marcc-hpc

#!/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

marcc-hpc

"""
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

3 3
-1.0 -8.0  0.0
-1.0  1.0 -5.0
 3.0  0.0  2.0

marcc-hpc

#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

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

#!/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

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

#!/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

#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