From 83654a04ae02309c24085b78c3ea3f84303ae6cd 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: Tue, 17 Dec 2019 08:12:06 +0100
Subject: [PATCH] modified: install/CENTOS7LATEST modified:
install/CONFIG modified: install/UBUNTULATEST deleted:
CentOS/7.5-ESPRESO/CentOS-7.5-Bootstrap deleted:
CentOS/7.5-ESPRESO/app/log_crawler.py deleted:
CentOS/7.5-ESPRESO/app/notifications_monitor.py deleted:
CentOS/7.5-ESPRESO/app/startup.py deleted:
CentOS/7.5-ESPRESO/app/wait_a_while.py deleted:
CentOS/7.5-ESPRESO/heat.cpp deleted: Debian/8.0/Debian-8.0-Bootstrap
deleted: Ubuntu/16.04-OpenFOAM/README deleted:
Ubuntu/16.04-OpenFOAM/Ubuntu-16.04-Bootstrap deleted:
Ubuntu/16.04-OpenFOAM/app/check deleted:
Ubuntu/16.04-OpenFOAM/app/monitor deleted:
Ubuntu/16.04-OpenFOAM/app/startup deleted:
Ubuntu/16.04-OpenFOAM/hpc_image deleted:
Ubuntu/16.04-OpenFOAM/openfoam6-linux deleted:
Ubuntu/16.04-OpenFOAM/openfoam_hacks/aliases deleted:
Ubuntu/16.04-OpenFOAM/openfoam_hacks/bashrc deleted:
Ubuntu/16.04-OpenFOAM/openfoam_hacks/exec deleted:
Ubuntu/16.04-OpenFOAM/recipe-openfoam.txt deleted:
Ubuntu/16.04-OpenFOAM/singularity_image.tar deleted:
Ubuntu/16.04/Ubuntu-16.04-Bootstrap
---
CentOS/7.5-ESPRESO/CentOS-7.5-Bootstrap | 58 -----
CentOS/7.5-ESPRESO/app/log_crawler.py | 151 ------------
.../7.5-ESPRESO/app/notifications_monitor.py | 65 ------
CentOS/7.5-ESPRESO/app/startup.py | 94 --------
CentOS/7.5-ESPRESO/app/wait_a_while.py | 64 ------
CentOS/7.5-ESPRESO/heat.cpp | 145 ------------
Debian/8.0/Debian-8.0-Bootstrap | 57 -----
Ubuntu/16.04-OpenFOAM/README | 74 ------
Ubuntu/16.04-OpenFOAM/Ubuntu-16.04-Bootstrap | 105 ---------
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/openfoam6-linux | 144 ------------
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 40960 -> 0 bytes
Ubuntu/16.04/Ubuntu-16.04-Bootstrap | 57 -----
install/CENTOS7LATEST | 6 +-
install/CONFIG | 8 +-
install/UBUNTULATEST | 6 +-
23 files changed, 8 insertions(+), 1840 deletions(-)
delete mode 100644 CentOS/7.5-ESPRESO/CentOS-7.5-Bootstrap
delete mode 100644 CentOS/7.5-ESPRESO/app/log_crawler.py
delete mode 100644 CentOS/7.5-ESPRESO/app/notifications_monitor.py
delete mode 100644 CentOS/7.5-ESPRESO/app/startup.py
delete mode 100644 CentOS/7.5-ESPRESO/app/wait_a_while.py
delete mode 100644 CentOS/7.5-ESPRESO/heat.cpp
delete mode 100644 Debian/8.0/Debian-8.0-Bootstrap
delete mode 100644 Ubuntu/16.04-OpenFOAM/README
delete mode 100644 Ubuntu/16.04-OpenFOAM/Ubuntu-16.04-Bootstrap
delete mode 100755 Ubuntu/16.04-OpenFOAM/app/check
delete mode 100755 Ubuntu/16.04-OpenFOAM/app/monitor
delete mode 100755 Ubuntu/16.04-OpenFOAM/app/startup
delete mode 100644 Ubuntu/16.04-OpenFOAM/hpc_image
delete mode 100644 Ubuntu/16.04-OpenFOAM/openfoam6-linux
delete mode 100755 Ubuntu/16.04-OpenFOAM/openfoam_hacks/aliases
delete mode 100755 Ubuntu/16.04-OpenFOAM/openfoam_hacks/bashrc
delete mode 100755 Ubuntu/16.04-OpenFOAM/openfoam_hacks/exec
delete mode 100644 Ubuntu/16.04-OpenFOAM/recipe-openfoam.txt
delete mode 100644 Ubuntu/16.04-OpenFOAM/singularity_image.tar
delete mode 100644 Ubuntu/16.04/Ubuntu-16.04-Bootstrap
diff --git a/CentOS/7.5-ESPRESO/CentOS-7.5-Bootstrap b/CentOS/7.5-ESPRESO/CentOS-7.5-Bootstrap
deleted file mode 100644
index d5fe1df..0000000
--- a/CentOS/7.5-ESPRESO/CentOS-7.5-Bootstrap
+++ /dev/null
@@ -1,58 +0,0 @@
-Bootstrap: docker
-From: centos:latest
-
-%post
-yum -y update && yum -y upgrade
-
-# CentOS repo
-yum -y install python gcc make wget vim mc procps tcl gcc-c++ gcc-gfortran pkg-config acl acpid alsa-lib alsa-lib-devel amtu apr aspell at atk atk-devel attr audit audit-libs audit-libs-python authconfig autoconf autofs automake avahi-glib avahi-libs basesystem bash bc bind-libs bind-utils binutils binutils-devel bison bison-devel bluez-libs bridge-utils busybox bzip2 bzip2-devel bzip2-libs ca-certificates cairo cairo-devel c-ares ccid cdparanoia-libs centos-indexhtml centos-release checkpolicy chkconfig cloog-ppl compat-libcap1 compat-libstdc++-33 compat-readline5 ConsoleKit ConsoleKit-libs coolkey coreutils coreutils-libs cpio cpp cppunit cpupowerutils cpuspeed cracklib cracklib-dicts crash crda cronie cronie-anacron crontabs cryptsetup-luks cryptsetup-luks-libs cups cups-libs curl cvs cyrus-sasl cyrus-sasl-devel cyrus-sasl-gssapi cyrus-sasl-lib cyrus-sasl-plain dash db4 db4-cxx db4-devel db4-utils dbus dbus-devel dbus-glib dbus-glib-devel dbus-libs dbus-python dejavu-fonts-common dejavu-lgc-sans-mono-fonts dejavu-sans-mono-fonts desktop-file-utils device-mapper device-mapper-event device-mapper-event-libs device-mapper-libs device-mapper-multipath device-mapper-multipath-libs device-mapper-persistent-data diffutils dmidecode dmraid dmraid-events dmz-cursor-themes docbook-dtds docbook-style-dsssl docbook-style-xsl docbook-utils dos2unix dosfstools dracut dracut-kernel dracut-network dump e2fsprogs e2fsprogs-devel e2fsprogs-libs ed eggdbus eject elfutils-libelf elfutils-libelf-devel elfutils-libs emacs emacs-common environment-modules ethtool expat expat-devel expect file file-devel file-libs filesystem findutils finger fipscheck fipscheck-lib flac fontconfig fontconfig-devel fontpackages-filesystem foomatic foomatic-db foomatic-db-filesystem foomatic-db-ppds freeglut freeglut-devel freetype freetype-devel ftp fuse fuse-libs gamin gamin-python gawk gcc gcc-c++ gcc-gfortran GConf2 GConf2-devel gd gdb gdbm gdbm-devel gdk-pixbuf2 gdk-pixbuf2-devel genisoimage gettext gettext-devel gettext-libs ghostscript ghostscript-fonts giflib git glib2 glib2-devel glibc glibc-common glibc-debuginfo glibc-debuginfo-common glibc-devel glibc-headers glx-utils gmp gmp-devel gnome-icon-theme gnome-keyring gnome-keyring-devel gnome-themes gnome-vfs2 gnome-vfs2-devel gnupg2 gnuplot gnuplot-common gnutls gnutls-devel gperf gpgme gpm gpm-libs grep groff grub grubby gstreamer gstreamer-plugins-base gstreamer-tools gtk2 gtk2-devel gtk2-engines gtk-doc gzip hal hal-devel hal-info hal-libs hdparm hesiod hicolor-icon-theme hunspell hwdata hwloc hwloc-devel ilmbase ImageMagick indent info initscripts iproute iptables iptables-ipv6 iptstate iputils irqbalance iscsi-initiator-utils iso-codes iw jasper-libs jwhois kbd kbd-misc kernel kernel kernel-devel kernel-firmware kernel-headers keyutils keyutils-libs keyutils-libs-devel kpartx krb5-devel krb5-libs krb5-workstation ksh lcms-libs less lftp libacl libacl-devel libaio libart_lgpl libart_lgpl-devel libasyncns libattr libattr-devel libbasicobjects libblkid libbonobo libbonobo-devel libbonoboui libbonoboui-devel libcanberra libcanberra-gtk2 libcap libcap-devel libcap-ng libcgroup libcollection libcom_err libcom_err-devel libcroco libcroco-devel libcxgb3 libcxgb4 libdaemon libdhash libdrm libdrm-devel libedit libedit-devel libevent libexif libffi libfontenc libgcc libgcj libgcrypt libgcrypt-devel libgfortran libglade2 libglade2-devel libgnome libgnomecanvas libgnomecanvas-devel libgnome-devel libgomp libgpg-error libgpg-error-devel libgsf libgsf-devel libgssglue libgudev1 libhugetlbfs libibcm libibcm-devel libibverbs libibverbs-devel libibverbs-devel-static libibverbs-utils libICE libICE-devel libicu libIDL libIDL-devel libidn libidn-devel libini_config libipa_hbac libjpeg-turbo libjpeg-turbo-devel libldb libmcpp libmlx4 libmlx5 libmng libmng-devel libmthca libmthca-static libnetfilter_conntrack libnfnetlink libnih libnl libnl-devel libnotify libogg liboil libotf libpath_utils libpcap libpciaccess libpciaccess-devel libpng libpng-devel libproxy libproxy-bin libproxy-python libref_array librsvg2 librsvg2-devel libselinux libselinux-devel libselinux-python libselinux-utils libsemanage libsepol libsepol-devel libSM libSM-devel libsndfile libss libssh2 libsss_idmap libstdc++ libstdc++-devel libsysfs libsysfs-devel libtalloc libtasn1 libtasn1-devel libtdb libtevent libthai libtheora libtiff libtiff-devel libtirpc libtool-ltdl libudev libudev-devel libunistring libusb libusb1 libusb-devel libuser libutempter libuuid libvisual libvorbis libwmf libwmf-lite libwnck libX11 libX11-common libX11-devel libXau libXau-devel libXaw libXaw-devel libxcb libxcb-devel libXcomposite libXcomposite-devel libXcursor libXcursor-devel libXdamage libXdamage-devel libXdmcp libXdmcp-devel libXext libXext-devel libXfixes libXfixes-devel libXfont libXft libXft-devel libXi libXi-devel libXinerama libXinerama-devel libxkbfile libxml2 libxml2-devel libxml2-python libXmu libXmu-devel libXp libXpm libXpm-devel libXrandr libXrandr-devel libXrender libXrender-devel libXres libXScrnSaver libXScrnSaver-devel libxslt libxslt-devel libXt libXt-devel libXtst libXtst-devel libXv libXv-devel libXxf86misc libXxf86misc-devel libXxf86vm libXxf86vm-devel lm_sensors-libs lockdev logrotate lsof lvm2 lvm2-libs lynx lzo m17n-db m17n-db-datafiles m17n-lib m2crypto m4 mailcap mailx make MAKEDEV man man-pages mc mcpp mcstrans mdadm mesa-dri1-drivers mesa-dri-drivers mesa-dri-filesystem mesa-libGL mesa-libGL-devel mesa-libGLU mesa-libGLU-devel mesa-private-llvm mgetty microcode_ctl mingetty mkbootdisk mlocate module-init-tools mpfr mtools mtr mysql-libs nano nc ncurses ncurses-base ncurses-devel ncurses-libs net-snmp net-snmp-libs net-tools newt newt-python nfs-utils nfs-utils-lib nmap notification-daemon nscd nspr nspr-devel nss nss_db nss-devel nss-softokn nss-softokn-debuginfo nss-softokn-devel nss-softokn-freebl nss-softokn-freebl-devel nss-sysinit nss-tools nss-util nss-util-devel ntp ntpdate ntsysv OpenEXR-libs OpenIPMI OpenIPMI-libs openjade openjpeg-libs openldap openldap-devel openmotif openmotif22 opensp openssh openssh-clients openssh-server ORBit2 ORBit2-devel p11-kit p11-kit-trust pam pam-devel pam_krb5 pam_passwdqc pam_pkcs11 pango pango-devel paps paps-libs parted passwd patch pax pciutils pciutils-devel pciutils-libs pcmciautils pcp pcp-conf pcp-libs pcre pcsc-lite pcsc-lite-libs perf perl perl-AppConfig perl-Authen-SASL perl-Bit-Vector perl-Carp-Clan perl-CGI perl-Class-Singleton perl-Compress-Raw-Zlib perl-Compress-Zlib perl-Convert-ASN1 perl-Crypt-PasswdMD5 perl-Date-Calc perl-Date-Manip perl-DateTime perl-DBD-Pg perl-DBI perl-devel perl-Digest-HMAC perl-Digest-SHA1 perl-Error perl-ExtUtils-MakeMaker perl-ExtUtils-ParseXS perl-File-Which perl-Git perl-GSSAPI perl-HTML-Parser perl-HTML-Tagset perl-IO-Compress-Base perl-IO-Compress-Zlib perl-IO-Socket-SSL perl-JSON perl-LDAP perl-libs perl-libwww-perl perl-List-MoreUtils perl-Module-Pluggable perl-Net-LibIDN perl-Net-SSLeay perl-Net-Telnet perl-Params-Validate perl-PCP-PMDA perl-Pod-Escapes perl-Pod-Simple perl-SGMLSpm perl-Socket6 perl-String-CRC32 perl-TermReadKey perl-Test-Harness perl-Test-Simple perl-Text-Iconv perl-Time-HiRes perl-URI perl-version perl-WWW-Curl perl-XML-Filter-BufferText perl-XML-LibXML perl-XML-NamespaceSupport perl-XML-Parser perl-XML-SAX perl-XML-SAX-Writer perl-XML-Simple perl-YAML-Syck pinentry pinfo pixman pixman-devel pkgconfig plymouth plymouth-core-libs plymouth-scripts pm-utils policycoreutils polkit poppler poppler-data poppler-utils popt popt-devel portreserve postfix postgresql postgresql-devel postgresql-libs postgresql-odbc ppl ppp prelink procmail procps psacct psmisc pth pulseaudio-libs pycairo pycairo-devel pygobject2 pygobject2-codegen pygobject2-devel pygobject2-doc pygpgme pygtk2 pygtk2-codegen pygtk2-devel pygtk2-doc pyOpenSSL pytalloc python python-argparse python-devel python-iniparse python-libs python-pcp python-pycurl python-setuptools python-sssdconfig python-urlgrabber qt qt3 qt-sqlite qt-x11 quota rarian rarian-compat rdate rdma readahead readline readline-devel redhat-logos redhat-lsb redhat-lsb-compat redhat-lsb-core redhat-lsb-graphics redhat-lsb-printing redhat-menus redhat-rpm-config rmt rootfiles rpcbind rpm rpm-devel rpm-libs rpm-python rp-pppoe rrdtool rsh rsync ruby ruby-libs samba samba4-libs samba-common samba-winbind samba-winbind-clients screen SDL SDL-devel sed selinux-policy setserial setup setuptool sgml-common sgpio shadow-utils shared-mime-info slang smartmontools snappy sos sound-theme-freedesktop sqlite sqlite-devel sssd sssd-ad sssd-client sssd-common sssd-common-pac sssd-ipa sssd-krb5 sssd-krb5-common sssd-ldap sssd-proxy startup-notification startup-notification-devel strace stunnel sudo swig symlinks sysfsutils syslinux syslinux-nonlinux sysstat system-gnome-theme system-icon-theme systemtap-devel sysvinit-tools t1lib talk tar tcl tcl-devel tcpdump tcp_wrappers tcp_wrappers-libs tcsh telnet time tk tmpwatch traceroute tree tunctl tzdata udev udftools unix2dos unixODBC unixODBC-devel unzip upstart urw-fonts usbutils usermode ustr util-linux-ng vconfig vim-common vim-enhanced vim-filesystem vim-minimal virt-what wget which wireless-tools words wpa_supplicant xcb-util xdg-utils xerces-c xerces-c-devel xinetd xkeyboard-config xml-common xmlrpc-c xmlrpc-c-client xorg-x11-fonts-100dpi xorg-x11-fonts-75dpi xorg-x11-font-utils xorg-x11-proto-devel xorg-x11-server-common xorg-x11-server-utils xorg-x11-xauth xorg-x11-xkb-utils xterm xz xz-libs xz-lzma-compat ypbind yp-tools yum yum-metadata-parser yum-plugin-auto-update-debug-info yum-plugin-fastestmirror yum-plugin-priorities yum-plugin-security yum-plugin-versionlock yum-utils zip zlib zlib-devel
-
-# Fedora repo
-yum -y install bash-completion pigz tmux
-
-yum -y groupinstall "Development Tools"
-
-cd /tmp
-
-# 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
-
-# pip
-curl -s -O https://bootstrap.pypa.io/get-pip.py
-python get-pip.py
-
-pip install setuptools numpy scipy pandas wheel --upgrade
-
-# lua
-wget http://dl.fedoraproject.org/pub/epel/7/x86_64/Packages/l/lua-posix-32-2.el7.x86_64.rpm
-wget http://dl.fedoraproject.org/pub/epel/7/x86_64/Packages/l/lua-filesystem-1.6.2-2.el7.x86_64.rpm
-wget http://mirror.centos.org/centos/7/os/x86_64/Packages/lua-devel-5.1.4-15.el7.x86_64.rpm
-wget http://dl.fedoraproject.org/pub/epel/7/x86_64/Packages/l/lua-bitop-1.0.2-3.el7.x86_64.rpm
-
-rpm -ihv lua-devel-5.1.4-15.el7.x86_64.rpm
-rpm -ihv lua-filesystem-1.6.2-2.el7.x86_64.rpm
-rpm -ihv lua-bitop-1.0.2-3.el7.x86_64.rpm
-rpm -ihv lua-posix-32-2.el7.x86_64.rpm
-
-# 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
-
-# APPS and SCRATCH
-mkdir /apps
-mkdir /scratch
-
-%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
diff --git a/CentOS/7.5-ESPRESO/app/log_crawler.py b/CentOS/7.5-ESPRESO/app/log_crawler.py
deleted file mode 100644
index e7146ea..0000000
--- a/CentOS/7.5-ESPRESO/app/log_crawler.py
+++ /dev/null
@@ -1,151 +0,0 @@
-import sys
-import time
-import os
-import json
-import logging
-import shutil
-
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger("Log crawler")
-
-PROGRESS_HEAD = '''<html>
- <head>
- <title>HPC job progress</title>
- <script type="text/javascript">
- function abort() {
- notify_running_job("ABORT");
- }
- </script>
- </head>'''
-
-PROGRESS_BODY='''<body style="margin: 20px; padding: 20px;">
- <h1>HPC job progress</h1>
- <div>
- <h3>This is a waiter. It's waiting on the HPC cluster. It has waited {}/{} seconds.</h3>
- <p>(Status from {}.)</p>
- <p>Click the Abort button to stop the waiter early. Please click only once,
- it will take a while until the request is processed. (The status might even
- update once more before the job is aborted.)</p>
- <input type="button" value="Abort" onclick="abort()">
- </div>
- </body>
-</html>
-'''
-
-PROGRESS_BODY_UNKNOWN='''<body style="margin: 20px; padding: 20px;">
- <h1>HPC job progress</h1>
- <div>
- <h3>This is a waiter. It's waiting on the HPC cluster. Its status is unknown.</h3>
- <input type="button" value="Abort job" onclick="abort()">
- </div>
- </body>
-</html>
-'''
-
-
-def main():
- fn_log = sys.argv[1]
- fn_status = sys.argv[2]
-
- crawl_log(fn_log, fn_status)
-
-
-def crawl_log(fn_log, fn_status):
- """Monitors a log file and creates html status pages from it
-
- The log file is expected to grow only by one line at a time, with new lines
- added to the end of the file. Each line is expected to be either a json
- string containing the fields 'timestamp', 'elapsed_time', and 'total_time',
- or the string 'FINISHED', which triggers the crawler to stop.
-
- Note that this crawler is "memory-less", meaning that it cares only about
- the last, newest line added to the log file while all prior lines are
- disregarded.
-
- Args:
- fn_log (str): Filename of the log file to monitor
- fn_status (str): Filename to write the status output to
- """
- logger.info("Log crawler starting up")
- cached_stamp = 0
- should_stop = False
- while not should_stop:
- if not os.path.exists(fn_log):
- logger.info("Log file doesn't exist")
- else:
- # Check if "last modified" time of the log file has changed
- stamp = os.stat(fn_log).st_mtime
- if not stamp != cached_stamp:
- logger.info("Log file hasn't changed since last check")
- else:
- logger.info("Log file has changed")
- cached_stamp = stamp
-
- status = get_last_line(fn_log)
- # We can stop crawling the logs if the main app is done
- if status.strip() == "FINISHED":
- should_stop = True
- logger.info("Found FINISHED log, will stop now!")
- # Otherwise, parse json and write status from it
- else:
- try:
- log = json.loads(status)
- write_status(log, fn_status)
- except json.JSONDecodeError:
- write_status_unknown(fn_status)
-
- time.sleep(1)
-
- logger.info("Log crawler terminating")
-
-
-def get_last_line(fn):
- """Returns the last line of a file
-
- Args:
- fn (str): File name of the file to read from
- """
- with open(fn, 'r') as fin:
- for line in fin:
- pass
- return line
-
-
-def write_status(log, fn_status):
- """Writes a status html page using the information in 'log'
-
- Args:
- log (dict): Log containing the field 'timestamp', 'elapsed_time', and
- 'total_time'
- fn_status (str): Filename to write the status html to
- """
- status = PROGRESS_HEAD + PROGRESS_BODY.format(
- log["elapsed_time"],
- log["total_time"],
- log["timestamp"],
- )
- # First write to a temporary file, then copy to actual status file. That
- # way, the status file won't be corrupt if the writing process takes a
- # while.
- fn_status_new = fn_status + '.new'
- with open(fn_status_new, 'w') as fout:
- fout.write(status)
- shutil.copyfile(fn_status_new, fn_status)
-
- logger.info("Wrote status file")
-
-
-def write_status_unknown(fn_status):
- """Writes a status html page when no actual status is known
-
- Args:
- fn_status (str): Filename to write the status html to
- """
- with open(fn_status, 'w') as fout:
- fout.write(PROGRESS_HEAD + PROGRESS_BODY_UNKNOWN)
-
- logger.info("Wrote unknown status")
-
-
-if __name__ == "__main__":
- main()
\ No newline at end of file
diff --git a/CentOS/7.5-ESPRESO/app/notifications_monitor.py b/CentOS/7.5-ESPRESO/app/notifications_monitor.py
deleted file mode 100644
index d12a92a..0000000
--- a/CentOS/7.5-ESPRESO/app/notifications_monitor.py
+++ /dev/null
@@ -1,65 +0,0 @@
-import os
-import time
-import sys
-import logging
-
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger("Notifications monitor")
-
-
-def main():
- fn_notifications = sys.argv[1]
- fn_abort = sys.argv[2]
-
- monitor(fn_notifications, fn_abort)
-
-
-def monitor(fn_notifications, fn_abort):
- """
- """
- logger.info("Notifications monitor starting up")
- cached_stamp = 0
- while True:
- if not os.path.exists(fn_notifications):
- logger.info("Notifications file doesn't exist")
- else:
- # Check if "last modified" time of the file has changed
- stamp = os.stat(fn_notifications).st_mtime
- if not stamp != cached_stamp:
- logger.info("Notifications file hasn't changed since last check")
- else:
- logger.info("Notifications file has changed")
- cached_stamp = stamp
-
- command = get_last_line(fn_notifications).strip()
-
- if command == "ABORT":
- logger.info("Received abort command")
- # Abort the main app by creating a specific file
- open(fn_abort, 'a').close()
- else:
- logger.info("Ignoring unknown command {}".format(command))
-
- time.sleep(1)
-
-
-def get_last_line(fn):
- """Returns the last line of a file
-
- Returns an empty string if the file is empty.
-
- Args:
- fn (str): File name of the file to read from
- """
- with open(fn, 'r') as fin:
- i = -1
- for i, line in enumerate(fin):
- pass
- if i >= 0:
- return line
- else:
- return ''
-
-
-if __name__ == "__main__":
- main()
\ No newline at end of file
diff --git a/CentOS/7.5-ESPRESO/app/startup.py b/CentOS/7.5-ESPRESO/app/startup.py
deleted file mode 100644
index 6c1018b..0000000
--- a/CentOS/7.5-ESPRESO/app/startup.py
+++ /dev/null
@@ -1,94 +0,0 @@
-import subprocess
-import sys
-import os
-import string
-import random
-import shutil
-import logging
-
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger("Startup")
-
-
-def main():
- # Input arguments
- seconds_to_wait = int(sys.argv[1])
- app_folder = sys.argv[2]
-
- # Pre-defined files for communication with the "outside world"
- fn_status = '/service/status.html'
- fn_result = '/service/result.txt'
- fn_notifications = '/service/notifications.txt'
-
- # Write dummy value into result file
- logger.info("Writing dummy result")
- with open(fn_result, 'w') as fout:
- fout.write("UNSET")
-
- # Define files for the main app in a unique folder
- ID = generate_id('/home')
- unique_folder = os.path.join('/home', ID)
- os.mkdir(unique_folder)
- fn_log = os.path.join(unique_folder, 'main_log.txt')
- fn_abort = os.path.join(unique_folder, 'main_abort.txt')
- logger.info("Created unique folder {}".format(unique_folder))
-
- # 1: Start log crawler as a background process
- # The log crawler monitors a single log file and creates status html pages
- # from it
- # The log crawler will automatically terminate when it reads the finishing
- # log from the main application
- logger.info("Starting log crawler")
- log_crawler_script = os.path.join(app_folder, 'log_crawler.py')
- command = ['python', log_crawler_script, fn_log, fn_status]
- proc_log = subprocess.Popen(command)
-
- # 2: Start the notifications monitor as a background process
- # It monitors the notifications file (which is written to when messages are
- # sent to the HPC service running this Singularity image) and translates
- # messages into comands to the main application. Here, this is done simply
- # by creating a specific file the main app looks for. Only a single command
- # (abort) is supported.
- # The notifications monitor does _not_ terminate by itself.
- logger.info("Starting notifications monitor")
- not_monitor_script = os.path.join(app_folder, 'notifications_monitor.py')
- command = ['python', not_monitor_script, fn_notifications, fn_abort]
- proc_not = subprocess.Popen(command)
-
- # 3: Start the main application as a foreground process
- # The main application will write to the log file monitored by the crawler,
- # and it will write its final result into the result file.
- # It will also check periodically for the existence of 'fn_abort' and quit
- # if this file exists. (This is a cheap way of sending a command to the
- # main app.)
- logger.info("Starting waiter")
- waiter_script = os.path.join(app_folder, 'wait_a_while.py')
- command = ['python', waiter_script, str(seconds_to_wait), fn_log,
- fn_result, fn_abort]
- subprocess.run(command)
- logger.info("Waiter finished, terminating processes")
-
- # 4: Terminate notifications monitor and remove log folders
- # As the main app is finished at this point, we can safely terminate the
- # notifications monitor
- proc_log.terminate()
- proc_not.terminate()
- shutil.rmtree(unique_folder)
-
- # (Optional) 5: Process end result
- # In case the final result of the main application (see step 3) is _not_
- # just a simple file, we should call another script here which processes
- # this end result and writes into the /service/result.txt file.
-
-
-def generate_id(folder, size=16, chars=string.ascii_uppercase + string.digits):
- """Generates a random ID string which guaranteed not to exist in a folder"""
- while True:
- ID = ''.join(random.choice(chars) for _ in range(size))
- if not os.path.exists(os.path.join(folder, ID)):
- break
- return ID
-
-
-if __name__ == "__main__":
- main()
\ No newline at end of file
diff --git a/CentOS/7.5-ESPRESO/app/wait_a_while.py b/CentOS/7.5-ESPRESO/app/wait_a_while.py
deleted file mode 100644
index 5f08b0e..0000000
--- a/CentOS/7.5-ESPRESO/app/wait_a_while.py
+++ /dev/null
@@ -1,64 +0,0 @@
-import sys
-import time
-import datetime
-import json
-import os
-import logging
-
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger("Waiter")
-
-
-def main():
- seconds_to_wait = int(sys.argv[1])
- fn_log = sys.argv[2]
- fn_result = sys.argv[3]
- fn_abort = sys.argv[4]
- logger.info("Waiter starting up, will wait {} seconds".format(seconds_to_wait))
-
- for current_time in range(seconds_to_wait):
- # Perform part of "complicated computation"
- time.sleep(1)
-
- # Write log
- write_log(fn_log, current_time, seconds_to_wait)
-
- # Check if we should abort
- if os.path.exists(fn_abort):
- write_final_log(fn_log)
- write_result(fn_result, current_time, aborted=True)
- return 0
-
- write_final_log(fn_log)
- write_result(fn_result, seconds_to_wait)
-
-
-def write_log(fn_log, elapsed_time, total_time):
- log = {
- 'timestamp': str(datetime.datetime.now()),
- 'elapsed_time': str(elapsed_time),
- 'total_time': str(total_time),
- }
- with open(fn_log, 'a') as fout:
- json.dump(log, fout)
- fout.write("\n")
- logger.info("Log written: {}/{} seconds waited".format(elapsed_time, total_time))
-
-
-def write_final_log(fn_log):
- with open(fn_log, 'a') as fout:
- fout.write("FINISHED\n")
- logger.info("Final log written")
-
-
-def write_result(fn, seconds_waited, aborted=False):
- with open(fn, 'w') as f:
- if aborted:
- f.write('Done. My waiting was aborted after {} seconds.'.format(seconds_waited))
- else:
- f.write('Done. I have waited {} seconds.'.format(seconds_waited))
- logger.info("Result written")
-
-
-if __name__ == "__main__":
- main()
diff --git a/CentOS/7.5-ESPRESO/heat.cpp b/CentOS/7.5-ESPRESO/heat.cpp
deleted file mode 100644
index e59fc15..0000000
--- a/CentOS/7.5-ESPRESO/heat.cpp
+++ /dev/null
@@ -1,145 +0,0 @@
-# ESPRESO Configuration File
-
-#BENCHMARK ARG0 [ TETRA4, TETRA10, PYRAMID5, PYRAMID13, PRISMA6, PRISMA15, HEXA8, HEXA20 ]
-#BENCHMARK ARG10 [ TOTAL_FETI, HYBRID_FETI ]
-
-DEFAULT_ARGS {
- 0 HEXA8;
-
- 1 1;
- 2 1;
- 3 1;
-
- 4 2;
- 5 2;
- 6 2;
-
- 7 5;
- 8 5;
- 9 5;
-
- 10 TOTAL_FETI;
-}
-
-INPUT GENERATOR;
-PHYSICS HEAT_TRANSFER_3D;
-
-DECOMPOSITION {
- BALANCE_CLUSTERS TRUE;
-}
-
-GENERATOR {
- SHAPE GRID;
-
- GRID {
- LENGTH_X 1;
- LENGTH_Y 1;
- LENGTH_Z 1;
-
- NODES {
- BOTTOM <1 , 1> <0 , 1> <0 , 1>;
- TOP <0 , 0> <0 , 1> <0 , 1>;
- }
-
- ELEMENT_TYPE [ARG0];
-
- BLOCKS_X 1;
- BLOCKS_Y 1;
- BLOCKS_Z 1;
-
- CLUSTERS_X [ARG1];
- CLUSTERS_Y [ARG2];
- CLUSTERS_Z [ARG3];
-
- DOMAINS_X [ARG4];
- DOMAINS_Y [ARG5];
- DOMAINS_Z [ARG6];
-
- ELEMENTS_X [ARG7];
- ELEMENTS_Y [ARG8];
- ELEMENTS_Z [ARG9];
- }
-}
-
-HEAT_TRANSFER_3D {
- LOAD_STEPS 1;
-
- MATERIALS {
- 1 {
- COORDINATE_SYSTEM {
- TYPE CYLINDRICAL;
- CENTER { X .5; Y .5; Z .5; }
- ROTATION { X 90; }
- }
-
- DENS 1;
- CP 1;
-
- THERMAL_CONDUCTIVITY {
- MODEL DIAGONAL;
-
- KXX 1;
- KYY 10;
- KZZ 10;
- }
- }
- }
-
- MATERIAL_SET {
- ALL_ELEMENTS 1;
- }
-
- INITIAL_TEMPERATURE {
- ALL_ELEMENTS 200;
- }
-
- STABILIZATION CAU;
- SIGMA 0;
-
- LOAD_STEPS_SETTINGS {
- 1 {
- DURATION_TIME 1;
- TYPE STEADY_STATE;
- MODE LINEAR;
- SOLVER FETI;
-
- FETI {
- METHOD [ARG10];
- PRECONDITIONER DIRICHLET;
- PRECISION 1E-08;
- ITERATIVE_SOLVER PCG;
- REGULARIZATION ANALYTIC;
- }
-
- TEMPERATURE {
- TOP 100;
- BOTTOM 300;
- }
- }
- }
-}
-
-OUTPUT {
- RESULTS_STORE_FREQUENCY EVERY_TIMESTEP;
- MONITORS_STORE_FREQUENCY EVERY_TIMESTEP;
-
- MONITORING {
- 1 {
- REGION TOP;
- STATISTICS MAX;
- PROPERTY TEMPERATURE;
- }
-
- 2 {
- REGION BOTTOM;
- STATISTICS MIN;
- PROPERTY TEMPERATURE;
- }
-
- 5 {
- REGION ALL_ELEMENTS;
- STATISTICS AVG;
- PROPERTY TEMPERATURE;
- }
- }
-}
diff --git a/Debian/8.0/Debian-8.0-Bootstrap b/Debian/8.0/Debian-8.0-Bootstrap
deleted file mode 100644
index 58dfc70..0000000
--- a/Debian/8.0/Debian-8.0-Bootstrap
+++ /dev/null
@@ -1,57 +0,0 @@
-Bootstrap: docker
-From: debian:jessie
-
-%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
-
-cd /bin
-rm sh && ln -s /bin/bash sh
-
-# APPS and SCRATCH
-mkdir /apps
-mkdir /scratch
-
-%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
diff --git a/Ubuntu/16.04-OpenFOAM/README b/Ubuntu/16.04-OpenFOAM/README
deleted file mode 100644
index b60452a..0000000
--- a/Ubuntu/16.04-OpenFOAM/README
+++ /dev/null
@@ -1,74 +0,0 @@
-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
deleted file mode 100644
index 449fb93..0000000
--- a/Ubuntu/16.04-OpenFOAM/Ubuntu-16.04-Bootstrap
+++ /dev/null
@@ -1,105 +0,0 @@
-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 apt-transport-https
-apt -y install dkms infiniband-diags libibverbs* ibacm librdmacm* libmlx4* libmlx5* mstflint libibcm.* libibmad.* libibumad* opensm srptools libmlx4-dev librdmacm-dev rdmacm-utils ibverbs-utils perftest vlan ibutils
-apt -y install libtool autoconf automake build-essential ibutils ibverbs-utils rdmacm-utils infiniband-diags perftest librdmacm-dev libibverbs-dev libmlx4-1 numactl libnuma-dev autoconf automake gcc g++ git libtool pkg-config
-apt -y install libnl-3-200 libnl-route-3-200 libnl-route-3-dev libnl-utils
-
-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
-
-cd /tmp
-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
-cd /tmp
-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
-cd /tmp
-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 \
- --enable-orterun-prefix-by-default \
- --enable-mpirun-prefix-by-default \
- --enable-static \
- --enable-shared \
- --with-verbs
-
-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 openfoam6
-echo '. /opt/openfoam6/etc/bashrc' >>$SINGULARITY_ENVIRONMENT
-
-### openfoam hacks ###
-
-#mv -f /opt/bashrc /opt/openfoam6/etc
-#mv -f /opt/aliases /opt/openfoam6/etc/config.sh
-#mv -f /opt/exec /.singularity.d/actions
-
-%environment
-source /opt/apps/lmod/7.7.7/init/profile
-clearMT
-export LD_LIBRARY_PATH=$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
deleted file mode 100755
index 41d9499..0000000
--- a/Ubuntu/16.04-OpenFOAM/app/check
+++ /dev/null
@@ -1,183 +0,0 @@
-#!/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
deleted file mode 100755
index 92943a2..0000000
--- a/Ubuntu/16.04-OpenFOAM/app/monitor
+++ /dev/null
@@ -1,62 +0,0 @@
-#!/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
deleted file mode 100755
index 0c2a461..0000000
--- a/Ubuntu/16.04-OpenFOAM/app/startup
+++ /dev/null
@@ -1,106 +0,0 @@
-#!/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
deleted file mode 100644
index 7072c94..0000000
--- a/Ubuntu/16.04-OpenFOAM/hpc_image
+++ /dev/null
@@ -1,71 +0,0 @@
-#!/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/openfoam6-linux b/Ubuntu/16.04-OpenFOAM/openfoam6-linux
deleted file mode 100644
index 619a88c..0000000
--- a/Ubuntu/16.04-OpenFOAM/openfoam6-linux
+++ /dev/null
@@ -1,144 +0,0 @@
-#!/bin/sh
-#------------------------------------------------------------------------------
-# ========= |
-# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox
-# \\ / O peration |
-# \\ / A nd | Copyright (C) 2017 OpenFOAM Foundation
-# \\/ M anipulation |
-#-------------------------------------------------------------------------------
-# License
-# This program 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.
-#
-# This program 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/>.
-#
-# Script
-# openfoam6-linux
-#
-# Description
-# Run script for an OpenFOAM 6 Docker image at:
-# https://hub.docker.com/r/openfoam
-#
-#------------------------------------------------------------------------------
-Script=${0##*/}
-VER=6
-
-usage () {
- exec 1>&2
- while [ "$#" -ge 1 ]; do echo "$1"; shift; done
- cat <<USAGE
-
-Usage: ${0##*/} [OPTIONS]
-options:
- -d | -dir host directory mounted (defaults to current directory)
- -x | -xhost use custom X authority and give container host network
- -h | -help help
-
-Launches the OpenFOAM ${VER} Docker image.
-- Requires installation of docker-engine.
-- Runs a "containerized" bash shell environment where the user can run OpenFOAM
- and, optionally, ParaView (see below).
-- The container mounts the user's file system so that case files are stored
- permanently. The container mounts the current directory by default, but the
- user can also specify a particular directory using the "-d" option.
-- Mounting the user's HOME directory is disallowed.
-- The '-xhost' option is useful when accessing the host via 'ssh -X'.
- This option should only be used when strictly necessary, as it relies on the
- option '--net=host' when launching the container in Docker, which will
- give to the container full access to the Docker host network stack and
- potentially the host's system services that rely on network communication,
- making it potentially insecure.
-
-Example:
-To store data in ${HOME}/OpenFOAM/${USER}-${VER}, the user can launch
-${Script} either by:
- cd ${HOME}/OpenFOAM/${USER}-${VER} && ${Script}
-or
- ${Script} -d ${HOME}/OpenFOAM/${USER}-${VER}
-
-Further Information:
-http://openfoam.org/download/6-linux
-
-Note:
-The container user name appears as "openfoam" but it is just an alias.
-
-USAGE
- exit 1
-}
-
-DOCKER_IMAGE='openfoam/openfoam6-paraview54'
-MOUNT_DIR=$(pwd)
-CUSTOM_XAUTH=""
-DOCKER_OPTIONS=""
-
-while [ "$#" -gt 0 ]
-do
- case "$1" in
- -d | -dir)
- [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
- MOUNT_DIR=$2
- shift 2
- ;;
- -x | -xhost)
- CUSTOM_XAUTH=yes
- shift
- ;;
- -h | -help)
- usage
- ;;
- *)
- usage "Invalid option '$1'"
- ;;
- esac
-done
-
-[ -d "$MOUNT_DIR" ] || usage "No directory exists: $MOUNT_DIR"
-MOUNT_DIR=$(cd "$MOUNT_DIR" && pwd -P)
-
-[ "$MOUNT_DIR" = "$(cd "$HOME" && pwd -P)" ] && \
- usage "Mount directory cannot be the user's home directory" \
- "Make a subdirectory and run from there, e.g." \
- " mkdir -p ${HOME}/OpenFOAM/$(whoami)-${VER}" \
- " ${Script} -d ${HOME}/OpenFOAM/$(whoami)-${VER}"
-
-if [ -n "$CUSTOM_XAUTH" ]
-then
- XAUTH_PATH="${MOUNT_DIR}/.docker.xauth.$$"
- touch "${XAUTH_PATH}"
-
- # Generate a custom X-authority file that allows any hostname
- xauth nlist "$DISPLAY" | sed -e 's/^..../ffff/' | \
- xauth -f "$XAUTH_PATH" nmerge -
-
- DOCKER_OPTIONS="-e XAUTHORITY=$XAUTH_PATH
- -v $XAUTH_PATH:$XAUTH_PATH
- --net=host"
-fi
-
-USER_ID=$(id -u 2> /dev/null)
-[ -n "$USER_ID" ] || usage "Cannot determine current user ID"
-GROUP_ID=$(id -g)
-
-HOME_DIR='/home/openfoam'
-
-echo "Launching $0"
-echo "User: \"$(id -un)\" (ID $USER_ID, group ID $GROUP_ID)"
-
-docker run -it \
- --rm \
- -e DISPLAY=$DISPLAY \
- -u $USER_ID:$GROUP_ID \
- -v /tmp/.X11-unix:/tmp/.X11-unix \
- -v $MOUNT_DIR:$HOME_DIR \
- $DOCKER_OPTIONS \
- $DOCKER_IMAGE
-
-[ -n "$CUSTOM_XAUTH" -a -e "${XAUTH_PATH}" ] && rm "${XAUTH_PATH}"
diff --git a/Ubuntu/16.04-OpenFOAM/openfoam_hacks/aliases b/Ubuntu/16.04-OpenFOAM/openfoam_hacks/aliases
deleted file mode 100755
index 098874b..0000000
--- a/Ubuntu/16.04-OpenFOAM/openfoam_hacks/aliases
+++ /dev/null
@@ -1,120 +0,0 @@
-#----------------------------------*-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
deleted file mode 100755
index d69506a..0000000
--- a/Ubuntu/16.04-OpenFOAM/openfoam_hacks/bashrc
+++ /dev/null
@@ -1,215 +0,0 @@
-#----------------------------------*-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" ] && . $WM_PROJECT_DIR/etc/config.sh/bash_completion
-
-#------------------------------------------------------------------------------
diff --git a/Ubuntu/16.04-OpenFOAM/openfoam_hacks/exec b/Ubuntu/16.04-OpenFOAM/openfoam_hacks/exec
deleted file mode 100755
index c24a5c6..0000000
--- a/Ubuntu/16.04-OpenFOAM/openfoam_hacks/exec
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/bash
-
-for script in /.singularity.d/env/*.sh; do
- if [ -f "$script" ]; then
- . "$script"
- fi
-done
-
-exec "$@"
diff --git a/Ubuntu/16.04-OpenFOAM/recipe-openfoam.txt b/Ubuntu/16.04-OpenFOAM/recipe-openfoam.txt
deleted file mode 100644
index 9e0c90d..0000000
--- a/Ubuntu/16.04-OpenFOAM/recipe-openfoam.txt
+++ /dev/null
@@ -1,48 +0,0 @@
-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' >>$SINGULARITY_ENVIRONMENT
-
- ### openfoam hacks ###
-
- mv -f /opt/bashrc /opt/openfoam5/etc
- mv -f /opt/aliases /opt/openfoam5/etc/config.sh
- mv -f /opt/exec /.singularity.d/actions
-
-
-%files
- app/startup opt/
- app/check opt/
- app/monitor opt/
- openfoam_hacks/bashrc opt/
- openfoam_hacks/aliases opt/
- openfoam_hacks/exec opt/
diff --git a/Ubuntu/16.04-OpenFOAM/singularity_image.tar b/Ubuntu/16.04-OpenFOAM/singularity_image.tar
deleted file mode 100644
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Bu0a3*
diff --git a/Ubuntu/16.04/Ubuntu-16.04-Bootstrap b/Ubuntu/16.04/Ubuntu-16.04-Bootstrap
deleted file mode 100644
index f35db22..0000000
--- a/Ubuntu/16.04/Ubuntu-16.04-Bootstrap
+++ /dev/null
@@ -1,57 +0,0 @@
-Bootstrap: docker
-From: ubuntu:latest
-
-%post
-apt -y update && apt -y upgrade
-apt -y install python curl wget gcc g++ make vim mc libncurses-dev rsync tclsh lua5.2 liblua5.2 gfortran ssh
-
-curl -s -O https://bootstrap.pypa.io/get-pip.py
-python get-pip.py
-pip install setuptools python-graph-core python-graph-dot tabulate numpy scipy pandas wheel --upgrade
-
-wget https://github.com/luarocks/luarocks/archive/v2.4.2.tar.gz
-tar xvf v2.4.2.tar.gz
-cd luarocks-2.4.2
-./configure
-make build
-make install
-mkdir ~/.luarocks
-echo "fs_use_modules = false" > ~/.luarocks/config.lua
-luarocks install luaposix
-luarocks install luafilesystem
-LUAROCKS_PREFIX=/usr/local
-export LUA_PATH="$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
-
-%environment
-source /opt/apps/lmod/7.7.7/init/profile
-clearMT
-export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
-export -f ml
-export -f module
-export -f clearMT
diff --git a/install/CENTOS7LATEST b/install/CENTOS7LATEST
index 29bd2a0..4e6a953 100644
--- a/install/CENTOS7LATEST
+++ b/install/CENTOS7LATEST
@@ -19,10 +19,10 @@ yum -y install libXdmcp libXfont2 libXxf86misc libxkbfile libXtst libX11-devel m
cd /tmp
# OpenMPI
-wget https://www.open-mpi.org/software/ompi/v2.1/downloads/openmpi-2.1.1.tar.gz
-tar xvf openmpi-2.1.1.tar.gz && cd openmpi-2.1.1
+wget https://www.open-mpi.org/software/ompi/v3.1/downloads/openmpi-3.1.5.tar.gz
+tar xvf openmpi-3.1.5.tar.gz && cd openmpi-3.1.5
./configure --prefix=/usr/local
-make -j 16
+make -j 36
make install
# pip
diff --git a/install/CONFIG b/install/CONFIG
index e8059ef..69fa6e8 100644
--- a/install/CONFIG
+++ b/install/CONFIG
@@ -1,10 +1,6 @@
-GPU_DRIVER_VERSION=390.30
-GPU_DRIVER_PATH=/apps/easybuild/sources/n/NVIDIA/NVIDIA-Linux-x86_64-390.30.run
-MPSS_PATH=/opt/mpss
-MIC_PATH=./rpm.tar.gz
-SINGULARITY_BIN_PATH=/apps/all/Singularity/3.4.1/bin
+SINGULARITY_BIN_PATH=/apps/all/Singularity/3.5.1/bin
IMAGE_PATH=/apps/all/OS
MODULEFILE_PATH=/apps/modules
USER_IMAGE=easybuild
EBROOTSQUASHFSMINTOOLS=/apps/all/squashfs-tools/4.3
-PATH=$PATH:/apps/all/Singularity/3.4.1/bin:/apps/all/squashfs-tools/4.3/bin
+PATH=$PATH:/apps/all/Singularity/3.5.1/bin:/apps/all/squashfs-tools/4.3/bin
diff --git a/install/UBUNTULATEST b/install/UBUNTULATEST
index 9d42e1d..2c12e90 100644
--- a/install/UBUNTULATEST
+++ b/install/UBUNTULATEST
@@ -36,10 +36,10 @@ cd Lmod-7.7.7
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
+wget https://www.open-mpi.org/software/ompi/v3.1/downloads/openmpi-3.1.5.tar.gz
+tar xvf openmpi-3.1.5.tar.gz && cd openmpi-3.1.5
./configure --prefix=/usr/local
-make -j 16
+make -j 36
make install
# APPS and SCRATCH
--
GitLab