Commits June 2016

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129 discussions

[svn:einsteintoolkit] www/about/releases/ (Rev. 1577)
by knarf＠cct.lsu.edu 15 Jun '16

15 Jun '16

User: knarf Date: 2016/06/15 04:26 AM Modified: /about/releases/ ET_2016_05_announcement.php Log: a more complete announcement File Changes: Directory: /about/releases/ =========================== File [modified]: ET_2016_05_announcement.php Delta lines: +30 -40 =================================================================== --- about/releases/ET_2016_05_announcement.php 2016-06-14 20:24:09 UTC (rev 1576) +++ about/releases/ET_2016_05_announcement.php 2016-06-15 09:26:07 UTC (rev 1577) @@ -15,12 +15,12 @@ simulating and analyzing general relativistic astrophysical systems that builds on numerous software efforts in the numerical relativity community including CactusEinstein, the Carpet AMR infrastructure and the relativistic -magneto-hydrodynamics code GRHydro. The Cactus Framework is used as the underlying -computational infrastructure providing large-scale parallelization, general -computational components, and a model for collaborative, portable code -development. The toolkit includes modules to build complete codes for -simulating black hole spacetimes as well as systems governed by relativistic -magneto-hydrodynamics.</p> +magneto-hydrodynamics code GRHydro. For parts of the toolkit, the Cactus +Framework is used as the underlying computational infrastructure providing +large-scale parallelization, general computational components, and a model for +collaborative, portable code development. The toolkit includes modules to build +complete codes for simulating black hole spacetimes as well as systems governed +by relativistic magneto-hydrodynamics.</p> <p>The Einstein Toolkit uses a distributed software model and its different modules are developed, distributed, and supported either by the core team of @@ -63,34 +63,28 @@ <li> Cactus Flesh <ul> - <li>While not a particular user-visible change, the Cactus version number was - bumped to 4.3.0, as a new version of Cactus was released at the same time - as this Einstein Toolkit release. - <li>Thorns can specify versions for capabilities they provide, and thorns - using them can depend on specific versions of those. - <li>pthread support got moved into a thorn (ExternalLibraries/pthreads) - </ul> + <li>Enable C++11 by default, and require it to be supported</li> + <li>Support bibtex in LaTeX thorn documentation</li> + <li>External libraries can specify additional paths (only) added as include + path for Fortran.</li> + <li>The 'checkout' target of 'make' has been removed, as it only supported + cvs, was unused and untested for a long time.</li> + </ul></li> + <li>IllinoisGRMHD/Convert_to_HydroBase: major update</li> + <li>SetMask_SphericalSurface: modify criterion for setting the mask to avoid problems with intermittant apparent horizon finder failures + <li>More examples in the Einstein Toolkit Gallery http://einsteintoolkit.org/about/gallery/</li> <li> - McLachlan + Simfactory <ul> - <li>re-write of the BSSN thorns: some parameter names changed. Backwards - compatible parameter names exist, but the old are deprecated now. Please - switch to the new, more consistent, parameter names. - </ul> - + <li>New configurations: acrcluster, centos, cori, minerva, sunnyvale</li> + <li>Updates to several machines (too many to list)</li> + </ul>stampede: fix core affinity settings + </li> <li> New thorns or tools <ul> - <li>IllinoisGRMHD (and connected thorns): a new GRMHD code within the Einstein - Toolkit. This isn't a drop-in replacement for GRHydro (as a lot of the - functionality, and parameters are different), but should be seen as - alternative. They are placed in the WVUThorns arrangement. - <li>CTThorns: Elliptic solver for Cactus/Carpet. This is a multi-grid solver, - and so far has mostly been used for cosmology-type simulations. - <li>AH2xdmf.py script (new utility within the AHFinderDirect thorn): - reads ASCII AHFinderDirect output files and combines data into hdf5 file - that can easily be visualized as time-series within tools like VisIt - <li>PITTNullCode/SphericalHarmonicReconGen: generic version of SphericalHarmonicRecon + <li>New thorn WatchDog: a thorn that terminates jobs that do not make progress + over a user-defined time frame, defined as time in between ANALYSIS steps.</li> </ul> </ul> @@ -112,28 +106,24 @@ <p>Supported (tested) machines include:</p> <ul> - <li> Default Debian, Ubuntu, Fedora and MacOS installations</li> + <li> Default Debian, Ubuntu, Fedora, CentOS, and MacOS installations</li> <li> Bethe</li> - <li> Bluewaters *</li> - <li> Carver</li> + <li> Bluewaters</li> <li> Comet</li> <li> Datura</li> - <li> Edison</li> - <li> Fermi</li> <li> Fionn</li> - <li> Galileo</li> <li> Gordon</li> + <li> GPC</li> <li> Gullimin</li> - <li> Hopper</li> + <li> MP2</li> <li> Nvidia</li> - <li> Philip</li> <li> Queenbee 2</li> <li> Shelob</li> <li> Supermike II</li> - <li> Stampede (CPU) *</li> + <li> Stampede (CPU)</li> + <li> Titan</li> <li> Zwicky</li> </ul> -<p>A * means that a small number of tests fail on that machine. Almost all tests pass on the other machines.</p> <ul> <li> Stampede: defs.local.ini needs to have sourcebasedir = $WORK and basedir = $SCRATCH/simulations configured for this machine. You need to determine $WORK and $SCRATCH by logging in to the machine.</li> </ul> @@ -142,7 +132,7 @@ marking this release. These release branches will be updated if severe errors are found.</p> -<p>The "Somerville" Release Team on behalf of the Einstein Toolkit Consortium (2016-06-15)</p> +<p>The "Brahe" Release Team on behalf of the Einstein Toolkit Consortium (2016-06-15)</p> <p>    Steven R. Brandt<br />

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[svn:einsteintoolkit] www/about/gallery/gw150914/ (Rev. 1576)
by barry.wardell＠gmail.com 14 Jun '16

14 Jun '16

User: barry.wardell Date: 2016/06/14 03:24 PM Modified: /about/gallery/gw150914/ index.php Log: gw150914: Fix URL for youtube embed File Changes: Directory: /about/gallery/gw150914/ =================================== File [modified]: index.php Delta lines: +1 -1 =================================================================== --- about/gallery/gw150914/index.php 2016-06-14 20:23:29 UTC (rev 1575) +++ about/gallery/gw150914/index.php 2016-06-14 20:24:09 UTC (rev 1576) @@ -102,7 +102,7 @@ <h4>Gravitational waves</h4> <a href="Strain.png"><img src="Strain_sm.png" srcset="Strain_sm_2x.png 2x" alt="h_+ at t=700M" width="400" height="300"/></a> -<iframe width="560" height="315" src="https://www.youtube.com/embed/videoseries?list=PLy_i7YBcuUSgp3GMUkmVqiWuP-j…" frameborder="0" allowfullscreen></iframe> +<iframe width="560" height="315" src="https://www.youtube.com/embed/videoseries?list=PLy_i7YBcuUSgp3GMUkmVqiWuP-j…" frameborder="0" allowfullscreen></iframe> <h4>Gravitational waveform</h4> <a href="waveform.png"><img src="waveform_sm.png" srcset="waveform.png 2x" alt="h_+^{2,2} at r=500M as a function of retarded time" width="542" height="188"/></a>

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[svn:einsteintoolkit] www/about/gallery/gw150914/ (Rev. 1575)
by barry.wardell＠gmail.com 14 Jun '16

14 Jun '16

User: barry.wardell Date: 2016/06/14 03:23 PM Modified: /about/gallery/gw150914/ index.php Log: gw150914: Only include a single youtube embed Use a playlist to show multiple movies in the same embed File Changes: Directory: /about/gallery/gw150914/ =================================== File [modified]: index.php Delta lines: +1 -2 =================================================================== --- about/gallery/gw150914/index.php 2016-06-14 16:17:00 UTC (rev 1574) +++ about/gallery/gw150914/index.php 2016-06-14 20:23:29 UTC (rev 1575) @@ -102,8 +102,7 @@ <h4>Gravitational waves</h4> <a href="Strain.png"><img src="Strain_sm.png" srcset="Strain_sm_2x.png 2x" alt="h_+ at t=700M" width="400" height="300"/></a> -<iframe width="560" height="315" src="https://www.youtube.com/embed/pabnzdDaf8A?rel=0" frameborder="0" allowfullscreen></iframe> -<iframe width="560" height="315" src="https://www.youtube.com/embed/GW7fQiG7caU?rel=0" frameborder="0" allowfullscreen></iframe> +<iframe width="560" height="315" src="https://www.youtube.com/embed/videoseries?list=PLy_i7YBcuUSgp3GMUkmVqiWuP-j…" frameborder="0" allowfullscreen></iframe> <h4>Gravitational waveform</h4> <a href="waveform.png"><img src="waveform_sm.png" srcset="waveform.png 2x" alt="h_+^{2,2} at r=500M as a function of retarded time" width="542" height="188"/></a>

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[svn:einsteintoolkit] www/about/releases/ (Rev. 1574)
by barry.wardell＠gmail.com 14 Jun '16

14 Jun '16

User: barry.wardell Date: 2016/06/14 11:17 AM Modified: /about/releases/ ET_2016_05_announcement.php Log: Add Fionn to the list of machines tested for the release File Changes: Directory: /about/releases/ =========================== File [modified]: ET_2016_05_announcement.php Delta lines: +1 -0 =================================================================== --- about/releases/ET_2016_05_announcement.php 2016-06-14 12:27:55 UTC (rev 1573) +++ about/releases/ET_2016_05_announcement.php 2016-06-14 16:17:00 UTC (rev 1574) @@ -120,6 +120,7 @@ <li> Datura</li> <li> Edison</li> <li> Fermi</li> + <li> Fionn</li> <li> Galileo</li> <li> Gordon</li> <li> Gullimin</li>

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[svn:einsteintoolkit] www/about/releases/ (Rev. 1573)
by knarf＠cct.lsu.edu 14 Jun '16

14 Jun '16

User: knarf Date: 2016/06/14 07:27 AM Added: /about/releases/ ET_2016_05_announcement.php Log: start working on release note File Changes: Directory: /about/releases/ =========================== File [added]: ET_2016_05_announcement.php Delta lines: +159 -0 =================================================================== --- about/releases/ET_2016_05_announcement.php (rev 0) +++ about/releases/ET_2016_05_announcement.php 2016-06-14 12:27:55 UTC (rev 1573) @@ -0,0 +1,159 @@ +<?php $title='Release Announcement'; +include_once($_SERVER['DOCUMENT_ROOT'].'/global/header.php');?> + +<p>We are pleased to announce the twelfth release (code name +"<a href="https://en.wikipedia.org/wiki/Tycho_Brahe">Brahe</a>") of the +Einstein Toolkit, an open, community developed software infrastructure for +relativistic astrophysics. This release includes, among other things, + +... + +In addition, bug fixes accumulated since the previous +release in November 2015 have been included.</p> + +<p>The Einstein Toolkit is a collection of software components and tools for +simulating and analyzing general relativistic astrophysical systems that builds +on numerous software efforts in the numerical relativity community including +CactusEinstein, the Carpet AMR infrastructure and the relativistic +magneto-hydrodynamics code GRHydro. The Cactus Framework is used as the underlying +computational infrastructure providing large-scale parallelization, general +computational components, and a model for collaborative, portable code +development. The toolkit includes modules to build complete codes for +simulating black hole spacetimes as well as systems governed by relativistic +magneto-hydrodynamics.</p> + +<p>The Einstein Toolkit uses a distributed software model and its different +modules are developed, distributed, and supported either by the core team of +Einstein Toolkit Maintainers, or by individual groups. Where modules are +provided by external groups, the Einstein Toolkit Maintainers provide quality +control for modules for inclusion in the toolkit and help coordinate support. +The Einstein Toolkit Maintainers currently involve postdocs and faculty from +six different institutions, and host weekly meetings that are open for anyone +to join in.</p> + +<p>Guiding principles for the design and implementation of the toolkit include: +open, community-driven software development; well thought out and stable +interfaces; separation of physics software from computational science +infrastructure; provision of complete working production code; training and +education for a new generation of researchers.</p> + +<p>For more information about using or contributing to the Einstein Toolkit, or to +join the Einstein Toolkit Consortium, please visit our web pages at +<<a href="http://einsteintoolkit.org">http://einsteintoolkit.org</a>>.</p> + +<p>The Einstein Toolkit is primarily supported by NSF +1212401/1212426/1212433/1212460 (Einstein Toolkit), and also by 0905046/0941653 +(PetaCactus) and 0710874 (LONI Grid).</p> + +<p>The Einstein Toolkit contains about 200 regression test cases. On a large +portion of the tested machines, almost all of these test suites pass, using both +MPI and OpenMP parallelization.</p> + +<h4>The changes between this and the previous release include:</h4> + +<ul><li><b>Larger changes since last release</b></li></ul> + +<ul> + <li> + Almost all repositories moved from the Einstein Toolkit subversion server + to bitbucket, with the ExternalLibraries being the only exception. Taking + this move as opportunity, some already existing thorns were moved to more + appropriate arrangements.</li> + + <li> + Cactus Flesh + <ul> + <li>While not a particular user-visible change, the Cactus version number was + bumped to 4.3.0, as a new version of Cactus was released at the same time + as this Einstein Toolkit release. + <li>Thorns can specify versions for capabilities they provide, and thorns + using them can depend on specific versions of those. + <li>pthread support got moved into a thorn (ExternalLibraries/pthreads) + </ul> + <li> + McLachlan + <ul> + <li>re-write of the BSSN thorns: some parameter names changed. Backwards + compatible parameter names exist, but the old are deprecated now. Please + switch to the new, more consistent, parameter names. + </ul> + + <li> + New thorns or tools + <ul> + <li>IllinoisGRMHD (and connected thorns): a new GRMHD code within the Einstein + Toolkit. This isn't a drop-in replacement for GRHydro (as a lot of the + functionality, and parameters are different), but should be seen as + alternative. They are placed in the WVUThorns arrangement. + <li>CTThorns: Elliptic solver for Cactus/Carpet. This is a multi-grid solver, + and so far has mostly been used for cosmology-type simulations. + <li>AH2xdmf.py script (new utility within the AHFinderDirect thorn): + reads ASCII AHFinderDirect output files and combines data into hdf5 file + that can easily be visualized as time-series within tools like VisIt + <li>PITTNullCode/SphericalHarmonicReconGen: generic version of SphericalHarmonicRecon + </ul> +</ul> + +<ul><li><b>How to upgrade from Somerville (ET_2015_11)</b></li></ul> + +<p>To upgrade from the previous release, use GetComponents with the new thornlist to check out the new version. Switching to the new branch is not possible for most repositories due to repository moves.</p> + +<p>See the <a href="http://einsteintoolkit.org/download/">Download</a> page on the Einstein Toolkit website for download instructions.</p> + +<ul><li><b>Remaining issues with this release</b></li></ul> + +<ul> + <li> Certain machines need to be configured specially in Simfactory because the remote directories cannot be determined automatically just from the user name. See the Machine notes below.</li> + <li> Recovering with Carpet: Carpet stores metadata (such as the simulation time) only for Carpet::max_timelevels time levels, although it is possible to allocate more time levels. These additional time levels then cannot be recovered; the symptom is an assertion failure during recovery. The solution is to either increase Carpet::max_timelevels, or to decrease the number of active time levels.</li> +</ul> + +<ul><li><b>Machine notes</b></li></ul> + +<p>Supported (tested) machines include:</p> + +<ul> + <li> Default Debian, Ubuntu, Fedora and MacOS installations</li> + <li> Bethe</li> + <li> Bluewaters *</li> + <li> Carver</li> + <li> Comet</li> + <li> Datura</li> + <li> Edison</li> + <li> Fermi</li> + <li> Galileo</li> + <li> Gordon</li> + <li> Gullimin</li> + <li> Hopper</li> + <li> Nvidia</li> + <li> Philip</li> + <li> Queenbee 2</li> + <li> Shelob</li> + <li> Supermike II</li> + <li> Stampede (CPU) *</li> + <li> Zwicky</li> +</ul> +<p>A * means that a small number of tests fail on that machine. Almost all tests pass on the other machines.</p> +<ul> + <li> Stampede: defs.local.ini needs to have sourcebasedir = $WORK and basedir = $SCRATCH/simulations configured for this machine. You need to determine $WORK and $SCRATCH by logging in to the machine.</li> +</ul> + +<p>All repositories participating in this release carry a branch ET_2016_05 +marking this release. These release branches will be updated if severe +errors are found.</p> + +<p>The "Somerville" Release Team on behalf of the Einstein Toolkit Consortium (2016-06-15)</p> + +<p> +   Steven R. Brandt<br /> +   Peter Diener<br /> +   Roland Haas<br /> +   Ian Hinder<br /> +   Frank LÃ¶ffler<br /> +   Bruno C. Mundim<br /> +   Erik Schnetter<br /> +   Barry Wardell<br /> +</p> + +<p>June 15, 2016</p> + +<?php include_once($_SERVER['DOCUMENT_ROOT'].'/global/footer.php');?>

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[svn:einsteintoolkit] tools/trunk/VirtualBox/ (Rev. 38)
by knarf＠cct.lsu.edu 14 Jun '16

14 Jun '16

User: knarf Date: 2016/06/14 06:54 AM Modified: /trunk/VirtualBox/ install_ET_2016_05 Log: son't use deleted without.run, but debian.sh as run script File Changes: Directory: /trunk/VirtualBox/ ============================= File [modified]: install_ET_2016_05 Delta lines: +1 -1 =================================================================== --- trunk/VirtualBox/install_ET_2016_05 2016-06-14 11:46:57 UTC (rev 37) +++ trunk/VirtualBox/install_ET_2016_05 2016-06-14 11:54:47 UTC (rev 38) @@ -16,7 +16,7 @@ fake_cores_per_core=`cat /proc/cpuinfo | grep "physical id" | sort | uniq | wc -l` cores=$((($logic_cores-$fake_cores_per_core)/$fake_cores_per_core+1)) -./simfactory/bin/sim setup-silent --optionlist=debian.cfg --ppn=$cores --submitscript=debian.sub --runscript=without.run +./simfactory/bin/sim setup-silent --optionlist=debian.cfg --ppn=$cores --submitscript=debian.sub --runscript=debian.sh mkdir -p ~/simulations set +e time ./simfactory/bin/sim build --thornlist ./thornlists/einsteintoolkit.th 2>&1 | tee ET_build.log

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[svn:einsteintoolkit] tools/ (Rev. 37)
by knarf＠cct.lsu.edu 14 Jun '16

14 Jun '16

User: knarf Date: 2016/06/14 06:46 AM Added: /trunk/VirtualBox/ install_ET_2016_05 Modified: /trunk/VirtualBox/ install_ET_2015_05 Log: fix URL, and add ET_2016_05 file Directory Changes: Directory: /svn:executable/ =========================== + * File Changes: Directory: /trunk/VirtualBox/ ============================= File [modified]: install_ET_2015_05 Delta lines: +1 -1 =================================================================== --- trunk/VirtualBox/install_ET_2015_05 2016-06-14 09:33:07 UTC (rev 36) +++ trunk/VirtualBox/install_ET_2015_05 2016-06-14 11:46:57 UTC (rev 37) @@ -8,7 +8,7 @@ RELEASE=ET_2015_05 wget --no-check-certificate https://github.com/gridaphobe/CRL/raw/$RELEASE/GetComponents chmod +x GetComponents -./GetComponents -p -a +./GetComponents -p -a https://bitbucket.org/einsteintoolkit/manifest/raw/$RELEASE/einsteintoolkit… cd Cactus # figure out how many cores we have File [added]: install_ET_2016_05 Delta lines: +27 -0 =================================================================== --- trunk/VirtualBox/install_ET_2016_05 (rev 0) +++ trunk/VirtualBox/install_ET_2016_05 2016-06-14 11:46:57 UTC (rev 37) @@ -0,0 +1,27 @@ +#!/bin/bash +set -e + +# necessary for mpich, but not openmpi +#perl -le 'printf "MPD_SECRETWORD=";print map { ("a".."z","A".."Z")[rand 52] } 1..40' > $HOME/.mpd.conf +#chmod 600 $HOME/.mpd.conf + +RELEASE=ET_2016_05 +wget --no-check-certificate https://github.com/gridaphobe/CRL/raw/$RELEASE/GetComponents +chmod +x GetComponents +./GetComponents -p -a https://bitbucket.org/einsteintoolkit/manifest/raw/$RELEASE/einsteintoolkit… +cd Cactus + +# figure out how many cores we have +logic_cores=`cat /proc/cpuinfo | grep "model name" | wc -l` +fake_cores_per_core=`cat /proc/cpuinfo | grep "physical id" | sort | uniq | wc -l` +cores=$((($logic_cores-$fake_cores_per_core)/$fake_cores_per_core+1)) + +./simfactory/bin/sim setup-silent --optionlist=debian.cfg --ppn=$cores --submitscript=debian.sub --runscript=without.run +mkdir -p ~/simulations +set +e +time ./simfactory/bin/sim build --thornlist ./thornlists/einsteintoolkit.th 2>&1 | tee ET_build.log +set -e +make sim +./simfactory/bin/sim create-run tests_1 --testsuite --procs 1 +./simfactory/bin/sim create-run tests_2 --testsuite --procs 2 + Property changes on: trunk/VirtualBox/install_ET_2016_05 ___________________________________________________________________

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[svn:einsteintoolkit] tools/trunk/VirtualBox/ (Rev. 36)
by knarf＠cct.lsu.edu 14 Jun '16

14 Jun '16

User: knarf Date: 2016/06/14 04:33 AM Modified: /trunk/VirtualBox/ create_ET Log: update debian disc image URL File Changes: Directory: /trunk/VirtualBox/ ============================= File [modified]: create_ET Delta lines: +1 -1 =================================================================== --- trunk/VirtualBox/create_ET 2015-11-09 17:18:12 UTC (rev 35) +++ trunk/VirtualBox/create_ET 2016-06-14 09:33:07 UTC (rev 36) @@ -10,7 +10,7 @@ #URL=http://cdimage.debian.org/mirror/cdimage/archive/7.8.0/amd64/iso-cd/debian-7.8.0-amd64-netinst.iso DIST=jessie -URL=http://cdimage.debian.org/debian-cd/8.2.0/amd64/iso-cd/debian-8.2.0-amd64-netinst.iso +URL=http://cdimage.debian.org/debian-cd/8.5.0/amd64/iso-cd/debian-8.5.0-amd64-netinst.iso #DIST=trusty #URL=http://archive.ubuntu.com/ubuntu/dists/trusty-updates/main/installer-amd64/current/images/netboot/mini.iso

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[ianhinder/Kranc]
by knarrff 14 Jun '16

14 Jun '16

Branch: refs/tags/ET_2016_05_v0 Home: https://github.com/ianhinder/Kranc

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[barrywardell/EinsteinExact]
by knarrff 14 Jun '16

14 Jun '16

Branch: refs/tags/ET_2016_05_v0 Home: https://github.com/barrywardell/EinsteinExact

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