Table of Contents
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Notes
Changes in this version from the one before include:
Updating build instructions and the io-500 hash
Pre-requisites
DAOS - See https://docs.daos.io/latest/admin/hardware/ for installation and setup instructions
MPI - any version / implementation
clush - See https://clustershell.readthedocs.io/en/latest/install.html for installation
Alternatives are possible, though examples are not provided in these instructions.
Build Paths
These instructions assume the following paths. For simplicity, you can set these variables to the actual locations where you have/want these installed.
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MY_DAOS_INSTALL_PATH=${HOME}/install/daos
MY_IO500_PATH=${HOME}/io500 |
Clone and Build IO-500
Clone the IO-500 repo
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git clone https://github.com/IO500/io500.git -b io500-isc24 "${MY_IO500_PATH}" &&
cd "${MY_IO500_PATH}" |
Edit prepare.sh to:
Point to the new pfind branch
Build ior with DFS support
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cat << EOF > io500_prepare.patch
diff --git a/prepare.sh b/prepare.sh
index e38cae6..54dbba5 100755
--- a/prepare.sh
+++ b/prepare.sh
@@ -8,7 +8,7 @@ echo It will output OK at the end if builds succeed
echo
IOR_HASH=bbfea005e2c05726da07171dfe3dfdd6c6011e14
-PFIND_HASH=778dca8
+PFIND_HASH=dfs_find
INSTALL_DIR=\$PWD
BIN=\$INSTALL_DIR/bin
@@ -59,7 +59,7 @@ function get_ior {
function get_pfind {
echo "Preparing parallel find"
- git_co https://github.com/VI4IO/pfind.git pfind \$PFIND_HASH
+ git_co https://github.com/mchaarawi/pfind pfind \$PFIND_HASH
}
function get_schema_tools {
@@ -73,7 +73,7 @@ function build_ior {
pushd "\$BUILD"/ior
./bootstrap
# Add here extra flags
- ./configure --prefix="\$INSTALL_DIR"
+ ./configure --prefix="\$INSTALL_DIR" --with-daos=\${MY_DAOS_INSTALL_PATH}
cd src
\$MAKE clean
\$MAKE install
EOF
git apply io500_prepare.patch |
Update the Makefile with correct paths
The Makefile needs to be updated to use the actual install location of DAOS. you can run:
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cat << EOF > io500_Makefile.patch
diff --git a/Makefile b/Makefile
index ee5cee9..d8fc0e4 100644
--- a/Makefile
+++ b/Makefile
@@ -1,10 +1,12 @@
CC = mpicc
CFLAGS += -std=gnu99 -Wall -Wempty-body -Werror -Wstrict-prototypes -Werror=maybe-uninitialized -Warray-bounds
+CFLAGS += -I\${MY_DAOS_INSTALL_PATH}/include
IORCFLAGS = \$(shell grep CFLAGS ./build/ior/src/build.conf | cut -d "=" -f 2-)
CFLAGS += -g3 -lefence -I./include/ -I./src/ -I./build/pfind/src/ -I./build/ior/src/
IORLIBS = \$(shell grep LDFLAGS ./build/ior/src/build.conf | cut -d "=" -f 2-)
LDFLAGS += -lm \$(IORCFLAGS) \$(IORLIBS) # -lgpfs # may need some additional flags as provided to IOR
+LDFLAGS += -L\${MY_DAOS_INSTALL_PATH}/lib64 -ldaos -ldaos_common -ldfs -lgurt -luuid -lirc
VERSION_GIT=\$(shell git describe --always --abbrev=12)
VERSION_TREE=\$(shell git diff src | wc -l | sed -e 's/ *//g' -e 's/^0//' | sed "s/\([0-9]\)/-\1/")
EOF
git apply io500_Makefile.patch |
Run the prepare.sh script
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${MY_IO500_PATH}/prepare.sh |
Run IO-500
Setup the config file
A sample config-full.ini file for reference: https://github.com/mchaarawi/io500/blob/main/config-full-isc22.ini
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For [find] the nprocs setting under that should be the same or less than the number of processes you want to run with the entire workflow (in io500.sh).
Create DAOS pool, container with type POSIX
For documentation on creating pools, see https://docs.daos.io/latest/admin/pool_operations/.
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dmg pool create -z 100G --label io500_pool daos container create --type POSIX --pool io500_pool --label=io500_cont |
Set the pool and cont environment variables
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export DAOS_POOL=io500_pool export DAOS_CONT=io500_cont |
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https://docs.daos.io/v2.0/user/mpi-io/?h=intel+mpi#intel-mpi
Substitute variables in the config file
This will replace $DAOS_POOL, $DAOS_CONT with their actual values.
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envsubst < config-full-isc22.ini > temp.ini |
Run the io500 in one of two ways:
Run the binary directly with or without the extended mode:
Code Block language bash mpirun -np 16 --hostfile ~/config/cli_hosts ./io500 temp.ini mpirun -np 16 --hostfile ~/config/cli_hosts ./io500 temp.ini --mode=extended
The extended mode is not required for an official submission and will extend your runtime significantly. After the run completes, you will need to tar up the result dir for that run.
Note that some versions of OpenMPI require setting the environment variables on the mpirun command line, so one needs to add the environment variables that are mentioned above on the mpirun command line with the following format:
Code Block language bash mpirun -np 16 -x env1=value1 -x env2=value2 --hostfile ~/config/cli_hosts ./io500 temp.ini
Run the io-500.sh script:
This requires mounting dfuse on the launch node only (not all the compute nodes):
Code Block language bash mkdir /tmp/dfuse dfuse --pool=$DAOS_POOL --container=$DAOS_CONT -m /tmp/dfuse/
Then, edit the io500.sh launch script with the mpirun command and change the local workdir, to add the dfuse prefix
Code Block language bash diff --git a/io500.sh b/io500.sh index 5f0bb89..dd62c35 100755 --- a/io500.sh +++ b/io500.sh @@ -12,10 +12,10 @@ # This script takes its parameters from the same .ini file as io500 binary. io500_ini="$1" # You can set the ini file here io500_mpirun="mpiexec" -io500_mpiargs="-np 2" +io500_mpiargs="-np 16 --hostfile ~/config/cli_hosts" function setup(){ - local workdir="$1" + local workdir="/tmp/dfuse/$1" local resultdir="$2" mkdir -p $workdir $resultdirNote that some versions of OpenMPI require setting the environment variables on the mpirun command line, so one needs to add the environment variables that are mentioned above on the mpirun command line in the script here with the following format:
Code Block language bash io500_mpiargs="-np 16 -x env1=value1 -x env2=value2 --hostfile ~/config/cli_hosts
Then run the io500.sh script which will tar the results for you at the end and place them in the result directory you specified in the ini file:
Code Block language bash ./io500.sh temp.ini
Lastly umount dfuse on the launch node:
Code Block language bash fusermount3 -u /tmp/dfuse/
Results
The tarball generated at the end (whether ran the binary or with the script) with the results can be submitted to the io500 committee for consideration.