new file: Ubuntu/16.04-OpenFOAM/README

	new file:   Ubuntu/16.04-OpenFOAM/Ubuntu-16.04-Bootstrap
	new file:   Ubuntu/16.04-OpenFOAM/app/check
	new file:   Ubuntu/16.04-OpenFOAM/app/monitor
	new file:   Ubuntu/16.04-OpenFOAM/app/startup
	new file:   Ubuntu/16.04-OpenFOAM/hpc_image
	new file:   Ubuntu/16.04-OpenFOAM/openfoam_hacks/aliases
	new file:   Ubuntu/16.04-OpenFOAM/openfoam_hacks/bashrc
	new file:   Ubuntu/16.04-OpenFOAM/openfoam_hacks/exec
	new file:   Ubuntu/16.04-OpenFOAM/recipe-openfoam.txt
	new file:   Ubuntu/16.04-OpenFOAM/singularity_image.tar
	new file:   install/CENTOS7
	new file:   install/CENTOS7GPU
	new file:   install/CENTOS7MIC
	modified:   install/install.sh
	deleted:    install/CENTOS74
	deleted:    install/CENTOS74GPU
	deleted:    install/CENTOS74MIC

Ubuntu/16.04-OpenFOAM/README

+A few instruction for building an openfoam image to be used on the CFG platform.
+Openfoam in this image can be used directly, by calling the solver, or through a python procedure useful to monitor the calculation on the CFG platform.
+
+Usually I build a sandbox writable image. When it's ok, I build a read-only image to be uploaded on CFG platform.
+
+openfoamdev/ is the sandbox image, to be used for development and debug
+openfoam.simg is a non-writable image deployable on CFG platform
+
+
+BUILDING OF THE IMAGE
+
+To build the writable image, use the recipe-openfoam.txt recipe as follows
+
+   sudo singularity build -s openfoamdev recipe-openfoam.txt
+   
+Files in folders app and openfoam_hacks are needed with this recipe.
+In the app folders there are files needed for checking and monitoring the calculation.
+They can be modified or not added.
+Files in openfoam_hacks are needed to allows openfoam to run in the container.
+
+
+TESTING OF THE IMAGE
+
+To test the container, the two mountpoints requested by the CGF platform are to be creted.
+Of course they can reside in a folder different than ~.
+
+  mkdir ~/scratch
+  mkdir ~/service
+  
+- Serial test (direct call of the solver). Specify the solver and the case folder (-case option)
+
+  singularity -B ~/service:service ~/scratch:/scratch exec --cleanenv openfoamdev ###SOLVER###
+
+- Parallel test (direct call of the solver). Specify the solver, the case folder (-case option) and the number of processors.
+Of course, modify the system/decomposeParDict file accordingly.
+
+  singularity -B ~/service:service ~/scratch:/scratch exec --cleanenv openfoamdev decomposePar
+  mpirun -np ###PROCS#### singularity -B ~/service:service ~/scratch:/scratch exec --cleanenv openfoamdev ###SOLVER### -parallel
+
+NOTE When executing directly a solver in parallel mode, this can be a truly MPI calculation.
+     Instead, when testing the python procedure, only processors on one single node can be used.
+
+- Python procedure test.
+When using the python procedure, the solver, the case folder and the number of processors are specified on command line.
+The decomposePar utility is executed, then the solver is started through an mpirun command and the the check utility is started.
+As stated before, in this way only processors on a single node can be used. This will hopefully change in future.
+A webpage is displayed in "~/service/status.html". The abort button can't work locally, but only on the CFG platform.
+Anyway, the interrupt procedure is implemented. See /app/notification file.
+
+  singularity -B ~/service:service ~/scratch:/scratch --cleanenv exec openfoamdev /app/startup -s SOLVER -f FOLDER -p NUMBER_OF_PROCESSORS
+
+The /app/check file is to be modified in order to display the desided webpage.
+The parsing procedure is taylored for interFoam solver and can fail when parsing output of different solvers, so please modify it and test it locally.
+
+
+DEPLOYMENT ON CFG PLATFORM
+
+To build to a non writable image:
+   sudo singularity build openfoam.simg recipe-openfoam.txt
+
+The hpc_image script can be used to upload and register the new image on the CFG platform, 
+or to unregister and delete. Specify username, password and project in the script before using it.
+To upload and register 
+  
+  ./hpc_image upload openfoam.simg
+
+To unregister and delete
+
+  ./hpc_image delete openfoam.simg
+
+
+
+
+

Ubuntu/16.04-OpenFOAM/Ubuntu-16.04-Bootstrap

+Bootstrap: docker
+From: ubuntu:16.04
+
+%post
+apt -y update && apt -y upgrade
+apt -y install python curl wget gcc g++ make vim mc libncurses-dev rsync tclsh lua5.2 liblua5.2 gfortran ssh
+
+curl -s -O https://bootstrap.pypa.io/get-pip.py
+python get-pip.py
+pip install setuptools python-graph-core python-graph-dot tabulate numpy scipy pandas wheel --upgrade
+
+wget https://github.com/luarocks/luarocks/archive/v2.4.2.tar.gz
+tar xvf v2.4.2.tar.gz
+cd luarocks-2.4.2
+./configure
+make build
+make install
+mkdir ~/.luarocks
+echo "fs_use_modules = false" > ~/.luarocks/config.lua
+luarocks install luaposix
+luarocks install luafilesystem
+LUAROCKS_PREFIX=/usr/local
+export LUA_PATH="$LUAROCKS_PREFIX/share/lua/5.1/?.lua;$LUAROCKS_PREFIX/share/lua/5.1/?/init.lua;;"
+export LUA_CPATH="$LUAROCKS_PREFIX/lib/lua/5.1/?.so;;"
+
+echo "# !/bin/bash" > /bin/logger
+echo "exit 0" >> /bin/logger
+chmod +x /bin/logger
+
+# Lmod
+wget https://github.com/TACC/Lmod/archive/7.7.7.tar.gz
+tar xvf 7.7.7.tar.gz
+cd Lmod-7.7.7
+./configure --prefix=/opt/apps
+make install
+
+# OpenMPI
+wget https://www.open-mpi.org/software/ompi/v2.1/downloads/openmpi-2.1.1.tar.gz
+tar xvf openmpi-2.1.1.tar.gz && cd openmpi-2.1.1
+./configure --prefix=/usr/local
+make -j 16
+make install
+
+# APPS and SCRATCH
+mkdir /apps
+mkdir /scratch
+
+cd /bin
+rm sh && ln -s /bin/bash sh
+
+
+### folders and files ###
+
+mkdir /service  
+mv /opt/startup /app
+mv /opt/check /app
+mv /opt/monitor /app
+
+### set-up python3 ###  
+
+apt install -y python3-pip python3-mpi4py
+pip3 install numpy matplotlib
+  
+### install openfoam ###
+
+apt install -y software-properties-common wget
+add-apt-repository "http://dl.openfoam.org/ubuntu"
+sh -c "wget -O - http://dl.openfoam.org/gpg.key | apt-key add -"
+apt update
+apt install -y openfoam5
+echo '. /opt/openfoam5/etc/bashrc' >>$SINGULARITY_ENVIRONMENT
+
+### openfoam hacks ###
+
+mv -f /opt/bashrc /opt/openfoam5/etc
+mv -f /opt/aliases /opt/openfoam5/etc/config.sh
+mv -f /opt/exec /.singularity.d/actions
+
+%environment
+source /opt/apps/lmod/7.7.7/init/profile
+clearMT
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
+export -f ml
+export -f module
+export -f clearMT
+
+%files
+app/startup opt/
+app/check   opt/
+app/monitor opt/
+openfoam_hacks/bashrc opt/
+openfoam_hacks/aliases opt/
+openfoam_hacks/exec opt/

Ubuntu/16.04-OpenFOAM/app/check

+#!/usr/bin/python3
+
+'''
+   This file parses the solver log file and produces the webpage displayed
+   during the simulation. Also a webpage result is written after the end of the
+   simulation.
+   
+   The webpage displays just the residuals and the abort button. Of course it 
+   can be customized.
+   
+
+
+
+
+'''
+
+import time
+import sys
+from subprocess import check_output
+from os.path import isfile, basename
+from os import getcwd
+from shutil import copy
+import logging
+import base64
+
+import re
+import matplotlib
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt
+
+
+
+PROGRESS_HEAD = '''<html>
+  <head>
+    <title>OPENFOAM job progress</title>
+    <script type="text/javascript">
+      function abort() {
+        notify_running_job("ABORT");
+      }
+    </script>
+  </head>'''
+  
+  
+PROGRESS_BODY='''<body style="margin: 20px; padding: 20px;">
+    <h3 align=center>Simulation {}</h3>
+    <p style="text-align:center;">
+<!--    Images to be embedded encoded in base64-->
+    <img src = "data:image/png;base64,{}" alt ="missing image">
+    </p>
+    <p style="text-align:center;">
+    <input type="button" value="Abort simulation" onclick="abort()">
+    </p>
+  </body>
+</html>
+'''
+
+'''
+  Regular expression needed to parse the log file
+'''
+_rx_dict = {
+    'time': re.compile(r'^Time = (?P<time>(\d+.\d+e[+-]\d+)|(\d+[.\d+]*))'),
+    'timestep': re.compile(r'^deltaT = (?P<timestep>(\d+.\d+e[+-]\d+)|(\d+[.\d+]*))'),
+    'residual': re.compile(r'''
+        ^\w+: \s+                                          # solver name
+        Solving \s for \s (?P<quantity>\w+(.\w+)*), \s     # field
+        Initial \s residual \s = \s                         
+        (?P<residual>(-?\d+.\d+e[+-]\d+)|(-?\d+[.\d+]*))   # residual value
+        ''',
+        re.VERBOSE),
+    'clock': re.compile(r'ExecutionTime = (?P<clock>\d+.\d+) s')
+    }
+    
+def _parse_line(line):
+    '''
+      Check if the line matches one of the regex in _rx_dict
+    '''
+    for key, rx in _rx_dict.items():
+        match = rx.search(line)
+        if match:
+            return key, match       
+    return None, None
+
+def give_nth_word(line,n):
+    try:
+        out = line.split()[n-1].strip(",")
+    except IndexError:
+        return ""
+    return out
+
+def parse_logfile(logfilename,data,offset=0):
+    '''
+      Parses the file LOGFILENAME starting from OFFSET line, putting requested 
+      data in list DATA and updating the OFFSET variable.
+      It is executed every 3 seconds (see main function).
+      Residuals, timestep, simulation time and clock time are parsed and 
+      appended to data, which is a list of list.
+    '''
+    time_data = {}
+    content = check_output(["cat",logfilename])
+    lines = content.decode("utf-8").splitlines(True)
+    for index,line in enumerate(lines):
+        if index > offset:
+            key, match = _parse_line(line)
+            if key == 'time':
+                time_data['time'] = float(match.group('time'))
+            if key == 'residual':
+                time_data[match.group('quantity')] = float(match.group('residual'))
+            if key == 'timestep':
+                time_data['timestep'] = float(match.group('timestep'))
+            if key == 'clock':
+                time_data['clock'] = float(match.group('clock'))
+                offset = index
+                data[0].append(time_data['time'])
+                data[1].append(time_data['timestep'])
+                data[2].append(time_data['Ux'])
+                data[3].append(time_data['Uy'])
+                data[4].append(time_data['Uz'])
+                data[5].append(time_data['p_rgh'])
+                data[6].append(time_data['clock'])
+    return offset
+
+def check_if_finished(logfilename):
+    with open(logfilename,'r') as logfile:
+        for line in logfile:
+            pass
+    if give_nth_word(line,1) == "Finalising":
+        return True
+    else:
+        return False
+
+def plot_images(data):
+    '''
+      Plot residual data and save it in a png file. This file will be embedded
+      in the webpage.
+    '''
+    try:
+        fig = plt.figure()
+        ax1 = fig.add_subplot(1,1,1)
+        ax1.set_xlabel('Time [s]')
+        ax1.set_ylabel('Residuals')
+        ax1.semilogy(data[0],data[2], label='ux')
+        ax1.semilogy(data[0],data[3], label='uy')
+        ax1.semilogy(data[0],data[4], label='uz')
+        ax1.semilogy(data[0],data[5], label='p')
+        leg = ax1.legend()
+        plt.savefig('/service/output.png')
+        plt.close()
+    except UserWarning:
+        return
+    return
+
+def main():
+    '''
+      Main function.
+      Every 3 seconds, che logfile is parsed, it is checked if the simulation is
+      finished, then the status webpage is updated.
+      In the end, the same webpage is written in the result file.
+    
+    '''
+    folder = sys.argv[1]
+    casename = basename((getcwd()))
+    logfilename = folder + '/' + casename + '.log'
+    statusfilename = '/service/status.html'
+    resultfilename = '/service/result.txt'
+    time.sleep(5)
+    finished = False
+    log_offset = 0
+    output_data = [[],[],[],[],[],[],[]]
+###    time, timestep, ux, uy, uz, pres, clock
+    while not finished:
+        time.sleep(3)
+        log_offset = parse_logfile(logfilename,output_data,log_offset)
+        finished = check_if_finished(logfilename)
+        plot_images(output_data)
+        with open('/service/output.png','rb') as imgfile:
+            b64image = base64.b64encode(imgfile.read()).decode()
+        with open(statusfilename,'w') as statfile:
+            statfile.write(str(PROGRESS_HEAD + PROGRESS_BODY.format(casename,b64image)))
+    with open(resultfilename,'w') as resfile:
+        resfile.write(str(PROGRESS_HEAD + PROGRESS_BODY.format(casename,b64image)))
+
+if __name__ == "__main__":
+    main()

Ubuntu/16.04-OpenFOAM/app/monitor

+#!/usr/bin/env python3
+
+
+'''
+  This file checks if something is written in the notification file
+  If the message ABORT is written, the controlDict file is modified in order to
+  stop the simulation.
+  Other answers to other command could be implemented, if needed.
+
+'''
+
+
+import os
+import sys
+import logging
+import time
+from subprocess import check_output
+
+logging.basicConfig(level=logging.DEBUG)
+logger = logging.getLogger("Notifications monitor")
+
+def modify_dict(dictionary,keyword,value):
+  spaces = " " * (16-len(keyword))
+  try:
+    with open(dictionary,"r") as old_filedict:
+      with open(dictionary+"new","w") as new_filedict:
+        for line in old_filedict:
+          keys = line.split()
+          if (len(keys) > 1) and not "//" in keys[0]:
+            if keyword == keys[0]:
+              line = keyword + spaces + str(value) + ";\n"
+          print(line,end='',file=new_filedict) 
+    os.remove(dictionary)
+    os.rename(dictionary+"new",dictionary)
+  except FileNotFoundError:
+    print("File " + dictionary + " not found.\n")
+    exit()
+  return 
+
+def main():
+
+    logger.info("Notification monitor started")
+    folder = sys.argv[1]
+    dictFile = folder + '/system/controlDict'
+    cached_stamp = 0
+
+    while True:
+        if os.path.exists('/service/notifications.txt'):
+            stamp = os.stat('/service/notifications.txt').st_mtime
+            if stamp != cached_stamp:
+                logger.info("New notifications received")
+                cached_stamp = stamp
+                command = check_output(["tail","-1","/service/notifications.txt"]).strip().decode()
+                if command == "ABORT":
+                    logger.info("Received abort command")
+                    modify_dict(dictFile,"stopAt","writeNow")
+                else:
+                    logger.info("Ignoring unknown command {}".format(command))
+        time.sleep(1)
+
+if __name__ == "__main__":
+    main()

Ubuntu/16.04-OpenFOAM/app/startup

+#!/usr/bin/env python3
+
+
+'''
+  This is the principal file.
+  It parses the command line, in which requested openFoam solver, case folder 
+  and number of processors are specified.
+  It decomposes the case, calls the check and monitor scripts, then calls 
+  the solver with the correct parameters and, finally, reconstructs the case.
+  
+  cmdline syntax:
+  
+    startup -s SOLVER [-f FOLDER] -p PROCESSORS
+    
+  The execution is parallel, but since mpi is called inside the container, 
+  processes are spawn only on one node, so there can be at maximum 16 processes
+  on Anselm ann 24 on Salomon.
+ 
+  A truly parallel execution would probably require an mpi4py procedure.
+  
+  (Leonardo) It seems that subprocess commands don't work in conjunction with 
+             an mpi4py script. I have no idea on how to launch an MPI
+             openfoam solver from inside a MPI python script.
+
+'''
+
+from subprocess import Popen, run, DEVNULL
+from os import getcwd, chdir, rename, remove
+from os.path import basename, abspath
+import logging
+import argparse
+
+logging.basicConfig(level=logging.DEBUG)
+logger = logging.getLogger("Openfoam image logger")
+
+def command_line():
+    '''
+      Define and parses the command line arguments.
+      
+    '''
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-solver',action='store',dest='solver')
+    parser.add_argument('-folder', action='store', dest='folder')
+    parser.add_argument('-processor',action='store', type=int, dest='np')
+    args = vars(parser.parse_args())
+    solver = args['solver']
+    folder = args['folder']
+    np = args['np']
+    return solver,folder,np
+    
+def modify_dict(dictionary,keyword,value):
+  '''
+   Modify the VALUE of the desired KEYWORD in the desider DICTIONARY
+  
+  '''    
+  spaces = " " * (16-len(keyword))
+  try:
+    with open(dictionary,"r") as old_filedict:
+      with open(dictionary+"new","w") as new_filedict:
+        for line in old_filedict:
+          keys = line.split()
+          if (len(keys) > 1) and not "//" in keys[0]:
+            if keyword == keys[0]:
+              line = keyword + spaces + str(value) + ";\n"
+          print(line,end='',file=new_filedict) 
+    remove(dictionary)
+    rename(dictionary+"new",dictionary)
+  except FileNotFoundError:
+    print("File " + dictionary + " not found.\n")
+    exit()
+  return 
+
+def main():
+    solver,folder,np = command_line()
+    # folder check
+    if folder is not None:
+        try:
+            chdir(folder)
+        except FileNotFoundError:
+            logger.error("Folder {} not found".format(folder))
+            exit()
+    else:
+        folder = getcwd()
+    folder = abspath(getcwd())
+    casename = basename(getcwd())
+    logfilename = folder + '/' + casename + '.log'
+    statusfilename = '/service/status.html'
+
+    with open(logfilename,'w') as logfile:
+        logger.info("Running decomposePar utility")
+        run(["decomposePar","-force"],stdout=logfile)
+        check_proc = Popen(["/app/check",folder])
+        monitor_proc = Popen(["/app/monitor",folder])
+        logger.info("Running {} on {} processors".format(solver,str(np)))
+        run(["mpirun","-np",str(np),solver,"-parallel","-case",folder],stdout=logfile)
+        logger.info("Running reconstructPar")
+        run(["reconstructPar"],stdout=DEVNULL)
+
+    monitor_proc.terminate()
+### in case of abort command, set the controlDict file in the original state
+    ctrlDict = folder + '/system/controlDict'
+    modify_dict(ctrlDict,"stopAt","endTime")
+    logger.info("Calculation ended")
+
+if __name__ == "__main__":
+    main()

Ubuntu/16.04-OpenFOAM/hpc_image

+#!/usr/bin/python3
+
+"""Ugly but working hard-coded test script for the HPC client"""
+""" 
+    For upload and register, hpc_image upload image_name
+    For unregister and delete, hpc_image delete image_name
+    
+    
+    N.B. Images are uploaded in /home/images folder in anselm cluster
+    N.B. Folder /home/images has to exist on the cluster
+    N.B. Username, password and project should be filled with needed values
+
+"""
+
+
+
+import os
+import filecmp
+import json
+
+import clfpy as cf
+import sys
+
+auth_url = "https://api.hetcomp.org/authManager/AuthManager?wsdl"
+hpc_url = "https://api.hetcomp.org/hpc_anselm/Images?wsdl"
+gss_url = "https://api.hetcomp.org/gss-0.1/FileUtilities?wsdl"
+username = ""
+password = ""
+project = ''
+
+
+print("Obtaining session token ...")
+auth = cf.AuthClient(auth_url)
+session_token = auth.get_session_token(username, project, password)
+
+gss = cf.GssClient(gss_url)
+hpc = cf.HpcImagesClient(hpc_url)
+
+
+
+def upload():
+    print("Uploading and registering a new image")
+    image_filepath = sys.argv[2]
+    gss_ID = "it4i_anselm://home/images/" + sys.argv[2]
+    print(gss.upload(gss_ID, session_token, image_filepath))
+    print(hpc.register_image(session_token, sys.argv[2], gss_ID))
+
+def delete():
+    print("Removing and deleting image")
+    print(hpc.delete_image(session_token, sys.argv[2]))  
+    gss_ID = "it4i_anselm://home/images/" + sys.argv[2]
+    print(gss.delete(gss_ID, session_token))
+
+
+def main():
+    if sys.argv[1] == "upload":
+        upload()
+    elif sys.argv[1] == "delete":
+        delete()
+        
+if __name__ == "__main__":
+    main()
+    
+
+
+
+
+
+
+
+

Ubuntu/16.04-OpenFOAM/openfoam_hacks/aliases

+#----------------------------------*-sh-*--------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
+#    \\/     M anipulation  |
+#------------------------------------------------------------------------------
+# License
+#     This file is part of OpenFOAM.
+#
+#     OpenFOAM is 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.
+#
+#     OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+#     ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+#     FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+#     for more details.
+#
+#     You should have received a copy of the GNU General Public License
+#     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+#
+# File
+#     etc/config.sh/aliases
+#
+# Description
+#     Aliases for working with OpenFOAM
+#     Sourced from OpenFOAM-<VERSION>/etc/bashrc and/or ~/.bashrc
+#
+#------------------------------------------------------------------------------
+
+# Change compiled version aliases
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+alias wmSet='. $WM_PROJECT_DIR/etc/bashrc'
+alias wm64='wmSet WM_ARCH_OPTION=64'
+alias wm32='wmSet WM_ARCH_OPTION=32'
+alias wmSP='wmSet WM_PRECISION_OPTION=SP'
+alias wmDP='wmSet WM_PRECISION_OPTION=DP'
+
+# Clear env
+alias wmUnset='. $WM_PROJECT_DIR/etc/config.sh/unset'
+
+# Toggle wmakeScheduler on/off
+#  - also need to set WM_HOSTS
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+alias wmSchedOn='export WM_SCHEDULER=$WM_PROJECT_DIR/wmake/wmakeScheduler'
+alias wmSchedOff='unset WM_SCHEDULER'
+
+# Change directory aliases
+# ~~~~~~~~~~~~~~~~~~~~~~~~
+alias foam='cd $WM_PROJECT_DIR'
+
+if [ -n "$WM_PROJECT_SITE" ]
+then
+    alias foamSite='cd $WM_PROJECT_SITE'
+else
+    alias foamSite='cd $WM_PROJECT_INST_DIR/site'
+fi
+
+alias src='cd $FOAM_SRC'
+alias lib='cd $FOAM_LIBBIN'
+alias app='cd $FOAM_APP'
+alias sol='cd $FOAM_SOLVERS'
+alias util='cd $FOAM_UTILITIES'
+alias tut='cd $FOAM_TUTORIALS'
+alias run='cd $FOAM_RUN'
+
+
+# Refresh the environment
+# ~~~~~~~~~~~~~~~~~~~~~~~
+
+
+
+# For backward-compatibility unalias wmRefresh if it is defined as an alias
+[ "$(type -t wmRefresh)" = "alias" ] && unalias wmRefresh || unset wmRefresh
+#if declare -f wmRefresh > /dev/null
+#then
+#    unset wmRefresh
+#else
+#    unalias wmRefresh 2> /dev/null
+#fi
+
+wmRefresh()
+{
+    wmProjectDir=$WM_PROJECT_DIR
+    foamSettings=$FOAM_SETTINGS
+    wmUnset
+    . $wmProjectDir/etc/bashrc $foamSettings
+}
+
+
+# Change OpenFOAM version
+# ~~~~~~~~~~~~~~~~~~~~~~~
+unset foamVersion
+foamVersion()
+{
+    if [ "$1" ]; then
+        foamInstDir=$FOAM_INST_DIR
+        wmUnset
+        . $foamInstDir/OpenFOAM-$1/etc/bashrc
+        foam
+        echo "Changed to OpenFOAM-$1" 1>&2
+    else
+        echo "OpenFOAM-$WM_PROJECT_VERSION" 1>&2
+    fi
+}
+
+
+# Change ParaView version
+# ~~~~~~~~~~~~~~~~~~~~~~~
+unset foamPV
+foamPV()
+{
+    . $WM_PROJECT_DIR/etc/config.sh/paraview ParaView_VERSION=$1
+    echo "paraview-$ParaView_VERSION  (major: $ParaView_MAJOR)" 1>&2
+}
+
+
+#------------------------------------------------------------------------------

Ubuntu/16.04-OpenFOAM/openfoam_hacks/bashrc

+#----------------------------------*-sh-*--------------------------------------
+# =========                 |
+# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+#  \\    /   O peration     |
+#   \\  /    A nd           | Copyright (C) 2011-2017 OpenFOAM Foundation
+#    \\/     M anipulation  |
+#------------------------------------------------------------------------------
+# License
+#     This file is part of OpenFOAM.
+#
+#     OpenFOAM is 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.
+#
+#     OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+#     ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+#     FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+#     for more details.
+#
+#     You should have received a copy of the GNU General Public License
+#     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+#
+# File
+#     etc/bashrc
+#
+# Description
+#     Startup file for OpenFOAM
+#     Sourced from ~/.profile or ~/.bashrc
+#     Should be usable by any POSIX-compliant shell (eg, ksh)
+#
+#------------------------------------------------------------------------------
+
+export WM_PROJECT=OpenFOAM
+export WM_PROJECT_VERSION=5.0
+
+################################################################################
+# USER EDITABLE PART: Changes made here may be lost with the next upgrade
+#
+# FOAM_INST_DIR is the location of the OpenFOAM installation which defaults to
+# the directory containing this file if sourced by a bash shell.
+#
+# Please set to the appropriate path if the default is not correct.
+#
+[ "$BASH" -o "$ZSH_NAME" ]
+#export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \
+export FOAM_INST_DIR=/opt
+# export FOAM_INST_DIR=~$WM_PROJECT
+# export FOAM_INST_DIR=/opt/$WM_PROJECT
+# export FOAM_INST_DIR=/usr/local/$WM_PROJECT
+#
+# END OF (NORMAL) USER EDITABLE PART
+################################################################################
+
+# The default environment variables below can be overridden in a prefs.sh file
+# located in ~/.OpenFOAM/$WM_PROJECT_VERSION, ~/.OpenFOAM,
+# $FOAM_INST_DIR/site/$WM_PROJECT_VERSION or $FOAM_INST_DIR/site
+
+#- Compiler location:
+#    WM_COMPILER_TYPE= system | ThirdParty (OpenFOAM)
+export WM_COMPILER_TYPE=system
+
+#- Compiler:
+#    WM_COMPILER = Gcc | Gcc48 ... Gcc62 | Clang | Icc
+export WM_COMPILER=Gcc
+unset WM_COMPILER_ARCH WM_COMPILER_LIB_ARCH
+
+#- Memory addressing:
+#    On a 64bit OS this can be 32bit or 64bit
+#    On a 32bit OS addressing is 32bit and this option is not used
+#    WM_ARCH_OPTION = 32 | 64
+export WM_ARCH_OPTION=64
+
+#- Precision:
+#    WM_PRECISION_OPTION = DP | SP
+export WM_PRECISION_OPTION=DP
+
+#- Label size:
+#    WM_LABEL_SIZE = 32 | 64
+export WM_LABEL_SIZE=32
+
+#- Optimised, debug, profiling:
+#    WM_COMPILE_OPTION = Opt | Debug | Prof
+export WM_COMPILE_OPTION=Opt
+
+#- MPI implementation:
+#    WM_MPLIB = SYSTEMOPENMPI | OPENMPI | SYSTEMMPI | MPICH | MPICH-GM | HPMPI
+#               | MPI | FJMPI | QSMPI | SGIMPI | INTELMPI
+export WM_MPLIB=SYSTEMOPENMPI
+
+#- Operating System:
+#    WM_OSTYPE = POSIX | ???
+export WM_OSTYPE=POSIX
+
+#- Floating-point signal handling:
+#    set or unset
+export FOAM_SIGFPE=
+
+#- memory initialisation:
+#    set or unset
+#export FOAM_SETNAN=
+
+################################################################################
+
+# The old dirs to be cleaned from the environment variables
+foamOldDirs="$WM_PROJECT_DIR $WM_THIRD_PARTY_DIR \
+    $HOME/$WM_PROJECT/$USER $FOAM_USER_APPBIN $FOAM_USER_LIBBIN \
+    $WM_PROJECT_SITE $FOAM_SITE_APPBIN $FOAM_SITE_LIBBIN"
+
+# Location of installation
+# ~~~~~~~~~~~~~~~~~~~~~~~~
+export WM_PROJECT_INST_DIR=$FOAM_INST_DIR
+export WM_PROJECT_DIR=$WM_PROJECT_INST_DIR/openfoam5
+
+# Location of third-party software
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+export WM_THIRD_PARTY_DIR=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION
+
+# Location of site-specific templates etc
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# unset is equivalent to $WM_PROJECT_INST_DIR/site
+if [ -d "$WM_PROJECT_SITE" ]
+then
+    export WM_PROJECT_SITE
+else
+    unset WM_PROJECT_SITE
+fi
+
+# Location of user files
+# ~~~~~~~~~~~~~~~~~~~~~~
+export WM_PROJECT_USER_DIR=$HOME/$WM_PROJECT/$USER-$WM_PROJECT_VERSION
+
+# Source initialization functions
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+. $WM_PROJECT_DIR/etc/config.sh/functions
+
+# Add in preset user or site preferences:
+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile prefs.sh`
+
+# Evaluate command-line parameters and record settings for later
+# these can be used to set/unset values, or specify alternative pref files
+export FOAM_SETTINGS="$@"
+
+# _foamEval $@
+
+# Clean standard environment variables (PATH, LD_LIBRARY_PATH, MANPATH)
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+foamClean=$WM_PROJECT_DIR/bin/foamCleanPath
+
+#- Clean PATH
+cleaned=`$foamClean "$PATH" "$foamOldDirs"` && PATH="$cleaned"
+
+#- Clean LD_LIBRARY_PATH
+cleaned=`$foamClean "$LD_LIBRARY_PATH" "$foamOldDirs"` \
+    && LD_LIBRARY_PATH="$cleaned"
+
+#- Clean MANPATH
+cleaned=`$foamClean "$MANPATH" "$foamOldDirs"` && MANPATH="$cleaned"
+
+export PATH LD_LIBRARY_PATH MANPATH
+
+# Source project setup files
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~
+_foamSource $WM_PROJECT_DIR/etc/config.sh/settings
+_foamSource $WM_PROJECT_DIR/etc/config.sh/aliases
+
+
+# Source user setup files for optional packages
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/mpi`
+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/paraview`
+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/ensight`
+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/gperftools`
+
+if [ ! -z "$FOAMY_HEX_MESH" ]
+then
+    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/CGAL`
+fi
+
+
+# Clean environment paths again. Only remove duplicates
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#- Clean PATH
+cleaned=`$foamClean "$PATH"` && PATH="$cleaned"
+
+#- Clean LD_LIBRARY_PATH
+cleaned=`$foamClean "$LD_LIBRARY_PATH"` && LD_LIBRARY_PATH="$cleaned"
+
+#- Clean MANPATH (trailing ':' to find system pages)
+cleaned=`$foamClean "$MANPATH"`: && MANPATH="$cleaned"
+
+export PATH LD_LIBRARY_PATH MANPATH
+
+#- Clean LD_PRELOAD
+if [ -n "$LD_PRELOAD" ]
+then
+    cleaned=`$foamClean "$LD_PRELOAD"` && LD_PRELOAD="$cleaned"
+    export LD_PRELOAD
+fi
+
+
+# Cleanup environment:
+# ~~~~~~~~~~~~~~~~~~~~
+unset cleaned foamClean foamOldDirs
+
+
+# Unload initialization functions:
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+. $WM_PROJECT_DIR/etc/config.sh/functions
+
+# Source the bash completion file:
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+[ "$BASH" ] && . $WM_PROJECT_DIR/etc/config.sh/bash_completion
+
+#------------------------------------------------------------------------------

Ubuntu/16.04-OpenFOAM/openfoam_hacks/exec

+#!/bin/bash
+
+for script in /.singularity.d/env/*.sh; do
+    if [ -f "$script" ]; then
+        . "$script"
+    fi
+done
+
+exec "$@"

Ubuntu/16.04-OpenFOAM/recipe-openfoam.txt

+Bootstrap: docker
+From: ubuntu:17.10
+
+%post
+
+  ### folders and files ###
+
+  mkdir /scratch
+  mkdir /service  
+  mkdir /app
+  mv /opt/startup /app
+  mv /opt/check /app
+  mv /opt/monitor /app
+
+  ### update & upgrade ###
+  
+  apt update
+  apt upgrade -y
+  apt install -y nano ssh
+  
+  ### set-up python3 ###  
+
+  apt install -y python3-pip python3-mpi4py
+  pip3 install numpy matplotlib
+  
+  ### install openfoam ###
+
+  apt install -y software-properties-common wget
+  add-apt-repository "http://dl.openfoam.org/ubuntu"
+  sh -c "wget -O - http://dl.openfoam.org/gpg.key | apt-key add -"
+  apt update
+  apt install -y openfoam5
+  echo '. /opt/openfoam5/etc/bashrc' >>$SINGULARITY_ENVIRONMENT
+
+  ### openfoam hacks ###
+
+  mv -f /opt/bashrc /opt/openfoam5/etc
+  mv -f /opt/aliases /opt/openfoam5/etc/config.sh
+  mv -f /opt/exec /.singularity.d/actions
+
+  
+%files
+ app/startup opt/
+ app/check   opt/
+ app/monitor opt/
+ openfoam_hacks/bashrc opt/
+ openfoam_hacks/aliases opt/
+ openfoam_hacks/exec opt/

install/install.sh

@@ -9,7 +9,7 @@ if [[ $# -eq 0 ]]; then
 	 printf "\e[31m
  ./install.sh\e[0m   ... create and build singularity image
 	-\e[33mi\e[0m OS (\e[33mCentOS\e[0m, \e[33mDebian\e[0m, \e[33mUbuntu\e[0m)
-	-\e[33mv\e[0m Version OS (CentOS \e[33m6.9\e[0m or CentOS \e[33m7.4\e[0m, Debian \e[33m8.0\e[0m, Ubuntu \e[33m16.04\e[0m)
+	-\e[33mv\e[0m Version OS (CentOS \e[33m6.9\e[0m or CentOS \e[33m7.5\e[0m, Debian \e[33m8.0\e[0m, Ubuntu \e[33m16.04\e[0m)
 	-\e[33mo\e[0m OpenMPI module (default is \e[31mOpenMPI/2.1.1-GCC-6.3.0-2.27\e[0m)
 	-\e[33mt\e[0m \e[33mclassic\e[0m, \e[33mGPU\e[0m, \e[33mMIC\e[0m (default is \e[31mclassic\e[0m)
  Example:
@@ -147,9 +147,9 @@ else
 fi
 
 if [ -z "$VERSION" ]; then
-   echo -e "Please, specify OS version (-v CentOS \e[31m6.9\e[0m or CentOS \e[31m7.4\e[0m, Debian \e[31m8.0\e[0m, Ubuntu \e[31m16.04\e[0m)"
+   echo -e "Please, specify OS version (-v CentOS \e[31m6.9\e[0m or CentOS \e[31m7.5\e[0m, Debian \e[31m8.0\e[0m, Ubuntu \e[31m16.04\e[0m)"
    exit 1
-elif ([ "$IMAGE" == "CentOS" ] && [ "$VERSION" == "6.9" ]) || ([ "$IMAGE" == "CentOS" ] && [ "$VERSION" == "7.4" ]) || ([ "$IMAGE" == "Debian" ] && [ "$VERSION" == "8.0" ]) || ([ "$IMAGE" == "Ubuntu" ] && [ "$VERSION" == "16.04" ]); then
+elif ([ "$IMAGE" == "CentOS" ] && [ "$VERSION" == "6.9" ]) || ([ "$IMAGE" == "CentOS" ] && [ "$VERSION" == "7.5" ]) || ([ "$IMAGE" == "Debian" ] && [ "$VERSION" == "8.0" ]) || ([ "$IMAGE" == "Ubuntu" ] && [ "$VERSION" == "16.04" ]); then
    echo -e "Version ................................ [\e[32mOK\e[0m]"
 else
    echo -e "Version ................................ [\e[31mERROR\e[0m]"
@@ -196,9 +196,9 @@ if [ "$IMAGE" == "CentOS" ]; then
       fi
    else
      if [ "$TYPE" == "classic" ]; then
-        BOOTSTRAP="CENTOS74"
+        BOOTSTRAP="CENTOS7"
      else
-        BOOTSTRAP="CENTOS74$TYPE"
+        BOOTSTRAP="CENTOS7$TYPE"
      fi
    fi
 elif [ "$IMAGE" == "Debian" ]; then