This page explains how to deploy MPI (and/or GNU parallel) cluster with NFS filesystem in the KASI cloud. Here, OpenMPI (https://www.open-mpi.org/) is used as an MPI implementation. If you like to use Intel oneAPI toolkit and its MPI implementation, see the tip section of the current page. Slurm (https://slurm.schedmd.com/) workload manager can be installed in the cluster too. This how-to assumes that users know how to use a single VM by following the guide given in KASI Science Cloud : VM instances. In particular, following KASI Science Cloud : VM instances#Step5.RemoteaccesstoVMinstancesviaSSHtunneling will help you access created clusters by using SSH. The basic usage scenario is: 1) user prepares codes and data in the created NFS volume, 2) compile or run the prepared code with OpenMPI (or Intel MPI) w/ or w/o Slurm, 3) output files are stored in the NFS volume, and 4) if needed, an external NAS volume is accessed in the VMs to receive/send the data between the created MPI cluster and the NAS (see KASI Science Cloud : VM instances#Step4.ConfiguretheVMinstanceforremotedesktop&externaldatastore). The same scenario also works in the case using GNU parallel with other codes. The related codes and shell scripts mentioned in this how-to are available in https://github.com/astromsshin/cloud_ex. Cloning the github repository to the NFS volume is the easies way to use the provided materials.
If you have questions and suggestions about this tutorial page and related problems, please, contact Min-Su Shin.
Step 1. Choose a cluster template: KASI-OpenMPI-Cluster or KASI-OpenMPI-Cluster-Slurm
As presented in the following figure, two options are available for the cluster. If you need Slurm in your cluster, choose KASI-OpenMPI-Cluster-Slurm template in Project → Cluster Infra → KASI Cluster Templates. If you simply need an MPI(or GNU parallel)-enabled cluster, choose KASI-OpenMPI-Cluster.
Click Next button in the following page after checking whether you are about to run a right cluster template.
Step 2. Configure a cluster by typing configuration parameters
- Stack Name: the name of the cluster which determines the hostnames of the master and slave VM nodes in the cluster.
- Password for user: password required to control the created cluster in certain situations.
- Image: VM system image.
- Flavor: VM flavor.
- Network: choose kasi-user-network.
- Minion VMs Number: the number of slave nodes. If you plan to use Slurm, it might be the number of Slurm work nodes which do not include the master node.
- NFS Mount Path: NFS directory path which will be prepared in all nodes including both master and slave nodes.
- NFS Size: the size of NFS volume.
- SSH Keys: ssh key used to access created VMs.
- Root Password: root password for root account in all nodes of the cluster. You may want to change the password after the cluster is created.
- User Script: shell commands that will be executed in all VM nodes of the cluster. Type custom commands as a single line (see https://dev.to/0xbf/run-multiple-commands-in-one-line-with-and-linux-tips-5hgm about how to use , ;, &&, ||). If you like to use GNU parallel in the cluster, type apt install parallel -y as shown above. If you are not familiar with apt command in Ubuntu OS, see https://ubuntu.com/server/docs/package-management.
Step 3. Checking the creation process
You can check the progress of creating the cluster in Cluster Infra → KASI Clusters, Compute → Instances, and Share → Shares as shown in the following figures.
Step 4. (Optional) tasks after creating the cluster
Because it takes time to build all VM nodes in the cluster, you may need to confirm that all nodes are ready with the required tools. The following is the shell script https://github.com/astromsshin/cloud_ex/blob/main/ex_mpi_check_mpirun.sh
#!/bin/bash
CLUSTERNAME="mycluster"
MINIONLASTIND="14"
echo "... checking ${CLUSTERNAME}-master"
res=$(which mpirun | wc -l)
if [ ${res} -ne "1" ]
then
echo "[WARNING] ${CLUSTERNAME}-master is not ready yet."
fi
for ind in $(seq 0 ${MINIONLASTIND})
do
echo "... checking ${CLUSTERNAME}-minion-${ind}"
res=$(ssh ${CLUSTERNAME}-minion-${ind} "which mpirun" | wc -l)
if [ ${res} -ne "1" ]
then
echo "[WARNING] ${CLUSTERNAME}-minion-${ind} is not ready yet."
fi
done
The above script tests whether mpirun is available or not in all cluster VM nodes. https://github.com/astromsshin/cloud_ex/blob/main/ex_mpi_check_munged_and_mpirun.sh conducts the similar test for Slurm as well as OpenMPI as shown below.
#!/bin/bash
CLUSTERNAME="mycluster"
MINIONLASTIND="14"
echo "... checking ${CLUSTERNAME}-master"
res=$(which munged mpirun | wc -l)
if [ ${res} -ne "2" ]
then
echo "[WARNING] ${CLUSTERNAME}-master is not ready yet."
fi
for ind in $(seq 0 ${MINIONLASTIND})
do
echo "... checking ${CLUSTERNAME}-minion-${ind}"
res=$(ssh ${CLUSTERNAME}-minion-${ind} "which munged mpirun" | wc -l)
if [ ${res} -ne "2" ]
then
echo "[WARNING] ${CLUSTERNAME}-minion-${ind} is not ready yet."
fi
done
Step 5. Erasing the cluster
Choose the cluster in Cluster Infra → KASI Clusters by clicking Delete Stacks. If some VM nodes are not erases cleanly, delete the VMs following the instruction given in KASI Science Cloud : VM instances.
Useful Tips
Running MPI codes
Without Slurm, you can simply run MPI codes by mpirun. The following example compile the example C++ MPI codes in https://github.com/astromsshin/cloud_ex and run them.
mpic++ -o a.out ex_mpi_hostname.cpp mpic++ -o a.out ex_mpi_montecarlo_pi.cpp mpirun --allow-run-as-root -np 32 --hostfile ./ex_mpirun_hostfile.txt ./a.out
See https://www.open-mpi.org/doc/v4.0/man1/mpirun.1.php or https://www.open-mpi.org/faq/?category=running for mpirun. You need to prepare a hostfile for mpirun, which is ex_mpirun_hostfile.txt in the above example. For example, the hostfile is like the following.
mycluster-master mycluster-minion-0 mycluster-minion-1
When your cluster is equipped with Slurm, you may need to use Slurm commands and follow the Slurm's way to submit jobs. See https://slurm.schedmd.com/sbatch.html or https://www.open-mpi.org/faq/?category=slurm. In the following example, ex_slurm_openmpi.job file is submitted via the sbatch command.
sbatch -N 3 -n 24 ex_slurm_openmpi.job
where ex_slurm_openmpi.job is the following
#!/bin/bash mpirun --allow-run-as-root ./a.out
Running GNU Parallel
You can run GNU parallel to execute jobs in remote hosts, i.e., cluster slave nodes. See https://www.gnu.org/software/parallel/parallel_tutorial.html#remote-execution (or https://www.biostars.org/p/63816/). The following example run some simple shell commands on nodes lsited in ex_parallel_hostfile.txt.
parallel --nonall --sshloginfile ex_parallel_hostfile.txt hostname
parallel --workdir /mnt/mpi --sshloginfile ex_parallel_hostfile.txt 'hostname; touch $RANDOM-$(hostname)-{}.txt' ::: 3 4 5 6 7 8 9 10 11 12
where ex_parallel_hostfile.txt is like the following
: mycluster-minion-0 mycluster-minion-1
Executing custom commands in multiple VM nodes (e.g., checking availability of Pythone modules in multiple VM nodes)
Because the created cluster has prepared environments allowing ssh access to all VM nodes for root account in a key-based login mode without password, the following script works via ssh remote execution in all remote VM nodes.
#!/bin/bash
RUNCMD='cd /tmp; /mnt/mpi/cloud_ex/tool_install_and_setup_conda_in_local_volume.sh'
CLUSTERNAME="mycluster"
MINIONLASTIND="2"
echo "... install on ${CLUSTERNAME}-master"
echo $RUNCMD | bash
for ind in $(seq 0 ${MINIONLASTIND})
do
echo "... install on ${CLUSTERNAME}-minion-${ind}"
ssh ${CLUSTERNAME}-minion-${ind} "${RUNCMD}"
done
This script is available at https://github.com/astromsshin/cloud_ex/blob/main/tool_execute_commands_all_nodes.sh . The script shows a typical case of executing custom commands in all VM nodes including a master node in the cluster. Other scripts in this tip section basically follow the same way as the above script in executing specific commands. If you are not familiar with executing multiple Linux shell commands in a single command-line, see https://dev.to/0xbf/run-multiple-commands-in-one-line-with-and-linux-tips-5hgm . One example of using the above method is checking availability of Python modules in multiple VM nodes including the cluster master. The following script (https://github.com/astromsshin/cloud_ex/blob/main/tool_test_whether_python_modules_available.sh) runs a short Python script (from tqdm import tqdm; from astropy.io import fits; from sklearn import mixture; import matplotlib.pyplot as plt; import numpy) which does not cause errors when the required modules are available.
#!/bin/bash
CLUSTERNAME="mycluster"
MINIONLASTIND="2"
RUNCMD='echo "Checking on $(hostname)"; python3 -c "from tqdm import tqdm; from astropy.io import fits; from sklearn import mixture; import matplotlib.pyplot as plt; import numpy; print(\"SUCCESS\")"'
echo "... install on ${CLUSTERNAME}-master"
echo $RUNCMD | bash
for ind in $(seq 0 ${MINIONLASTIND})
do
echo "... install on ${CLUSTERNAME}-minion-${ind}"
ssh ${CLUSTERNAME}-minion-${ind} "${RUNCMD}"
done
Changing root password in multiple VM nodes
SSH remote execution can be used to change root passowrds in all VM nodes as described in https://github.com/astromsshin/cloud_ex/blob/main/tool_change_password_all_nodes.sh:
#!/bin/bash
CLUSTERNAME="mycluster"
MINIONLASTIND="14"
PWUSER="root"
NEWPASSWORD="xxxxxxxxxx"
echo "... changing ${CLUSTERNAME}-master : ${PWUSER}"
echo -e "${NEWPASSWORD}\n${NEWPASSWORD}" | passwd ${PWUSER}
for ind in $(seq 0 ${MINIONLASTIND})
do
echo "... changing ${CLUSTERNAME}-minion-${ind} : ${PWUSER}"
ssh ${CLUSTERNAME}-minion-${ind} "echo -e \"${NEWPASSWORD}\n${NEWPASSWORD}\" | passwd ${PWUSER}"
done
where PWUSER is a user account and NEWPASSWORD is a new password.
Changing password of ubuntu account and preparing key-based ssh login environment in multiple VM nodes
Ubuntu account is available as a default account in addition to root account. You may want to use the ubuntu account as your main account to use the created cluster. The following script (https://github.com/astromsshin/cloud_ex/blob/main/tool_change_password_for_ubuntu_all_nodes_and_setup_sshkey.sh) helps you setup the environment with the ubuntu account by changing a password for the ubuntu account and adding a generated ssh key file to the right directory.
#!/bin/bash
# this script should be executed by root in the master node.
CLUSTERNAME="mycluster"
MINIONLASTIND="4"
PWUSER="ubuntu"
NEWPASSWORD="xxxxxxxxxx"
NFSDIR="/mnt/mpi"
# changing password of ubuntu account.
echo "... changing ${CLUSTERNAME}-master : ${PWUSER}"
echo -e "${NEWPASSWORD}\n${NEWPASSWORD}" | passwd ${PWUSER}
for ind in $(seq 0 ${MINIONLASTIND})
do
echo "... changing ${CLUSTERNAME}-minion-${ind} : ${PWUSER}"
ssh ${CLUSTERNAME}-minion-${ind} "echo -e \"${NEWPASSWORD}\n${NEWPASSWORD}\" | passwd ${PWUSER}"
done
# generate ssh-key
rm -f ${NFSDIR}/id_ed25519 ${NFSDIR}/id_ed25519.pub
### you should type empty passwords by entering twice.
ssh-keygen -t ed25519 << endskey
${NFSDIR}/id_ed25519
endskey
# setup the environemnt for ssh access without password among the cluster nodes
# for ubuntu account
### master
echo "setup the master: ${CLUSTERNAME}-master"
cp -f ${NFSDIR}/id_ed25519 /home/ubuntu/.ssh/
cp -f ${NFSDIR}/id_ed25519.pub /home/ubuntu/.ssh/
chown ubuntu:ubuntu /home/ubuntu/.ssh/id_ed25519*
chmod 600 /home/ubuntu/.ssh/id_ed25519
chmod 644 /home/ubuntu/.ssh/id_ed25519.pub
cat /home/ubuntu/.ssh/id_ed25519.pub >> /home/ubuntu/.ssh/authorized_keys
### slaves
for ind in $(seq 0 ${MINIONLASTIND})
do
echo "setup the slave: ${CLUSTERNAME}-minion-${ind}"
ssh ${CLUSTERNAME}-minion-${ind} "cp -f ${NFSDIR}/id_ed25519 /home/ubuntu/.ssh/; cp -f ${NFSDIR}/id_ed25519.pub /home/ubuntu/.ssh/; chown ubuntu:ubuntu /home/ubuntu/.ssh/id_ed25519*; chmod 600 /home/ubuntu/.ssh/id_ed25519; chmod 644 /home/ubuntu/.ssh/id_ed25519.pub; cat /home/ubuntu/.ssh/id_ed25519.pub >> /home/ubuntu/.ssh/authorized_keys"
done
The above script should be executed by root account. If you like to use a different type in stead of ed25519, you should modify the script.
Install Intel oneAPI and use its MPI
It is possible to install Intel oneAPI and use its MPI implementation instead of OpenMPI. The following script (https://github.com/astromsshin/cloud_ex/blob/main/tool_install_intel_oneapi_ubuntu_all_nodes.sh) can be used to install Intel oneAPI Base and HPC Toolkits in all VM nodes of the cluster.
#!/bin/bash
# See
# https://www.intel.com/content/www/us/en/develop/documentation/installation-guide-for-intel-oneapi-toolkits-linux/top/installation/install-
using-package-managers/apt.html
install_intel_oneapi='cd /tmp; wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB; apt-key add GPG-PUB-KEY-IN
TEL-SW-PRODUCTS.PUB; rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB; echo "deb https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.lis
t.d/oneAPI.list; add-apt-repository "deb https://apt.repos.intel.com/oneapi all main"; apt install -y intel-basekit intel-hpckit'
CLUSTERNAME="mycluster"
MINIONLASTIND="14"
echo "... install on ${CLUSTERNAME}-master"
echo $install_intel_oneapi | bash
for ind in $(seq 0 ${MINIONLASTIND})
do
echo "... install on ${CLUSTERNAME}-minion-${ind}"
ssh ${CLUSTERNAME}-minion-${ind} "${install_intel_oneapi}"
done
After installing the Intel toolkits, you need to setup the shell environment for the Intel tools. See https://www.intel.com/content/www/us/en/develop/documentation/oneapi-programming-guide/top/oneapi-development-environment-setup/use-the-setvars-script-with-linux-or-macos/use-a-config-file-for-setvars-sh-on-linux-or-macos.html for the guide to setup the environment. Here, simply source /opt/intel/oneapi/setvars.sh. As shown below, you can compile and test MPI programs by using the installed Intel toolkits.
> which mpiicpc /opt/intel/oneapi/mpi/2021.5.1/bin/mpiicpc > mpiicpc ./ex_mpi_montecarlo_pi.cpp > ldd ./a.out > which mpirun /opt/intel/oneapi/mpi/2021.5.1/bin/mpirun
See https://www.intel.com/content/www/us/en/develop/documentation/mpi-developer-guide-linux/top.html to figure out how to compile and run MPI programs with Intel toolkits.
Installing softwares with apt
You may want to install software by using apt commands in Ubunut Linux environment. As described above, you can type a specific command such as "apt install parallel -y" in the cluster template as we do for installing GNU parallel in all cluster nodes. Using the custom commands in the cluster template is one way to install apt packages in all cluster nodes. If you want to install apt packages after your cluster is built, you can use the following script (https://github.com/astromsshin/cloud_ex/blob/main/tool_install_apt_packages_all_nodes.sh).
#!/bin/bash
pkgs=(astropy-utils python3-astropy python3-astropy-affiliated python3-astropy-healpix python3-astropy-helpers python3-sklearn python3-skimage python3-statsmodels python3-matplotlib)
CLUSTERNAME="mycluster"
MINIONLASTIND="14"
echo "... install on ${CLUSTERNAME}-master"
apt update -y
for pkg in ${pkgs[@]}
do
apt install $pkg -y
done
for ind in $(seq 0 ${MINIONLASTIND})
do
echo "... install on ${CLUSTERNAME}-minion-${ind}"
ssh ${CLUSTERNAME}-minion-${ind} "apt update -y"
for pkg in ${pkgs[@]}
do
ssh ${CLUSTERNAME}-minion-${ind} "apt install ${pkg} -y"
done
done
Installing conda and preparing conda environtmens
The following script is available at https://github.com/astromsshin/cloud_ex/blob/main/tool_install_and_setup_conda_in_shared_volume.sh which install miniconda and setup a specific conda environment by using the network-shared volume.
#!/bin/bash
CLUSTERNAME="mycluster"
NFSDIR="/mnt/mpi"
CONDAENV="xclass"
CONDAURL="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"
# additional apt packages
apt install zip
# installation of miniconda
cd ${NFSDIR}
wget "${CONDAURL}" -O ./miniconda.sh
bash ./miniconda.sh -b -p ${NFSDIR}/miniconda
eval "$(${NFSDIR}/miniconda/bin/conda shell.bash hook)"
conda init
conda update -y -n base -c defaults conda
# creating the environment
conda create -y -n ${CONDAENV} python=2.7
# adding new conda packages
conda install -y -n ${CONDAENV} numpy
conda install -y -n ${CONDAENV} scipy
conda install -y -n ${CONDAENV} matplotlib
conda install -y -n ${CONDAENV} astropy
conda install -y -n ${CONDAENV} sqlite
# adding pip packages
conda activate ${CONDAENV}
pip install pyfits
echo "Do the following things to use the environment ${CONDAENV}"
echo "1) source ~/.bashrc"
echo "2) conda activate ${CONDAENV}"
You can imagine installing conda and preparing environments in your local home directory. The script https://github.com/astromsshin/cloud_ex/blob/main/tool_install_and_setup_conda_in_local_volume.sh can be used.
#!/bin/bash
CLUSTERNAME="mycluster"
TMPDIR="/tmp"
CONDAENV="xclass"
CONDAURL="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"
# additional apt packages
apt install zip
# installation of miniconda
cd ${TMPDIR}
wget "${CONDAURL}" -O ./miniconda.sh
bash ./miniconda.sh -b -p ${HOME}/miniconda
eval "$(${HOME}/miniconda/bin/conda shell.bash hook)"
conda init
conda update -y -n base -c defaults conda
# creating the environment
conda create -y -n ${CONDAENV} python=2.7
# adding new conda packages
conda install -y -n ${CONDAENV} numpy
conda install -y -n ${CONDAENV} scipy
conda install -y -n ${CONDAENV} matplotlib
conda install -y -n ${CONDAENV} astropy
conda install -y -n ${CONDAENV} sqlite
# adding pip packages
conda activate ${CONDAENV}
pip install pyfits
echo "Do the following things to use the environment ${CONDAENV}"
echo "1) source ~/.bashrc"
echo "2) conda activate ${CONDAENV}"
Downloading/uploading files from/to the external storage
The following script show how to download files from the external storage, which is described in KASI Science Cloud : VM instances#Step4.ConfiguretheVMinstanceforremotedesktop&externaldatastore, in the the network-shared volume. A typical usage includes downloading compiled binary codes, related scripts, configuration files, and data from the external storage. The script is available at https://github.com/astromsshin/cloud_ex/blob/main/tool_download_from_external_storage.sh.
#!/bin/bash
# edit the folloiwing variables
TARGETDIR="/mnt/mpi"
# assuming webdav accesses
WEBDAVIP="xxxx"
WEBDAVID="xxxx"
WEBDAVPW="xxxx"
# array of filenames that will be downloaded and saved
SRCFNARR=("XCLASS.zip" "ins_custom.sh")
DESTFNARR=("XCLASS.zip" "ins_custom.sh")
cd ${TARGETDIR}
CNT=0
for SRCFN in ${SRCFNARR[@]}
do
DESTFN=${DESTFNARR[$CNT]}
wget -O ${DESTFN} --no-check-certificate -r -c --user ${WEBDAVID} --password ${WEBDAVPW} https://${WEBDAVIP}/home/${SRCFN}
CNT=$((CNT+1))
done
You can also upload files from the cluster to the external storage as shown in the following example script (https://github.com/astromsshin/cloud_ex/blob/main/tool_upload_to_external_storage.sh).
#!/bin/bash
# edit the folloiwing variables
# assuming webdav accesses
WEBDAVIP="xxxx"
WEBDAVID="xxxx"
WEBDAVPW="xxxx"
# array of filenames that will be downloaded and saved
SRCFNARR=("/root/.ssh/id_rsa.pub")
DESTFNARR=("cluster_master_id_rsa.pub")
CNT=0
for SRCFN in ${SRCFNARR[@]}
do
DESTFN=${DESTFNARR[$CNT]}
curl --insecure -u ${WEBDAVID}:${WEBDAVPW} -T ${SRCFN} https://${WEBDAVIP}/home/${DESTFN}
CNT=$((CNT+1))
done