Daisuke Miyamoto DaisukeMiyamoto

myPresto5 Screening Tutorial on AWS ParallelCluster with SGE

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。

testing VirtualFlow tutorial on AWS ParallelCluster

[aws]

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

	#!/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 \

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

	TAG_KEY = 'ClusterName'


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

	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()

	#!/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

	#!/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

	#!/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"

	#!/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
	#