, then this number is 25
io500_info_num_metadata_storage_devices='xxx' # if you have 2 metadata servers, and each has 5 drives, then this number is 10
io500_info_data_storage_type='xxx' # HDD, SSD, persistent memory, etc, feel free to put specific models
io500_info_metadata_storage_type='xxx' # HDD, SSD, persistent memory, etc, feel free to put specific models
io500_info_storage_network='xxx' # infiniband, omnipath, ethernet, etc
io500_info_storage_interface='xxx' # SAS, SATA, NVMe, etc
# miscellaneous
io500_info_whatever='WhateverElseYouThinkRelevant'
}
main
- ior_easy_read
-
IOR-3.1.0: MPI Coordinated Test of Parallel I/O
ior WARNING: fsync() only available in POSIX/MMAP. Using value of 0.
Began: Mon Jun 18 14:57:43 2018
Command line used: /home/users/kunkel/io-500-dev/bin/ior -r -R -C -Q 1 -g -G 27 -k -e -t 2048k -b 20g -F -o /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38/ior_easy/ior_file_easy
Machine: Linux host168.jc.rl.ac.uk
Test 0 started: Mon Jun 18 14:57:43 2018
Summary:
api = MPIIO (version=3, subversion=1)
test filename = /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38/ior_easy/ior_file_easy
access = file-per-process
ordering in a file = sequential offsets
ordering inter file= constant task offsets = 1
clients = 128 (2 per node)
repetitions = 1
xfersize = 2 MiB
blocksize = 20 GiB
aggregate filesize = 2560 GiB
access bw(MiB/s) block(KiB) xfer(KiB) open(s) wr/rd(s) close(s) total(s) iter
------ --------- ---------- --------- -------- -------- -------- -------- ----
read 1842.38 20971520 2048.00 0.274555 1422.58 0.002902 1422.86 0
Max Read: 1842.38 MiB/sec (1931.87 MB/sec)
Summary of all tests:
Operation Max(MiB) Min(MiB) Mean(MiB) StdDev Max(OPs) Min(OPs) Mean(OPs) StdDev Mean(s) Test# #Tasks tPN reps fPP reord reordoff reordrand seed segcnt blksiz xsize aggsize API RefNum
read 1842.38 1842.38 1842.38 0.00 921.19 921.19 921.19 0.00 1422.85774 0 128 2 1 1 1 1 0 0 1 21474836480 2097152 2748779069440 MPIIO 0
Finished: Mon Jun 18 15:21:26 2018
- ior_easy_write
-
IOR-3.1.0: MPI Coordinated Test of Parallel I/O
ior WARNING: fsync() only available in POSIX/MMAP. Using value of 0.
Began: Mon Jun 18 13:30:46 2018
Command line used: /home/users/kunkel/io-500-dev/bin/ior -w -C -Q 1 -g -G 27 -k -e -t 2048k -b 20g -F -o /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38/ior_easy/ior_file_easy
Machine: Linux host168.jc.rl.ac.uk
Test 0 started: Mon Jun 18 13:30:46 2018
Summary:
api = MPIIO (version=3, subversion=1)
test filename = /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38/ior_easy/ior_file_easy
access = file-per-process
ordering in a file = sequential offsets
ordering inter file= constant task offsets = 1
clients = 128 (2 per node)
repetitions = 1
xfersize = 2 MiB
blocksize = 20 GiB
aggregate filesize = 2560 GiB
access bw(MiB/s) block(KiB) xfer(KiB) open(s) wr/rd(s) close(s) total(s) iter
------ --------- ---------- --------- -------- -------- -------- -------- ----
write 4012 20971520 2048.00 0.339175 653.10 0.006481 653.44 0
Max Write: 4011.75 MiB/sec (4206.62 MB/sec)
Summary of all tests:
Operation Max(MiB) Min(MiB) Mean(MiB) StdDev Max(OPs) Min(OPs) Mean(OPs) StdDev Mean(s) Test# #Tasks tPN reps fPP reord reordoff reordrand seed segcnt blksiz xsize aggsize API RefNum
write 4011.75 4011.75 4011.75 0.00 2005.87 2005.87 2005.87 0.00 653.44060 0 128 2 1 1 1 1 0 0 1 21474836480 2097152 2748779069440 MPIIO 0
Finished: Mon Jun 18 13:41:39 2018
- ior_hard_read
-
IOR-3.1.0: MPI Coordinated Test of Parallel I/O
ior WARNING: fsync() only available in POSIX/MMAP. Using value of 0.
Began: Mon Jun 18 15:22:45 2018
Command line used: /home/users/kunkel/io-500-dev/bin/ior -r -R -C -Q 1 -g -G 27 -k -e -t 47008 -b 47008 -s 7000 -o /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38/ior_hard/IOR_file
Machine: Linux host168.jc.rl.ac.uk
Test 0 started: Mon Jun 18 15:22:45 2018
Summary:
api = MPIIO (version=3, subversion=1)
test filename = /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38/ior_hard/IOR_file
access = single-shared-file
ordering in a file = sequential offsets
ordering inter file= constant task offsets = 1
clients = 128 (2 per node)
repetitions = 1
xfersize = 47008 bytes
blocksize = 47008 bytes
aggregate filesize = 39.23 GiB
access bw(MiB/s) block(KiB) xfer(KiB) open(s) wr/rd(s) close(s) total(s) iter
------ --------- ---------- --------- -------- -------- -------- -------- ----
read 51.23 45.91 45.91 0.260798 783.86 0.006161 784.12 0
Max Read: 51.23 MiB/sec (53.71 MB/sec)
Summary of all tests:
Operation Max(MiB) Min(MiB) Mean(MiB) StdDev Max(OPs) Min(OPs) Mean(OPs) StdDev Mean(s) Test# #Tasks tPN reps fPP reord reordoff reordrand seed segcnt blksiz xsize aggsize API RefNum
read 51.23 51.23 51.23 0.00 1142.68 1142.68 1142.68 0.00 784.12326 0 128 2 1 0 1 1 0 0 7000 47008 47008 42119168000 MPIIO 0
Finished: Mon Jun 18 15:35:49 2018
- ior_hard_write
-
IOR-3.1.0: MPI Coordinated Test of Parallel I/O
ior WARNING: fsync() only available in POSIX/MMAP. Using value of 0.
Began: Mon Jun 18 13:51:02 2018
Command line used: /home/users/kunkel/io-500-dev/bin/ior -w -C -Q 1 -g -G 27 -k -e -t 47008 -b 47008 -s 7000 -o /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38/ior_hard/IOR_file
Machine: Linux host168.jc.rl.ac.uk
Test 0 started: Mon Jun 18 13:51:02 2018
Summary:
api = MPIIO (version=3, subversion=1)
test filename = /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38/ior_hard/IOR_file
access = single-shared-file
ordering in a file = sequential offsets
ordering inter file= constant task offsets = 1
clients = 128 (2 per node)
repetitions = 1
xfersize = 47008 bytes
blocksize = 47008 bytes
aggregate filesize = 39.23 GiB
access bw(MiB/s) block(KiB) xfer(KiB) open(s) wr/rd(s) close(s) total(s) iter
------ --------- ---------- --------- -------- -------- -------- -------- ----
write 12.89 45.91 45.91 0.312685 3116.40 0.654598 3117.36 0
Max Write: 12.89 MiB/sec (13.51 MB/sec)
Summary of all tests:
Operation Max(MiB) Min(MiB) Mean(MiB) StdDev Max(OPs) Min(OPs) Mean(OPs) StdDev Mean(s) Test# #Tasks tPN reps fPP reord reordoff reordrand seed segcnt blksiz xsize aggsize API RefNum
write 12.89 12.89 12.89 0.00 287.42 287.42 287.42 0.00 3117.36321 0 128 2 1 0 1 1 0 0 7000 47008 47008 42119168000 MPIIO 0
Finished: Mon Jun 18 14:43:00 2018
- mdtest_easy_delete
-
-- started at 06/18/2018 15:36:02 --
mdtest-1.9.3 was launched with 128 total task(s) on 64 node(s)
Command line used: /home/users/kunkel/io-500-dev/bin/mdtest -r -F -d /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38/mdt_easy -n 200000 -u -L
Path: /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38
FS: 200.0 TiB Used FS: 4.7% Inodes: 409600.0 Mi Used Inodes: 4.7%
128 tasks, 25600000 files
SUMMARY: (of 1 iterations)
Operation Max Min Mean Std Dev
--------- --- --- ---- -------
File creation : 0.000 0.000 0.000 0.000
File stat : 0.000 0.000 0.000 0.000
File read : 0.000 0.000 0.000 0.000
File removal : 44972.581 44972.581 44972.581 0.000
Tree creation : 0.000 0.000 0.000 0.000
Tree removal : 0.282 0.282 0.282 0.000
-- finished at 06/18/2018 15:45:34 --
- mdtest_easy_stat
-
-- started at 06/18/2018 15:21:29 --
mdtest-1.9.3 was launched with 128 total task(s) on 64 node(s)
Command line used: /home/users/kunkel/io-500-dev/bin/mdtest -T -F -d /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38/mdt_easy -n 200000 -u -L
Path: /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38
FS: 200.0 TiB Used FS: 4.7% Inodes: 409600.0 Mi Used Inodes: 4.7%
128 tasks, 25600000 files
SUMMARY: (of 1 iterations)
Operation Max Min Mean Std Dev
--------- --- --- ---- -------
File creation : 0.000 0.000 0.000 0.000
File stat : 347540.711 347540.711 347540.711 0.000
File read : 0.000 0.000 0.000 0.000
File removal : 0.000 0.000 0.000 0.000
Tree creation : 0.000 0.000 0.000 0.000
Tree removal : 0.000 0.000 0.000 0.000
-- finished at 06/18/2018 15:22:43 --
- mdtest_easy_write
-
-- started at 06/18/2018 13:41:41 --
mdtest-1.9.3 was launched with 128 total task(s) on 64 node(s)
Command line used: /home/users/kunkel/io-500-dev/bin/mdtest -C -F -d /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38/mdt_easy -n 200000 -u -L
Path: /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38
FS: 200.0 TiB Used FS: 4.7% Inodes: 409600.0 Mi Used Inodes: 4.7%
128 tasks, 25600000 files
SUMMARY: (of 1 iterations)
Operation Max Min Mean Std Dev
--------- --- --- ---- -------
File creation : 45957.001 45957.001 45957.001 0.000
File stat : 0.000 0.000 0.000 0.000
File read : 0.000 0.000 0.000 0.000
File removal : 0.000 0.000 0.000 0.000
Tree creation : 11.722 11.722 11.722 0.000
Tree removal : 0.000 0.000 0.000 0.000
-- finished at 06/18/2018 13:50:58 --
- mdtest_hard_delete
-
-- started at 06/18/2018 15:45:46 --
mdtest-1.9.3 was launched with 128 total task(s) on 64 node(s)
Command line used: /home/users/kunkel/io-500-dev/bin/mdtest -r -t -F -w 3901 -e 3901 -d /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38/mdt_hard -n 8000
Path: /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38
FS: 200.0 TiB Used FS: 4.7% Inodes: 409600.0 Mi Used Inodes: 4.7%
128 tasks, 1024000 files
SUMMARY: (of 1 iterations)
Operation Max Min Mean Std Dev
--------- --- --- ---- -------
File creation : 0.000 0.000 0.000 0.000
File stat : 0.000 0.000 0.000 0.000
File read : 0.000 0.000 0.000 0.000
File removal : 1133.062 1133.062 1133.062 0.000
Tree creation : 0.000 0.000 0.000 0.000
Tree removal : 5.977 5.977 5.977 0.000
-- finished at 06/18/2018 16:00:50 --
- mdtest_hard_read
-
-- started at 06/18/2018 15:45:37 --
mdtest-1.9.3 was launched with 128 total task(s) on 64 node(s)
Command line used: /home/users/kunkel/io-500-dev/bin/mdtest -E -t -F -w 3901 -e 3901 -d /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38/mdt_hard -n 8000
Path: /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38
FS: 200.0 TiB Used FS: 4.7% Inodes: 409600.0 Mi Used Inodes: 4.7%
128 tasks, 1024000 files
SUMMARY: (of 1 iterations)
Operation Max Min Mean Std Dev
--------- --- --- ---- -------
File creation : 0.000 0.000 0.000 0.000
File stat : 0.000 0.000 0.000 0.000
File read : 142073.997 142073.997 142073.997 0.000
File removal : 0.000 0.000 0.000 0.000
Tree creation : 0.000 0.000 0.000 0.000
Tree removal : 0.000 0.000 0.000 0.000
-- finished at 06/18/2018 15:45:44 --
- mdtest_hard_stat
-
-- started at 06/18/2018 15:35:54 --
mdtest-1.9.3 was launched with 128 total task(s) on 64 node(s)
Command line used: /home/users/kunkel/io-500-dev/bin/mdtest -T -t -F -w 3901 -e 3901 -d /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38/mdt_hard -n 8000
Path: /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38
FS: 200.0 TiB Used FS: 4.7% Inodes: 409600.0 Mi Used Inodes: 4.7%
128 tasks, 1024000 files
SUMMARY: (of 1 iterations)
Operation Max Min Mean Std Dev
--------- --- --- ---- -------
File creation : 0.000 0.000 0.000 0.000
File stat : 175626.263 175626.263 175626.263 0.000
File read : 0.000 0.000 0.000 0.000
File removal : 0.000 0.000 0.000 0.000
Tree creation : 0.000 0.000 0.000 0.000
Tree removal : 0.000 0.000 0.000 0.000
-- finished at 06/18/2018 15:36:00 --
- mdtest_hard_write
-
-- started at 06/18/2018 14:43:04 --
mdtest-1.9.3 was launched with 128 total task(s) on 64 node(s)
Command line used: /home/users/kunkel/io-500-dev/bin/mdtest -C -t -F -w 3901 -e 3901 -d /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38/mdt_hard -n 8000
Path: /home/users/kunkel/io-500-dev/datafiles/io500.2018.06.18-13.30.38
FS: 200.0 TiB Used FS: 4.7% Inodes: 409600.0 Mi Used Inodes: 4.7%
128 tasks, 1024000 files
SUMMARY: (of 1 iterations)
Operation Max Min Mean Std Dev
--------- --- --- ---- -------
File creation : 1324.414 1324.414 1324.414 0.000
File stat : 0.000 0.000 0.000 0.000
File read : 0.000 0.000 0.000 0.000
File removal : 0.000 0.000 0.000 0.000
Tree creation : 209.431 209.431 209.431 0.000
Tree removal : 0.000 0.000 0.000 0.000
-- finished at 06/18/2018 14:55:57 --
- result_summary
-
[RESULT] BW phase 1 ior_easy_write 3.918 GB/s : time 653.44 seconds
[RESULT] IOPS phase 1 mdtest_easy_write 45.957 kiops : time 558.94 seconds
[RESULT] BW phase 2 ior_hard_write 0.013 GB/s : time 3117.36 seconds
[RESULT] IOPS phase 2 mdtest_hard_write 1.324 kiops : time 776.51 seconds
[RESULT] IOPS phase 3 find 1.370 kiops : time 105.15 seconds
[RESULT] BW phase 3 ior_easy_read 1.799 GB/s : time 1422.86 seconds
[RESULT] IOPS phase 4 mdtest_easy_stat 347.541 kiops : time 76.09 seconds
[RESULT] BW phase 4 ior_hard_read 0.050 GB/s : time 784.12 seconds
[RESULT] IOPS phase 5 mdtest_hard_stat 175.626 kiops : time 10.95 seconds
[RESULT] IOPS phase 6 mdtest_easy_delete 44.973 kiops : time 574.36 seconds
[RESULT] IOPS phase 7 mdtest_hard_read 142.074 kiops : time 9.34 seconds
[RESULT] IOPS phase 8 mdtest_hard_delete 1.133 kiops : time 906.01 seconds
[SCORE] Bandwidth 0.258125 GB/s : IOPS 20.9315 kiops : TOTAL 2.32442