Jason Rigby jasonrig

jasonrig / parse_pubmed.py

Created March 21, 2023 12:21

Verify and extract abstracts from PubMed

	import csv
	import glob
	import gzip
	import hashlib
	import xml.sax

	import tqdm

	file_list = glob.glob("./pubmed/*.xml.gz")

jasonrig / remac.sh

Created November 9, 2019 03:34

A shell script to toggle NIC MAC addresses between the factory default and a new random one

	#!/bin/bash

	if [ "$#" -ne 1 ]; then
	echo "Network device must be specified"
	exit 1
	fi

	DEVICE="$1"

	OLD_MAC=$(ifconfig \| grep "$DEVICE:" -A3 \| grep ether \| head -1 \| cut -d ' ' -f 2)

jasonrig / run_spark_cluster.sh

Created August 9, 2019 03:47

Example SLURM job script to start a Spark cluster

	#!/bin/bash
	#SBATCH --job-name spark-cluster
	#SBATCH --account=qh82
	#SBATCH --time=02:00:00
	# --- Master resources ---
	#SBATCH --nodes=1
	#SBATCH --mem-per-cpu=1G
	#SBATCH --cpus-per-task=1
	#SBATCH --ntasks-per-node=1
	# --- Worker resources ---

jasonrig / spark-2.4.3-hadoop2.7.tcl

Created August 9, 2019 03:45

Example modulefile for Spark on HPC clusters

	#%Module1.0
	## Spark 2.4.3 modulefile
	##
	proc ModulesHelp { } {
	puts stderr "Provides the Spark environment for large-scale data processing"
	puts stderr "This version has been prebuilt with Scala 2.11."
	}

	module-whatis "Apache Spark™ is a unified analytics engine for large-scale data processing."

jasonrig / GoogleCloudStorage-wiki.en.vec.tsv

Created April 27, 2018 15:32

Upload wiki.en.vec to Google Cloud Storage

We can make this file beautiful and searchable if this error is corrected: It looks like row 2 should actually have 1 column, instead of 3 in line 1.

	TsvHttpData-1.0
	https://s3-us-west-1.amazonaws.com/fasttext-vectors/wiki.en.vec 6597238061 RBesTphc+YsGkOD1gBEqaA==