From a64014e4ca1d28f85b32a0d00de81a30f53c3faf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= <lukas.krupcik@vsb.cz>
Date: Thu, 19 Jul 2018 13:44:41 +0200
Subject: [PATCH] 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 | 74 +++++++
Ubuntu/16.04-OpenFOAM/Ubuntu-16.04-Bootstrap | 93 ++++++++
Ubuntu/16.04-OpenFOAM/app/check | 183 ++++++++++++++++
Ubuntu/16.04-OpenFOAM/app/monitor | 62 ++++++
Ubuntu/16.04-OpenFOAM/app/startup | 106 +++++++++
Ubuntu/16.04-OpenFOAM/hpc_image | 71 ++++++
Ubuntu/16.04-OpenFOAM/openfoam_hacks/aliases | 120 +++++++++++
Ubuntu/16.04-OpenFOAM/openfoam_hacks/bashrc | 215 +++++++++++++++++++
Ubuntu/16.04-OpenFOAM/openfoam_hacks/exec | 9 +
Ubuntu/16.04-OpenFOAM/recipe-openfoam.txt | 48 +++++
Ubuntu/16.04-OpenFOAM/singularity_image.tar | Bin 0 -> 40960 bytes
install/{CENTOS74 => CENTOS7} | 0
install/{CENTOS74GPU => CENTOS7GPU} | 0
install/{CENTOS74MIC => CENTOS7MIC} | 0
install/install.sh | 10 +-
15 files changed, 986 insertions(+), 5 deletions(-)
create mode 100644 Ubuntu/16.04-OpenFOAM/README
create mode 100644 Ubuntu/16.04-OpenFOAM/Ubuntu-16.04-Bootstrap
create mode 100755 Ubuntu/16.04-OpenFOAM/app/check
create mode 100755 Ubuntu/16.04-OpenFOAM/app/monitor
create mode 100755 Ubuntu/16.04-OpenFOAM/app/startup
create mode 100644 Ubuntu/16.04-OpenFOAM/hpc_image
create mode 100755 Ubuntu/16.04-OpenFOAM/openfoam_hacks/aliases
create mode 100755 Ubuntu/16.04-OpenFOAM/openfoam_hacks/bashrc
create mode 100755 Ubuntu/16.04-OpenFOAM/openfoam_hacks/exec
create mode 100644 Ubuntu/16.04-OpenFOAM/recipe-openfoam.txt
create mode 100644 Ubuntu/16.04-OpenFOAM/singularity_image.tar
rename install/{CENTOS74 => CENTOS7} (100%)
rename install/{CENTOS74GPU => CENTOS7GPU} (100%)
rename install/{CENTOS74MIC => CENTOS7MIC} (100%)
diff --git a/Ubuntu/16.04-OpenFOAM/README b/Ubuntu/16.04-OpenFOAM/README
new file mode 100644
index 0000000..b60452a
--- /dev/null
+++ b/Ubuntu/16.04-OpenFOAM/README
@@ -0,0 +1,74 @@
+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
+
+
+
+
+
diff --git a/Ubuntu/16.04-OpenFOAM/Ubuntu-16.04-Bootstrap b/Ubuntu/16.04-OpenFOAM/Ubuntu-16.04-Bootstrap
new file mode 100644
index 0000000..6224f5d
--- /dev/null
+++ b/Ubuntu/16.04-OpenFOAM/Ubuntu-16.04-Bootstrap
@@ -0,0 +1,93 @@
+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/
diff --git a/Ubuntu/16.04-OpenFOAM/app/check b/Ubuntu/16.04-OpenFOAM/app/check
new file mode 100755
index 0000000..41d9499
--- /dev/null
+++ b/Ubuntu/16.04-OpenFOAM/app/check
@@ -0,0 +1,183 @@
+#!/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()
diff --git a/Ubuntu/16.04-OpenFOAM/app/monitor b/Ubuntu/16.04-OpenFOAM/app/monitor
new file mode 100755
index 0000000..92943a2
--- /dev/null
+++ b/Ubuntu/16.04-OpenFOAM/app/monitor
@@ -0,0 +1,62 @@
+#!/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()
diff --git a/Ubuntu/16.04-OpenFOAM/app/startup b/Ubuntu/16.04-OpenFOAM/app/startup
new file mode 100755
index 0000000..0c2a461
--- /dev/null
+++ b/Ubuntu/16.04-OpenFOAM/app/startup
@@ -0,0 +1,106 @@
+#!/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()
diff --git a/Ubuntu/16.04-OpenFOAM/hpc_image b/Ubuntu/16.04-OpenFOAM/hpc_image
new file mode 100644
index 0000000..7072c94
--- /dev/null
+++ b/Ubuntu/16.04-OpenFOAM/hpc_image
@@ -0,0 +1,71 @@
+#!/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()
+
+
+
+
+
+
+
+
+
diff --git a/Ubuntu/16.04-OpenFOAM/openfoam_hacks/aliases b/Ubuntu/16.04-OpenFOAM/openfoam_hacks/aliases
new file mode 100755
index 0000000..098874b
--- /dev/null
+++ b/Ubuntu/16.04-OpenFOAM/openfoam_hacks/aliases
@@ -0,0 +1,120 @@
+#----------------------------------*-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
+}
+
+
+#------------------------------------------------------------------------------
diff --git a/Ubuntu/16.04-OpenFOAM/openfoam_hacks/bashrc b/Ubuntu/16.04-OpenFOAM/openfoam_hacks/bashrc
new file mode 100755
index 0000000..d69506a
--- /dev/null
+++ b/Ubuntu/16.04-OpenFOAM/openfoam_hacks/bashrc
@@ -0,0 +1,215 @@
+#----------------------------------*-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" ] && . $WM_PROJECT_DIR/etc/config.sh/bash_completion
+
+#------------------------------------------------------------------------------
diff --git a/Ubuntu/16.04-OpenFOAM/openfoam_hacks/exec b/Ubuntu/16.04-OpenFOAM/openfoam_hacks/exec
new file mode 100755
index 0000000..c24a5c6
--- /dev/null
+++ b/Ubuntu/16.04-OpenFOAM/openfoam_hacks/exec
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+for script in /.singularity.d/env/*.sh; do
+ if [ -f "$script" ]; then
+ . "$script"
+ fi
+done
+
+exec "$@"
diff --git a/Ubuntu/16.04-OpenFOAM/recipe-openfoam.txt b/Ubuntu/16.04-OpenFOAM/recipe-openfoam.txt
new file mode 100644
index 0000000..9e0c90d
--- /dev/null
+++ b/Ubuntu/16.04-OpenFOAM/recipe-openfoam.txt
@@ -0,0 +1,48 @@
+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/
diff --git a/Ubuntu/16.04-OpenFOAM/singularity_image.tar b/Ubuntu/16.04-OpenFOAM/singularity_image.tar
new file mode 100644
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Bu0a3*
literal 0
HcmV?d00001
diff --git a/install/CENTOS74 b/install/CENTOS7
similarity index 100%
rename from install/CENTOS74
rename to install/CENTOS7
diff --git a/install/CENTOS74GPU b/install/CENTOS7GPU
similarity index 100%
rename from install/CENTOS74GPU
rename to install/CENTOS7GPU
diff --git a/install/CENTOS74MIC b/install/CENTOS7MIC
similarity index 100%
rename from install/CENTOS74MIC
rename to install/CENTOS7MIC
diff --git a/install/install.sh b/install/install.sh
index d056fd2..ceb5281 100755
--- a/install/install.sh
+++ b/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
--
GitLab