BinWang0213

OpenFoam 6.0 install on SuperMike II

Follow the guide @ http://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-6/CentOS_SL_RHEL#CentOS_6.10_.28without_SCL.29

#Using node for faster compile
qsub -I -l nodes=2:ppn=16,walltime=00:120:00 -q workq -A hpc_startup_xjwang

#enable module
sh /usr/local/packages/Modules/module_setup.sh

BinWang0213

#!/bin/bash
#PBS -A hpc_cdss01
#PBS -q workq
#PBS -l nodes=2:ppn=16
#PBS -l walltime=30:00:00
#PBS -V
#PBS -j oe
#PBS -N TransmissionLine

#-----------------Environment setup---------------------

BinWang0213

*
 * CSR_convert.H - part of the SpeedIT Classic toolkit
 * Copyright 2010 (C) Vratis Ltd
 * email: support@vratis.com
 * 
 * SpeedIT Classic toolkit is a free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License as published 
 * by the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 

BinWang0213

```
Solver
======
Type:             FGMRES(30)
Unknowns:         4898600
Memory footprint: 2.26 G

Preconditioner
==============
Schur complement (two-stage preconditioner)

BinWang0213

import os

def list_files(startpath):
    for root, dirs, files in os.walk(startpath):
        if '.git' in dirs: # don't go into any .git directories.
            dirs.remove('.git')
        level = root.replace(startpath, '').count(os.sep)
        indent = ' ' * 4 * (level)
        dirname=os.path.basename(root).replace('_','\_')
        #print('{}{}{}.'.format(indent, '.%d '%(level+1),os.path.basename(root)))

BinWang0213

//
//https://github.com/InteractiveComputerGraphics/Discregrid


#include <Discregrid/All>
#include <Eigen/Dense>

#include "resource_path.hpp"

#include <string>

BinWang0213

1. Show available containers 

sudo docker ps

2. Start container with shared root in local machine  $(pwd):/media/home/Fenics/ to container root  /home/fenics/shared 

docker run --shm-size=1g -ti --name notebook -w /home/fenics -v F:/fenics/run_examples:/home/fenics/shared -d -p 127.0.0.1:8888:8888 quay.io/fenicsproject/stable 'jupyter-notebook --ip=0.0.0.0'

docker run --shm-size=1g -ti --name fenics -v F:/fenics/run_examples:/home/fenics/shared quay.io/fenicsproject/stable

notebook usage

docker inspect notebook #find ip address ip:8888

BinWang0213

import shutil
import glob, os
import subprocess

#Find all job files
os.chdir("./")
bash_files=[]
for file in glob.glob("*.sh"):
    #print(file)
    bash_files+=[file]

BinWang0213

Install OpenFOAM7 in Docker

Install Openfoam and setup linux environment

#Download openfoam7
docker run --shm-size=1g -ti --name of7 -v F:/hybridPorousFoam/:/home/openfoam openfoam/openfoam7-paraview56

#Re-login as root user
exit
docker exec -u 0 -it of7  bash

BinWang0213

Install opengeosys in Docker

Install opengeosys and setup linux environment

#Download build system
docker run --shm-size=1g -ti --name ogs6 -v F:/ogs/:/home ogs6/gcc


#Download and build ogs
git clone --filter=blob:limit=100k -b 6.3.2 https://gitlab.opengeosys.org/ogs/ogs.git