- io500
-
#!/bin/bash
#PJM -L rscgrp=ofptest-all
#PJM -L node=2048
#PJM --mpi proc=16384
#PJM -L elapse=2:00:00
#PJM -g gz02
#PJM -j
#
# 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.
set -euo pipefail # better error handling
#DIR=/cache/xg17i000/x10007/io-500-dev
DIR=$PJM_O_CACHEDIR
export I_MPI_PIN_PROCESSOR_EXCLUDE_LIST=0,68,136,204
# turn these to True successively while you debug and tune this benchmark.
# for each one that you turn to true, go and edit the appropriate function.
# to find the function name, see the 'main' function.
# These are listed in the order that they run.
io500_run_ior_easy="True" # does the write phase and enables the subsequent read
io500_run_md_easy="True" # does the creat phase and enables the subsequent stat
io500_run_ior_hard="True" # does the write phase and enables the subsequent read
io500_run_md_hard="True" # does the creat phase and enables the subsequent read
io500_run_find="True"
io500_run_ior_easy_read="True"
io500_run_md_easy_stat="True"
io500_run_ior_hard_read="True"
io500_run_md_hard_stat="True"
io500_run_md_hard_read="True"
io500_run_md_easy_delete="True" # turn this off if you want to just run find by itself
io500_run_md_hard_delete="True" # turn this off if you want to just run find by itself
io500_run_mdreal="False" # this one is optional
io500_cleanup_workdir="False" # this flag is currently ignored. You'll need to clean up your data files manually if you want to.
function main {
setup_directories
setup_paths
setup_ior_easy # required if you want a complete score
setup_ior_hard # required if you want a complete score
setup_mdt_easy # required if you want a complete score
setup_mdt_hard # required if you want a complete score
setup_find # required if you want a complete score
setup_mdreal # optional
run_benchmarks
}
function setup_directories {
# set directories for where the benchmark files are created and where the results will go.
# If you want to set up stripe tuning on your output directories or anything similar, then this is good place to do it.
timestamp=`date +%Y.%m.%d-%H.%M.%S` # create a uniquifier
io500_workdir=$DIR/datafiles/io500.$timestamp # directory where the data will be stored
io500_result_dir=$DIR/results/$timestamp # the directory where the output results will be kept
mkdir -p $io500_workdir $io500_result_dir
}
function setup_paths {
# Set the paths to the binaries. If you ran ./utilities/prepare.sh successfully, then binaries are in ./bin/
io500_ior_cmd=$DIR/bin/ior
io500_mdtest_cmd=$DIR/bin/mdtest
io500_mdreal_cmd=$DIR/bin/md-real-io
io500_mpirun="mpiexec.hydra"
io500_mpiargs="-n ${PJM_MPI_PROC}"
}
function setup_ior_easy {
io500_ior_easy_params="-t 2048k -b 16g -F" # 2M writes, 2 GB per proc, file per proc
}
function setup_mdt_easy {
io500_mdtest_easy_params="-u -L" # unique dir per thread, files only at leaves
io500_mdtest_easy_files_per_proc=650
}
function setup_ior_hard {
io500_ior_hard_writes_per_proc=300000
}
function setup_mdt_hard {
io500_mdtest_hard_files_per_proc=40
}
function setup_find {
#
# setup the find command. This is an area where innovation is allowed.
# There are three default options provided. One is a serial find, one is python
# parallel version, one is C parallel version. Current default is to use serial.
# But it is very slow. We recommend to either customize or use the C parallel version.
# Instructions below.
# If a custom approach is used, please provide enough info so others can reproduce.
# the serial version that should run (SLOWLY) without modification
io500_find_mpi="False"
io500_find_cmd=$DIR/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="$DIR/bin/pfind"
io500_find_cmd_args="-s 300 -r $io500_result_dir/pfind_results"
# a parallel version that might require some work, it is a python3 program
# if you used utilities/prepare.sh, it should already be there.
# change the stonewall to 300 to get a valid score
#set +u
#export PYTHONPATH=$PYTHONPATH:$PWD/bin/lib
#io500_find_mpi="True"
#io500_find_cmd="$PWD/bin/pfind -stonewall 1"
#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 ./bin/io500_fixed.sh 2>&1 | tee $io500_result_dir/io-500-summary.$timestamp.txt
}
# Add key/value pairs defining your system if you want
# This function needs to exist although it doesn't have to output anything if you don't want
function extra_description {
echo "System_name='JCAHPC Oakforest-PACS'"
}
main
#rm -rf $io500_workdir
- ior_easy_read
-
IOR-3.1.0: MPI Coordinated Test of Parallel I/O
ior WARNING: fsync() only available in POSIX. Using value of 0.
Began: Thu May 3 21:00:12 2018
Command line used: /cache/0/gz02/z30218/io-500-dev/bin/ior -r -R -C -Q 1 -g -G 27 -k -e -t 2048k -b 128g -F -o /cache/0/gz02/z30218/io-500-dev/datafiles/io500.2018.05.03-20.36.21/ior_easy/ior_file_easy
Machine: Linux c0001.ofp
Test 0 started: Thu May 3 21:00:12 2018
Summary:
api = MPIIO (version=3, subversion=1)
test filename = /cache/0/gz02/z30218/io-500-dev/datafiles/io500.2018.05.03-20.36.21/ior_easy/ior_file_easy
access = file-per-process
ordering in a file = sequential offsets
ordering inter file= constant task offsets = 1
clients = 2048 (1 per node)
repetitions = 1
xfersize = 2 MiB
blocksize = 128 GiB
aggregate filesize = 262144 GiB
access bw(MiB/s) block(KiB) xfer(KiB) open(s) wr/rd(s) close(s) total(s) iter
------ --------- ---------- --------- -------- -------- -------- -------- ----
read 680415 134217728 2048.00 0.237256 394.27 0.006414 394.52 0
Max Read: 680414.54 MiB/sec (713466.36 MB/sec)
Summary of all tests:
Operation Max(MiB) Min(MiB) Mean(MiB) StdDev Mean(s) Test# #Tasks tPN reps fPP reord reordoff reordrand seed segcnt blksiz xsize aggsize API RefNum
read 680414.54 680414.54 680414.54 0.00 394.51752 0 2048 1 1 1 1 1 0 0 1 137438953472 2097152 281474976710656 MPIIO 0
Finished: Thu May 3 21:06:47 2018
- ior_easy_write
-
IOR-3.1.0: MPI Coordinated Test of Parallel I/O
ior WARNING: fsync() only available in POSIX. Using value of 0.
Began: Thu May 3 20:36:45 2018
Command line used: /cache/0/gz02/z30218/io-500-dev/bin/ior -w -C -Q 1 -g -G 27 -k -e -t 2048k -b 128g -F -o /cache/0/gz02/z30218/io-500-dev/datafiles/io500.2018.05.03-20.36.21/ior_easy/ior_file_easy
Machine: Linux c0001.ofp
Test 0 started: Thu May 3 20:36:45 2018
Summary:
api = MPIIO (version=3, subversion=1)
test filename = /cache/0/gz02/z30218/io-500-dev/datafiles/io500.2018.05.03-20.36.21/ior_easy/ior_file_easy
access = file-per-process
ordering in a file = sequential offsets
ordering inter file= constant task offsets = 1
clients = 2048 (1 per node)
repetitions = 1
xfersize = 2 MiB
blocksize = 128 GiB
aggregate filesize = 262144 GiB
access bw(MiB/s) block(KiB) xfer(KiB) open(s) wr/rd(s) close(s) total(s) iter
------ --------- ---------- --------- -------- -------- -------- -------- ----
write 762634 134217728 2048.00 0.177675 350.31 1.50 351.98 0
Max Write: 762634.11 MiB/sec (799679.83 MB/sec)
Summary of all tests:
Operation Max(MiB) Min(MiB) Mean(MiB) StdDev Mean(s) Test# #Tasks tPN reps fPP reord reordoff reordrand seed segcnt blksiz xsize aggsize API RefNum
write 762634.11 762634.11 762634.11 0.00 351.98459 0 2048 1 1 1 1 1 0 0 1 137438953472 2097152 281474976710656 MPIIO 0
Finished: Thu May 3 20:42:37 2018
- ior_hard_read
-
IOR-3.1.0: MPI Coordinated Test of Parallel I/O
ior WARNING: fsync() only available in POSIX. Using value of 0.
Began: Thu May 3 21:08:26 2018
Command line used: /cache/0/gz02/z30218/io-500-dev/bin/ior -r -R -C -Q 1 -g -G 27 -k -e -t 47008 -b 47008 -s 2400000 -o /cache/0/gz02/z30218/io-500-dev/datafiles/io500.2018.05.03-20.36.21/ior_hard/IOR_file
Machine: Linux c0001.ofp
Test 0 started: Thu May 3 21:08:26 2018
Summary:
api = MPIIO (version=3, subversion=1)
test filename = /cache/0/gz02/z30218/io-500-dev/datafiles/io500.2018.05.03-20.36.21/ior_hard/IOR_file
access = single-shared-file
ordering in a file = sequential offsets
ordering inter file= constant task offsets = 1
clients = 2048 (1 per node)
repetitions = 1
xfersize = 47008 bytes
blocksize = 47008 bytes
aggregate filesize = 215185.55 GiB
access bw(MiB/s) block(KiB) xfer(KiB) open(s) wr/rd(s) close(s) total(s) iter
------ --------- ---------- --------- -------- -------- -------- -------- ----
read 293979 45.91 45.91 0.196741 749.33 0.018433 749.54 0
Max Read: 293978.72 MiB/sec (308259.03 MB/sec)
Summary of all tests:
Operation Max(MiB) Min(MiB) Mean(MiB) StdDev Mean(s) Test# #Tasks tPN reps fPP reord reordoff reordrand seed segcnt blksiz xsize aggsize API RefNum
read 293978.72 293978.72 293978.72 0.00 749.54404 0 2048 1 1 0 1 1 0 0 2400000 47008 47008 231053721600000 MPIIO 0
Finished: Thu May 3 21:20:56 2018
- ior_hard_write
-
IOR-3.1.0: MPI Coordinated Test of Parallel I/O
ior WARNING: fsync() only available in POSIX. Using value of 0.
Began: Thu May 3 20:48:12 2018
Command line used: /cache/0/gz02/z30218/io-500-dev/bin/ior -w -C -Q 1 -g -G 27 -k -e -t 47008 -b 47008 -s 2400000 -o /cache/0/gz02/z30218/io-500-dev/datafiles/io500.2018.05.03-20.36.21/ior_hard/IOR_file
Machine: Linux c0001.ofp
Test 0 started: Thu May 3 20:48:12 2018
Summary:
api = MPIIO (version=3, subversion=1)
test filename = /cache/0/gz02/z30218/io-500-dev/datafiles/io500.2018.05.03-20.36.21/ior_hard/IOR_file
access = single-shared-file
ordering in a file = sequential offsets
ordering inter file= constant task offsets = 1
clients = 2048 (1 per node)
repetitions = 1
xfersize = 47008 bytes
blocksize = 47008 bytes
aggregate filesize = 215185.55 GiB
access bw(MiB/s) block(KiB) xfer(KiB) open(s) wr/rd(s) close(s) total(s) iter
------ --------- ---------- --------- -------- -------- -------- -------- ----
write 709364 45.91 45.91 0.139181 310.33 0.156248 310.63 0
Max Write: 709364.13 MiB/sec (743822.20 MB/sec)
Summary of all tests:
Operation Max(MiB) Min(MiB) Mean(MiB) StdDev Mean(s) Test# #Tasks tPN reps fPP reord reordoff reordrand seed segcnt blksiz xsize aggsize API RefNum
write 709364.13 709364.13 709364.13 0.00 310.63031 0 2048 1 1 0 1 1 0 0 2400000 47008 47008 231053721600000 MPIIO 0
Finished: Thu May 3 20:53:23 2018
- mdtest_easy_delete
-
-- started at 05/03/2018 21:21:50 --
mdtest-1.9.3 was launched with 2048 total task(s) on 2048 node(s)
Command line used: /cache/0/gz02/z30218/io-500-dev/bin/mdtest -r -F -d /cache/0/gz02/z30218/io-500-dev/datafiles/io500.2018.05.03-20.36.21/mdt_easy -n 5200 -u -L
Path:
FS: 23597.0 TiB Used FS: 15.9% Inodes: 12312.0 Mi Used Inodes: 7.8%
2048 tasks, 10649600 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 : 22182.094 22182.094 22182.094 0.000
Tree creation : 0.000 0.000 0.000 0.000
Tree removal : 0.683 0.683 0.683 0.000
-- finished at 05/03/2018 21:29:52 --
- mdtest_easy_stat
-
-- started at 05/03/2018 21:07:10 --
mdtest-1.9.3 was launched with 2048 total task(s) on 2048 node(s)
Command line used: /cache/0/gz02/z30218/io-500-dev/bin/mdtest -T -F -d /cache/0/gz02/z30218/io-500-dev/datafiles/io500.2018.05.03-20.36.21/mdt_easy -n 5200 -u -L
Path:
FS: 23597.0 TiB Used FS: 15.9% Inodes: 12312.0 Mi Used Inodes: 7.8%
2048 tasks, 10649600 files
SUMMARY: (of 1 iterations)
Operation Max Min Mean Std Dev
--------- --- --- ---- -------
File creation : 0.000 0.000 0.000 0.000
File stat : 202010.929 202010.929 202010.929 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 05/03/2018 21:08:03 --
- mdtest_easy_write
-
-- started at 05/03/2018 20:43:00 --
mdtest-1.9.3 was launched with 2048 total task(s) on 2048 node(s)
Command line used: /cache/0/gz02/z30218/io-500-dev/bin/mdtest -C -F -d /cache/0/gz02/z30218/io-500-dev/datafiles/io500.2018.05.03-20.36.21/mdt_easy -n 5200 -u -L
Path:
FS: 23597.0 TiB Used FS: 15.9% Inodes: 12312.0 Mi Used Inodes: 7.7%
2048 tasks, 10649600 files
SUMMARY: (of 1 iterations)
Operation Max Min Mean Std Dev
--------- --- --- ---- -------
File creation : 37014.661 37014.661 37014.661 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 : 3.686 3.686 3.686 0.000
Tree removal : 0.000 0.000 0.000 0.000
-- finished at 05/03/2018 20:47:48 --
- mdtest_hard_delete
-
-- started at 05/03/2018 21:30:42 --
mdtest-1.9.3 was launched with 2048 total task(s) on 2048 node(s)
Command line used: /cache/0/gz02/z30218/io-500-dev/bin/mdtest -r -t -F -w 3901 -e 3901 -d /cache/0/gz02/z30218/io-500-dev/datafiles/io500.2018.05.03-20.36.21/mdt_hard -n 320
Path:
FS: 23597.0 TiB Used FS: 15.9% Inodes: 12312.0 Mi Used Inodes: 7.7%
2048 tasks, 655360 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 : 755.741 755.741 755.741 0.000
Tree creation : 0.000 0.000 0.000 0.000
Tree removal : 41.370 41.370 41.370 0.000
-- finished at 05/03/2018 21:45:09 --
- mdtest_hard_read
-
-- started at 05/03/2018 21:30:15 --
mdtest-1.9.3 was launched with 2048 total task(s) on 2048 node(s)
Command line used: /cache/0/gz02/z30218/io-500-dev/bin/mdtest -E -t -F -w 3901 -e 3901 -d /cache/0/gz02/z30218/io-500-dev/datafiles/io500.2018.05.03-20.36.21/mdt_hard -n 320
Path:
FS: 23597.0 TiB Used FS: 15.9% Inodes: 12312.0 Mi Used Inodes: 7.7%
2048 tasks, 655360 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 : 266706.060 266706.060 266706.060 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 05/03/2018 21:30:17 --
- mdtest_hard_stat
-
-- started at 05/03/2018 21:21:19 --
mdtest-1.9.3 was launched with 2048 total task(s) on 2048 node(s)
Command line used: /cache/0/gz02/z30218/io-500-dev/bin/mdtest -T -t -F -w 3901 -e 3901 -d /cache/0/gz02/z30218/io-500-dev/datafiles/io500.2018.05.03-20.36.21/mdt_hard -n 320
Path:
FS: 23597.0 TiB Used FS: 15.9% Inodes: 12312.0 Mi Used Inodes: 7.8%
2048 tasks, 655360 files
SUMMARY: (of 1 iterations)
Operation Max Min Mean Std Dev
--------- --- --- ---- -------
File creation : 0.000 0.000 0.000 0.000
File stat : 67241.783 67241.783 67241.783 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 05/03/2018 21:21:29 --
- mdtest_hard_write
-
-- started at 05/03/2018 20:53:45 --
mdtest-1.9.3 was launched with 2048 total task(s) on 2048 node(s)
Command line used: /cache/0/gz02/z30218/io-500-dev/bin/mdtest -C -t -F -w 3901 -e 3901 -d /cache/0/gz02/z30218/io-500-dev/datafiles/io500.2018.05.03-20.36.21/mdt_hard -n 320
Path:
FS: 23597.0 TiB Used FS: 15.9% Inodes: 12312.0 Mi Used Inodes: 7.8%
2048 tasks, 655360 files
SUMMARY: (of 1 iterations)
Operation Max Min Mean Std Dev
--------- --- --- ---- -------
File creation : 1959.867 1959.867 1959.867 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 : 363.238 363.238 363.238 0.000
Tree removal : 0.000 0.000 0.000 0.000
-- finished at 05/03/2018 20:59:20 --
- result_summary
-
[RESULT] BW phase 1 ior_easy_write 744.760 GB/s : time 351.98 seconds
[RESULT] IOPS phase 1 mdtest_easy_write 37.015 kiops : time 310.99 seconds
[RESULT] BW phase 2 ior_hard_write 692.738 GB/s : time 310.63 seconds
[RESULT] IOPS phase 2 mdtest_hard_write 1.960 kiops : time 356.55 seconds
[RESULT] IOPS phase 3 find 394.980 kiops : time 28.63 seconds
[RESULT] BW phase 3 ior_easy_read 664.468 GB/s : time 394.52 seconds
[RESULT] IOPS phase 4 mdtest_easy_stat 202.011 kiops : time 75.58 seconds
[RESULT] BW phase 4 ior_hard_read 287.089 GB/s : time 749.54 seconds
[RESULT] IOPS phase 5 mdtest_hard_stat 67.242 kiops : time 32.99 seconds
[RESULT] IOPS phase 6 mdtest_easy_delete 22.182 kiops : time 503.00 seconds
[RESULT] IOPS phase 7 mdtest_hard_read 266.706 kiops : time 25.69 seconds
[RESULT] IOPS phase 8 mdtest_hard_delete 0.756 kiops : time 891.32 seconds
[SCORE] Bandwidth 560.104 GB/s : IOPS 33.8903 kiops : TOTAL 18982.0925