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Singularity36 #2

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Nov 23, 2020
Merged

Singularity36 #2

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f9e7cb2
update to singularity 3.6
MontrealSergiy Nov 10, 2020
f6f2ad5
saner size
MontrealSergiy Nov 23, 2020
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6 changes: 3 additions & 3 deletions Vagrantfile
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
# backwards compatibility). Please don't change it unless you know what
# you're doing.
Vagrant.configure(2) do |config|
config.vm.box = "ubuntu/xenial64"
config.vm.box = "sylabs/singularity-3.6-ubuntu-bionic64"

config.vm.network "forwarded_port", guest: 3000, host: 3000
# config.vm.network "public_network"
Expand All @@ -25,7 +25,7 @@ Vagrant.configure(2) do |config|
exec "vagrant " + ARGV.join(' ')
end

config.disksize.size="10GB"
config.disksize.size="10MB"

config.vm.provider "virtualbox" do |vb|
vb.memory = "8129"
Expand Down Expand Up @@ -53,6 +53,6 @@ Vagrant.configure(2) do |config|
cd ~/cbrain/BrainPortal
echo "Please login in to the portal for the first time as user 'admin'"
cat /tmp/cbinit.txt
# rails server thin -e development -p 3000 > ~/cbrain.log &
# rails server puma -e development -p 3000 -b 0.0.0.0> ~/cbrain.log &
SHELL
end
18 changes: 3 additions & 15 deletions provision/setup.sh
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Expand Up @@ -27,7 +27,7 @@ echo "-----------------------------------------------" >> $logFile

cd $HOME

apt-get install libsodium-dev gnupg2 -y
sudo apt-get install curl libsodium-dev gnupg2 -y
gpg --keyserver hkp://pool.sks-keyservers.net --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3 7D2BAF1CF37B13E2069D6956105BD0E739499BDB
# \curl -sSL https://rvm.io/pkuczynski.asc | gpg --import - >> $logFile
\curl -sSL https://get.rvm.io | bash -s stable >> $logFile
Expand Down Expand Up @@ -114,27 +114,15 @@ dockerLog=/tmp/docker-install.log
sudo apt-get install docker.io -y > $dockerLog
sudo usermod -a -G docker ubuntu >> $dockerLog

## install singularity
singLog=/tmp/singularity.log

mkdir $HOME/singTemp; cd $HOME/singTemp
sudo apt-get install python dh-autoreconf build-essential -y > $singLog
wget https://github.com/singularityware/singularity/releases/download/2.4.1/singularity-2.4.1.tar.gz >> $singLog
tar -xvzf singularity-2.4.1.tar.gz >> $singLog
cd singularity-2.4.1
./configure --prefix=/usr/local --sysconfdir=/etc >> $singLog
make >> $singLog
sudo make install >> $singLog

cd $HOME
rm -rf $HOME/singTemp


#### Set up the BrainPortal Cache and timezone
cd $HOME/cbrain/BrainPortal

echo $HOME | xargs -I {} echo 'p=RemoteResource.first; p.dp_cache_dir="{}/BPCache"; p.save' | rails c >> $logFile
timezone=`timedatectl status | grep 'Time zone' | awk '{print $3}'`
echo $timezone | xargs -I {} echo 'p=User.first; p.time_zone = "{}"; p.save' | rails c >> $logFile
echo $timezne | xargs -I {} echo 'p=User.first; p.time_zone = "{}"; p.save' | rails c >> $logFile

### Setup local DataProvider

Expand Down