DaisukeMiyamoto

#!/bin/bash -x

. /etc/parallelcluster/cfnconfig

nvidia-smi
if [ $? = 0 ] ; then
CLUSTER_NAME=$(echo ${stack_name} | sed -e "s/parallelcluster-//g")
sudo pip install boto3 pynvml
wget -P /tmp https://s3.amazonaws.com/aws-bigdata-blog/artifacts/GPUMonitoring/gpumon.py
sed \

DaisukeMiyamoto

# -- coding: utf-8 --
import boto3
import logging
import json

TAG_KEY = 'ClusterName'


logger = logging.getLogger()
logger.setLevel(logging.INFO)

DaisukeMiyamoto

import json
import logging
import base64
import gzip
import urllib.request

LOG_STREAM = 'ip-10-0-1-xxx.i-08f68c623be216d6e.slurmctld'
SLACK_WEB_HOOK = 'https://hooks.slack.com/services/XXXX'

logger = logging.getLogger()

DaisukeMiyamoto

#!/bin/bash -xe
# Based on this site:
# https://software.intel.com/content/www/us/en/develop/documentation/installation-guide-for-intel-oneapi-toolkits-linux/top/installation/install-using-package-managers/apt.html

# use wget to fetch the Intel repository public key
cd /tmp
wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
# add to your apt sources keyring so that archives signed with this key will be trusted.
sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
# remove the public key

DaisukeMiyamoto

#!/bin/bash

# module load intelmpi
module load openmpi

wget http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.6.2.tar.gz
tar zxvf ./osu-micro-benchmarks-5.6.2.tar.gz
cd osu-micro-benchmarks-5.6.2/
./configure CC=mpicc CXX=mpicxx
make -j 4

DaisukeMiyamoto

#!/bin/bash

wget https://ftp.gromacs.org/pub/benchmarks/ADH_bench_systems.tar.gz
tar xvzf ADH_bench_systems.tar.gz
docker run -ti --runtime nvidia -v $(pwd)/ADH/adh_cubic:/benchmark --workdir /benchmark nvcr.io/hpc/gromacs:2020.2 sh -c "gmx grompp -f pme_verlet.mdp"
time docker run -ti --runtime nvidia -v $(pwd)/ADH/adh_cubic:/benchmark --workdir /benchmark nvcr.io/hpc/gromacs:2020.2 sh -c "gmx mdrun -v -nsteps 100000 -resetstep 90000 -noconfout -ntmpi 4 -ntomp 10 -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400 -s topol.tpr" 

DaisukeMiyamoto

#!/bin/bash -xe                                                                                                                                                  
#
# Usage:
# $ chmod +x set-up-nicedcv-centos.sh
# $ sudo ./set-up-nicedcv-centos.sh
#
# after executing this script, you need to set password for user
# e.g.
# sudo passwd centos
#

DaisukeMiyamoto

myPresto5 Screening Tutorial on AWS ParallelCluster with SGE

• 2020/10/30 EBS容量設定を増加
• 2020/08/07 ドキュメント作成

このドキュメントは参考情報として提供されるものであり、動作は保証されない。

DaisukeMiyamoto

testing VirtualFlow tutorial on AWS ParallelCluster

https://docs.virtual-flow.org/tutorials/-LdE94b2AVfBFT72zK-v/

set up AWS ParallelCluster

• example config file for AWS ParallelCluster

[aws]

DaisukeMiyamoto

myPresto5 Screening Tutorial on AWS ParallelCluster with SGE

based on myPresto5.0 -in silico screening- tutorial 180112

set up AWS ParallelCluster

install AWS ParallelCluster