crabba

#include <chrono>
#include <iostream>
#include <thread>
#include <unistd.h>
#include <vector>

void whoami(int i) {
  int sleep_ms = rand() % 5000;

  std::thread::id this_id = std::this_thread::get_id();

crabba

#! /bin/bash

# install-singularity-al2.sh
# Install Singularity (also Apptainer, your choice) runtime on ParallelCluster with Amazon Linux 2
# Assumes this script is installed on a shared home directory: uses srun to call nodes

set -o errexit   # abort on nonzero exitstatus
# set -o nounset   # abort on unbound variable
set -o pipefail  # don't hide errors within pipes

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#! /usr/bin/env bash

# Set up venv inside a wdl directory
mkdir wdl
cd wdl
python3 -m venv venv
source ./venv/bin/activate

# AL2 version of openssl causes error
# miniwdl-run urllib3 v2.0 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with 'OpenSSL 1.0.2k-fips  26 Jan 2017'.

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# Process to build R with MKL support on Amazon Linux 2

# Install R v4
sudo amazon-linux-extras install R4
wget https://mac.r-project.org/benchmarks/R-benchmark-25.R
which R  # /usr/bin/R
R --version  # 4.0.2

# Install Intel MKL library
# https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl-download.html?operatingsystem=linux&distributions=yumpackagemanager

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#! /bin/bash

# Detect OS and set useful environment variables
# Sets:
#   AWS_ACCOUNT_ID
#   AWS_REGION

TOKEN=$(curl -X PUT "http://169.254.169.254/latest/api/token" -H "X-aws-ec2-metadata-token-ttl-seconds: 21600")
curl http://169.254.169.254/latest/meta-data/profile -H "X-aws-ec2-metadata-token: $TOKEN"

crabba

#! /usr/bin/env python3

import argparse
import boto3
import logging

parser = argparse.ArgumentParser(description='Retrieve Omics test run results')
parser.add_argument('-p', '--profile', dest='profile', metavar='PROFILE', help='AWS profile to use')
parser.add_argument('-n', '--name', dest='name', metavar='NAME', help='Name of test (run prefix)')
parser.add_argument('-v', '--verbose', dest='verbose', action='count', default=0, help='Verbosity (up to 3x)')

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#!/bin/bash

user=$1
echo "User: $user"

user_policies=$(aws iam list-user-policies --user-name $user --query 'PolicyNames[*]' --output text)

echo "Deleting user policies: $user_policies"
for policy in $user_policies ;
do

crabba

#! /usr/bin/env python3

import boto3
import sys

s3client = boto3.client('s3')

def s3_object_exists(bucket, key):
  ret = False
  try:

crabba

#!/bin/bash

# Specify the desired volume size in GiB as a command line argument. If not specified, default to 50 GiB.
SIZE=${1:-50}

# Get the ID of the environment host Amazon EC2 instance.
INSTANCEID=$(curl http://169.254.169.254/latest/meta-data/instance-id)

# Get the ID of the Amazon EBS volume associated with the instance.
VOLUMEID=$(aws ec2 describe-instances \

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from datetime import datetime, timezone, timedelta
# Using Boto 3 EC2
launch_time = ec2.launch_time
print("launch_time {} tz {}".format(launch_time, launch_time.tzinfo))
now = datetime.now()
print("now         {} tz {}".format(now, now.tzinfo))
try:
    diff = now - launch_time
except TypeError as err:
    print("Error: {}".format(err))