Commits July 2017

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commit/EinsteinAnalysis: eschnett: QuasiLocalModes: Simplify VTK output routine to speed up build times
by Bitbucket 17 Jul '17

17 Jul '17

1 new commit in EinsteinAnalysis: https://bitbucket.org/einsteintoolkit/einsteinanalysis/commits/56a98ded290e/ Changeset: 56a98ded290e Branch: master User: eschnett Date: 2017-07-17 17:45:56+00:00 Summary: QuasiLocalModes: Simplify VTK output routine to speed up build times Affected #: 2 files Repository URL: https://bitbucket.org/einsteintoolkit/einsteinanalysis/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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[svn:einsteintoolkit] tools/trunk/VirtualBox/ (Rev. 41)
by rhaas＠tapir.caltech.edu 15 Jul '17

15 Jul '17

User: rhaas Date: 2017/07/15 12:33 PM Removed: /trunk/VirtualBox/ late_command.sh /trunk/VirtualBox/data/ Modified: /trunk/VirtualBox/ create_ET, postseed, preseed.cfg Log: revert r39 File Changes: Directory: /trunk/VirtualBox/ ============================= File [modified]: create_ET Delta lines: +10 -29 =================================================================== --- trunk/VirtualBox/create_ET 2017-07-15 17:28:02 UTC (rev 40) +++ trunk/VirtualBox/create_ET 2017-07-15 17:33:10 UTC (rev 41) @@ -9,12 +9,9 @@ #DIST=wheezy #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/8.7.1/i386/iso-cd/debian-8.7.1-i386-netinst.iso +DIST=jessie +URL=http://cdimage.debian.org/debian-cd/8.5.0/amd64/iso-cd/debian-8.5.0-amd64-netinst.iso -DIST=stretch -URL=https://cdimage.debian.org/debian-cd/current/i386/iso-cd/debian-9.0.0-i386-netinst.iso - #DIST=trusty #URL=http://archive.ubuntu.com/ubuntu/dists/trusty-updates/main/installer-amd64/current/images/netboot/mini.iso @@ -29,14 +26,11 @@ ISOLINUX=isolinux/ fi cd $CD_DST - -# debian stretch defaults to a gfx based install perl -pi -e 's/initrd\.gz/initrd\.gz auto-install\/enable=true debconf\/priority=critical preseed\/file=\/cdrom\/preseed.cfg/' ${ISOLINUX}txt.cfg -perl -pi -e 's/initrd\.gz/initrd\.gz auto-install\/enable=true debconf\/priority=critical preseed\/file=\/cdrom\/preseed.cfg/' ${ISOLINUX}gtk.cfg perl -pi -e 's/timeout 0/timeout 1/' ${ISOLINUX}isolinux.cfg -cp ../preseed.cfg ../late_command.sh ../postseed . - -cp ../data/*.tar ./ +cp ../preseed.cfg ../postseed . +mkdir et_misc +cp ../install_$RELEASE et_misc/ md5sum `find ! -name "md5sum.txt" ! -path "./isolinux/*" -follow -type f` > md5sum.txt # Ubuntu's mini.iso does not mount the iso image itself during installation, so we have to @@ -58,14 +52,13 @@ VMNAME=${DIST}_$RELEASE -VBoxManage unregistervm $VMNAME --delete || true VBoxManage createvm --name $VMNAME --register # standard settings -VBoxManage modifyvm $VMNAME --ostype Debian --acpi on --biosbootmenu disabled --rtcuseutc on +VBoxManage modifyvm $VMNAME --ostype Debian_64 --acpi on --biosbootmenu disabled --rtcuseutc on ### minimal system -VBoxManage modifyvm $VMNAME --memory 1024 --cpus 1 --vram 32 +VBoxManage modifyvm $VMNAME --memory 1024 --cpus 1 ### workstation class #VBoxManage modifyvm $VMNAME --memory 4096 --cpus 8 --ioapic on --vram 64 --usb on @@ -74,22 +67,10 @@ VBoxManage storagectl $VMNAME --name "IDE Controller" --add ide --controller PIIX4 VBoxManage storagectl $VMNAME --name "SATA Controller" --add sata --controller IntelAhci VBoxManage storageattach $VMNAME --storagectl "IDE Controller" --port 0 --device 0 --type dvddrive --medium `pwd`/$VMNAME.iso -# we limit the partition to 8GB initially and offer the user the option to -# increase it to the full size VBoxManage createhd --filename $VMNAME.vdi --size 32768 -VBoxManage storageattach $VMNAME --storagectl "SATA Controller" --port 0 --device 0 --type hdd --medium $VMNAME.vdi --discard on -VBoxManage modifyvm $VMNAME --nic1 nat --nictype1 virtio --cableconnected1 on -VBoxManage modifyvm $VMNAME --natpf1 "ssh,tcp,127.0.0.1,2222,,22" -# this does likely not work since it is a privileged port and Windows cannot connect to any other -VBoxManage modifyvm $VMNAME --natpf2 "smb,tcp,127.0.0.1,415,,415" -# use for SMB share inside of VM -# cannot be used since ti aborts unless the users does something else first -# VBoxManage modifyvm $VMNAME --nic2 hostonly --nictype2 virtio --cableconnected2 on --hostonlyadapter2 vboxnet0 +VBoxManage storageattach $VMNAME --storagectl "SATA Controller" --port 0 --device 0 --type hdd --medium $VMNAME.vdi +VBoxManage modifyvm $VMNAME --nic1 nat --nictype1 82540EM +VBoxManage modifyvm $VMNAME --natpf1 "ssh,tcp,,2222,,22" VBoxManage modifyvm $VMNAME --audio alsa -VBoxManage modifyvm $VMNAME --clipboard bidirectional VBoxManage modifyvm $VMNAME --boot1 disk --boot2 dvd --boot3 net --boot4 none VBoxManage startvm $VMNAME - -VBoxManage modifyhd --compact $VMNAME.vdi -rm -f $VMNAME.ova -VBoxManage export $VMNAME --output $VMNAME.ova File [removed]: late_command.sh Delta lines: +0 -32 =================================================================== --- trunk/VirtualBox/late_command.sh 2017-07-15 17:28:02 UTC (rev 40) +++ trunk/VirtualBox/late_command.sh 2017-07-15 17:33:10 UTC (rev 41) @@ -1,32 +0,0 @@ -#!/bin/sh - -# finish setup inside of started system -cp /cdrom/postseed /target/etc/init.d/ -chroot /target update-rc.d postseed defaults - -# installing packages from backports is tricky since its deps are not -# automatically pulled from backports when one uses preseed -#chroot /target apt-get install -y -t jessie-backports jupyter-notebook python-notebook - -# enable file sharing to windows clients, disable passwords -sed -i '/^\[homes\]/{:loop;n;/^ *read only *=/s/yes/no/;s/^ *valid users/ public = yes\n;&/;/^\[/!b loop}' /target/etc/samba/smb.conf -# prepare for host-only network -echo -e 'auto eth1\niface eth1 inet dhcp' >>/target/etc/network/interfaces - -# prepare to make enlarging the partition possible -# we need to remove the dummy partition we created to make partman happy -umount /dev/sda2 ; sed -i '/delme/d' /target/etc/fstab ; rmdir /target/home/et/delme -sfdisk /dev/sda --dump | awk '/sda1/{start=$4;size=$6} /sda2/{$1="/dev/sda1";$4=start;$6=($6+size)",";print} {next}' | sfdisk --force /dev/sda - -# don't ask for passwd for et user to become root -sed -i '/^%sudo/s!ALL$!NOPASSWD: ALL!' /target/etc/sudoers - -# Boot into et user desktop (and stay there) -sed -i 's!NODM_ENABLED=false!NODM_ENABLED=true!;s!NODM_USER=root!NODM_USER=et!' /target/etc/default/nodm - -# set up user $HOME directory -for i in /cdrom/*.tar ; do - tar -xf $i -C /target/home/et/ -done - -chroot /target chown -R et:et /home/et File [modified]: postseed Delta lines: +6 -48 =================================================================== --- trunk/VirtualBox/postseed 2017-07-15 17:28:02 UTC (rev 40) +++ trunk/VirtualBox/postseed 2017-07-15 17:33:10 UTC (rev 41) @@ -9,52 +9,10 @@ # Default-Stop: ### END INIT INFO -# purge packages only needed to compile virtualbox module -apt-get install -y linux-headers-686-pae virtualbox-guest-dkms/sid virtualbox-guest-utils/sid virtualbox-guest-x11/sid -apt-get remove -y --purge linux-headers-686-pae -apt-get autoremove -y --purge -apt-get autoclean -apt-get clean - +chown -R et /home/et/misc +chgrp -R et /home/et/misc +chmod -R +w /home/et/misc +# give the system time to get network up +sleep 5 +sudo -i -u et /home/et/misc/install_ET_* 2>&1 | tee /var/log/ET_install update-rc.d postseed remove - -# install ET 2016_11, do this after isntallation finishes so that eg network is -# correct -sudo -u et bash <<"EOF" -cd /home/et - -RELEASE=master -wget --no-check-certificate https://github.com/gridaphobe/CRL/raw/$RELEASE/GetComponents -chmod +x GetComponents -./GetComponents -p -a --shallow https://bitbucket.org/einsteintoolkit/manifest/raw/$RELEASE/einsteintoolkit… -cd Cactus - -# reduce build time and redce file sizes by leaving out big thorns and making -# sure that system libraries are used -sed 's!^CactusUtils/Formaline!!#DISABLED &!' manifest/einsteintoolkit.th >thornlists/et.th -cp simfactory/mdb/optionlists/debian.cfg simfactory/mdb/optionlists/et.cfg -echo "PAPI_DIR=NO_BUILD" >>simfactory/mdb/optionlists/et.cfg - -# figure out how many cores we have -logic_cores=`cat /proc/cpuinfo | grep "model name" | wc -l` -fake_cores_per_core=`cat /proc/cpuinfo | grep "physical id" | sort | uniq | wc -l` -cores=$((($logic_cores-$fake_cores_per_core)/$fake_cores_per_core+1)) - -./simfactory/bin/sim setup-silent --optionlist=et.cfg --ppn=$cores --submitscript=debian.sub --runscript=debian.sh -mkdir -p ~/simulations -set +e -( time ./simfactory/bin/sim build --mdbkey make "make -j $cores" --thornlist ./thornlists/et.th ) >ET_build.log 2>&1 -set -e -find configs/sim $ -name \*.a -or -name \*.d $ -delete -rm -rf exe/sim exe/cactus_sim configs/sim/piraha - -cd /home/et -cp -r --reflink=always Cactus Cactus.original -EOF - -# wipe unused blocks to zero -dd if=/dev/zero bs=1M of=/zero -sync ; sync ; sync -rm /zero - -shutdown -h now File [modified]: preseed.cfg Delta lines: +5 -28 =================================================================== --- trunk/VirtualBox/preseed.cfg 2017-07-15 17:28:02 UTC (rev 40) +++ trunk/VirtualBox/preseed.cfg 2017-07-15 17:33:10 UTC (rev 41) @@ -11,36 +11,23 @@ d-i mirror/http/hostname string httpredir.debian.org d-i mirror/http/directory string /debian d-i mirror/http/proxy string -d-i apt-setup/contrib boolean true -d-i apt-setup/local0/repository string http://ftp.debian.org/debian sid contrib d-i passwd/root-password password et d-i passwd/root-password-again password et d-i passwd/user-fullname string Einstein Toolkit User d-i passwd/username string et d-i passwd/user-password password et d-i passwd/user-password-again password et -d-i passwd/user-default-groups string sudo d-i user-setup/allow-password-weak boolean true d-i clock-setup/utc boolean true d-i time/zone string US/Central #d-i partman-auto/init_automatically_partition select biggest_free -# this creates a partition 8GB in size -# we need to put in a dummy paritition at the end to stop debian from gobbling -# up the remaing space. This is a bug since 2010 ! -# (https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=297201) d-i partman-auto/expert_recipe string \ root :: \ - 8000 8000 8000 ext3 \ + 5000 1000000000 1000000000 ext3 \ $primary{ } $bootable{ } \ method{ format } format{ } \ - use_filesystem{ } filesystem{ btrfs } \ - mountpoint{ / } \ - . \ - 0 80000 1000000 ext3 \ - $primary{ } \ - method{ format } format{ } \ use_filesystem{ } filesystem{ ext3 } \ - mountpoint{ /home/et/delme } \ + mountpoint{ / } \ . d-i partman-basicfilesystems/no_swap boolean false d-i partman-auto/method string regular @@ -52,20 +39,10 @@ d-i grub-installer/only_debian boolean true d-i grub-installer/bootdev string /dev/sda d-i finish-install/reboot_in_progress note -# Configure APT to not install recommended packages by default. Use of this -# option can result in an incomplete system and should only be used by very -# experienced users. -d-i base-installer/install-recommends boolean false tasksel tasksel/first multiselect d-i pkgsel/upgrade select full-upgrade #d-i debian-installer/exit/halt boolean true #d-i debian-installer/exit/poweroff boolean true -popularity-contest popularity-contest/participate boolean false -d-i preseed/late_command string sh /cdrom/late_command.sh -d-i pkgsel/include string sudo curl perl python subversion git gfortran g++ libfftw3-dev libgsl0-dev libatlas-base-dev libjpeg-dev libssl-dev libhdf5-serial-dev hdf5-tools libopenmpi-dev libpapi-dev openmpi-bin make pkg-config \ - openssh-server openssh-client rsync samba psmisc policykit-1 \ - qupzilla thunar tango-icon-theme thunar-volman xorg nodm xfwm4 xfdesktop4 xfce4-panel xfce4-terminal xfce4-session mousepad vim-gtk emacs24 less \ - atril ffmpeg vlc eom \ - jupyter-notebook python-jupyter-client python3-jupyter-client \ - python3-matplotlib python3-tk python3-numpy python3-h5py python3-scipy \ - python-matplotlib python-tk python-numpy python-h5py python-scipy +pularity-contest popularity-contest/participate boolean false +d-i preseed/late_command string cp /cdrom/postseed /target/etc/init.d/; chroot /target update-rc.d postseed defaults; cp -r /cdrom/et_misc /target/home/et/misc +d-i pkgsel/include string sudo perl python subversion git gfortran g++ libfftw3-dev libgsl0-dev libatlas-base-dev libjpeg-dev libssl-dev libhdf5-serial-dev hdf5-tools libopenmpi-dev openmpi-bin make

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[svn:einsteintoolkit] tools/branches/ (Rev. 40)
by rhaas＠tapir.caltech.edu 15 Jul '17

15 Jul '17

User: rhaas Date: 2017/07/15 12:28 PM Added: /branches/ /branches/etk_ncsa_2017/ Log: create branch for 2017 ET workshop at NCSA

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[svn:einsteintoolkit] tools/trunk/VirtualBox/ (Rev. 39)
by rhaas＠tapir.caltech.edu 15 Jul '17

15 Jul '17

User: rhaas Date: 2017/07/15 12:19 PM Added: /trunk/VirtualBox/ late_command.sh /trunk/VirtualBox/data/ ET_background.jpg, ET_background.xcf, MountSharedFolder.sh, et.tar Modified: /trunk/VirtualBox/ create_ET, postseed, preseed.cfg Log: scripts and data to create virtualbox appliance for etk2017 File Changes: Directory: /trunk/VirtualBox/ ============================= File [modified]: create_ET Delta lines: <Unavailable> File [added]: late_command.sh Delta lines: <Unavailable> File [modified]: postseed Delta lines: <Unavailable> File [modified]: preseed.cfg Delta lines: <Unavailable> Directory: /trunk/VirtualBox/data/ ================================== File [added]: ET_background.jpg Delta lines: <Unavailable> File [added]: ET_background.xcf Delta lines: <Unavailable> File [added]: MountSharedFolder.sh Delta lines: <Unavailable> File [added]: et.tar Delta lines: <Unavailable>

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[ianhinder/Kranc] 14a543: Schedule so that GPU is assigned *before* thorn's ...
by David M. Koppelman 14 Jul '17

14 Jul '17

Branch: refs/heads/dmk-chemora Home: https://github.com/ianhinder/Kranc Commit: 14a54305a97572f3c05e0fa2494ac0bd0ae602d4 https://github.com/ianhinder/Kranc/commit/14a54305a97572f3c05e0fa2494ac0bd0… Author: David M. Koppelman <koppel(a)ece.lsu.edu> Date: 2017-07-14 (Fri, 14 Jul 2017) Changed paths: M Tools/CodeGen/CaKernel.m Log Message: ----------- Schedule so that GPU is assigned *before* thorn's storage is allocated. CaKernelSchedule: Schedule after CaCUDA_Startup rather than after Accelerator_SetDevice.

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commit/manifest: knarrff: use release tags in thornlist
by Bitbucket 13 Jul '17

13 Jul '17

1 new commit in manifest: https://bitbucket.org/einsteintoolkit/manifest/commits/b0910d48a840/ Changeset: b0910d48a840 Branch: ET_2017_06 User: knarrff Date: 2017-07-13 23:16:06+00:00 Summary: use release tags in thornlist Affected #: 1 file Repository URL: https://bitbucket.org/einsteintoolkit/manifest/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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[ianhinder/Kranc]
by knarrff 13 Jul '17

13 Jul '17

Branch: refs/tags/ET_2017_06_v0 Home: https://github.com/ianhinder/Kranc

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[barrywardell/EinsteinExact]
by knarrff 13 Jul '17

13 Jul '17

Branch: refs/tags/ET_2017_06_v0 Home: https://github.com/barrywardell/EinsteinExact

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[ianhinder/Kranc]
by knarrff 13 Jul '17

13 Jul '17

Branch: refs/heads/ET_2017_06 Home: https://github.com/ianhinder/Kranc

1 0

[barrywardell/EinsteinExact]
by knarrff 13 Jul '17

13 Jul '17

Branch: refs/heads/ET_2017_06 Home: https://github.com/barrywardell/EinsteinExact

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Commits July 2017