marcc-hpc’s gists

marcc-hpc / Makefile

Created January 31, 2018 03:36

Building FastQTL on MARCC - Makefile

	#PLEASE SPECIFY THE R path here where you built the R math library standalone
	RMATH=/cm/shared/apps/R/3.4.3/gcc/5.4/lib

	#compiler
	CXX=g++ -std=c++11

	#internal paths
	VPATH=$(shell for file in `find src -name *.cpp`; do echo $$(dirname $$file); done)
	PATH_TABX=lib/Tabix
	PATH_EIGN=lib/Eigen

marcc-hpc / pyrosetta_job.sh

Last active April 26, 2018 22:43

Singularity PyRosetta Script

	#!/bin/bash
	#SBATCH -p shared
	#SBATCH --reservation=t-jgray21
	#SBATCH -t 4:0:0
	#SBATCH -N 1
	#SBATCH -n 20
	#SBATCH -J pyrosetta_job

	# important presets for pyrosetta
	export AMINO_SURFACE_CALL="--job_title HAp_FEP --surface_type HAp_010 --aa_type A --batches 500 --batch_size 100"

marcc-hpc / singularity_pyrosetta

Last active August 12, 2023 18:56

PyRosetta Singularity File with Anaconda and OpenMPI

	Bootstrap: docker
	From: centos:centos7

	%environment
	PATH="/opt/software/bin:$PATH"
	export PATH
	LD_LIBRARY_PATH="/opt/software/lib/openmpi:$LD_LIBRARY_PATH"
	export LD_LIBRARY_PATH

	%files

marcc-hpc / install_run_sircel.sh

Last active May 6, 2018 08:54

Installing Sircel on MARCC

	#!/bin/bash

	# this module is specific to MARCC
	module load anaconda-python/3.6

	# create anaconda environment and use it
	conda create -y -n sircel python
	source activate sircel

	# install kallisto, redis

marcc-hpc / .vimrc

Created May 1, 2018 15:46

YAML vimrc

	set autoindent
	set tabstop=2
	set shiftwidth=2
	autocmd FileType yaml setlocal ai ts=2 sw=2 et
	autocmd FileType yml setlocal ai ts=2 sw=2 et

marcc-hpc / test_lapack.cpp

Created July 13, 2018 17:17

	#include <iostream>
	#include <fstream>


	using namespace std;

	// dgeev_ is a symbol in the LAPACK library files
	extern "C" {
	extern int dgeev_(char,char,int,double,int,double, double, double, int, double, int, double, int, int);
	}

marcc-hpc / test_lapack_matrix.txt

Created July 13, 2018 17:26

Matching test matrix for test_lapack.cpp

marcc-hpc / example_lapack.py

Created August 7, 2018 14:03

An example of generating a random matrix solver on MARCC

	"""
	Running LAPACK with Anaconda Python
	Copyright 2016 Ohio Supercomputer Center (OSC)
	Copyright 2017 Maryland Advanced Research Computing Center (MARCC)

	Attributions:
	This example was inspired by
	"Numerical Computing with Modern Fortran" (SIAM, 2013) by Hanson & Hopkins

	"""

marcc-hpc / example_lapack.job

Created August 7, 2018 14:05

Matching job script for example_lapack.py

	#!/bin/bash -l
	#SBATCH --job-name=test_with_gnu_parallel
	#SBATCH --partition=parallel
	#SBATCH --time=1:0:0
	#SBATCH --nodes=1
	#SBATCH --ntasks=4
	#SBATCH --cores=6

	# in this example we are using multithreading via MKL threads
	# if you have single core tasks set ntasks=24