[CCPPETMR/CCPPETMR_VM] update to Ubuntu 18.04 (#104)

[Kris Thielemans]

---

You can view, comment on, or merge this pull request online at:

  https://github.com/CCPPETMR/CCPPETMR_VM/pull/104

Commit Summary

• additional packages for ubuntu18.04
• add path to local user binary directory
• Added vagrantfile for 18.04
• use ubuntu18.04 branch of SIRF-SuperBuild
• remove install of gcc 6

File Changes

• M scripts/INSTALL_prerequisites_with_apt-get.sh (7)
• M scripts/UPDATE.sh (1)
• M vagrant/Vagrantfile (29)

Patch Links:

• https://github.com/CCPPETMR/CCPPETMR_VM/pull/104.patch
• https://github.com/CCPPETMR/CCPPETMR_VM/pull/104.diff

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[Kris Thielemans]

@KrisThielemans pushed 2 commits.

• 2466063 Merge branch 'master' into ubuntu18.04
• 4896b68 remove checkout of ubuntu18.04 SIF-SuperBuild tag

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[Kris Thielemans]

@KrisThielemans pushed 1 commit.

• d2de514 Fix and improve pip-install of python packages

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[Kris Thielemans]

@KrisThielemans pushed 1 commit.

• c3dc47e Use system boost

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[Edoardo Pasca]

Vagrant suggests to use bento boxes as base boxes for different linux flavours.

We could/should change to bento/ubuntu-18.04.

[Edoardo Pasca]

I'm trying to vagrant up but it's failing like

A customization command failed:

["storageattach", :id, "--storagectl", "IDE", "--port", "1", "--device", "0", "--type", "dvddrive", "--medium", "emptydrive"]

The following error was experienced:

#<Vagrant::Errors::VBoxManageError: There was an error while executing `VBoxManage`, a CLI used by Vagrant
for controlling VirtualBox. The command and stderr is shown below.

Command: ["storageattach", "d7c7b264-e7bd-48e5-a8e2-f991b116557b", "--storagectl", "IDE", "--port", "1", "--device", "0", "--type", "dvddrive", "--medium", "emptydrive"]

Stderr: VBoxManage.exe: error: Could not find a controller named 'IDE'
>

Please fix this customization and try again.

[Edoardo Pasca]

@paskino pushed 4 commits.

• e4f971c updates
• 683df4f Merge branch 'ubuntu18.04' of https://github.com/CCPPETMR/CCPPETMR_VM into ubuntu18.04
• 133cb34 use bento box
• dcb103e Merge branch 'ubuntu18.04' of https://github.com/CCPPETMR/CCPPETMR_VM into ubuntu18.04

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[Edoardo Pasca]

@paskino pushed 2 commits.

• ab1d82f Added 50Gb VDI disk image
• 1a1fb9f builds VM with vagrant

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[Edoardo Pasca]

That error is due to the name of the "--storagectl", "IDE" which should be IDE Controller

[Edoardo Pasca]

@paskino pushed 2 commits.

• b0a6e76 add port forwarding, add 32 Mb video ram, 50 Gb HDD
• 9c41fb5 use system boost

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[Edoardo Pasca]

@paskino pushed 1 commit.

• b10f200 delete sirf_disk.vdi

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[Edoardo Pasca]

@paskino pushed 1 commit.

• ad2d659 removed links to specific VM and SuperBuild branches

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[Edoardo Pasca]

This branch creates a VM that works fine with ubuntu18.04 SuperBuild branch.

Tests and notebooks (running on VM and accessed from host) work.

Requires CCPPETMR/SIRF-SuperBuild#149

[Edoardo Pasca]

CCPPETMR/SIRF-SuperBuild#149 is superseded by
CCPPETMR/SIRF-SuperBuild#205 (merged)

[Kris Thielemans]

@KrisThielemans commented on this pull request.

Looks fine to me (some trailing white spaces) but I haven't tested it.

Please add lines to CHANGES.md (upgrade ubuntu, do port forwarding, don't install firefox)

[Kris Thielemans]

@KrisThielemans pushed 2 commits.

• 8d9ba4f use globbing for resetting *URL and *TAG
• 486eb75 set USE_ITK=ON

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[Edoardo Pasca]

@paskino pushed 3 commits.

• 8f8139f created function find_boost_version
• f3a789b moved shell provision script to file
• b906864 Merge branch 'ubuntu18.04' of https://github.com/CCPPETMR/CCPPETMR_VM into ubuntu18.04

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[Edoardo Pasca]

@paskino pushed 3 commits.

• a02da85 install libhdf5-dev
• d14060a vram is in modifyvm section
• 2ff11bf indentation fix

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[Edoardo Pasca]

@paskino pushed 1 commit.

• 0bba490 removed comment

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[Edoardo Pasca]

@paskino pushed 2 commits.

• b331644 separate the install steps
• 8f478bb multi line install

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[Edoardo Pasca]

@paskino pushed 1 commit.

• 7472310 added bootstrap_ubuntu.sh script

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[Edoardo Pasca]

@paskino pushed 1 commit.

• dd8098c install missing boost libraries

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[Edoardo Pasca]

closes #94

[Edoardo Pasca]

@paskino pushed 2 commits.

• e69cca8 removes autosuspend notification
• 116ac49 add info on 2.0rc1

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[Edoardo Pasca]

@paskino pushed 1 commit.

• e2b60c1 builds ubuntu18.04 SuperBuild

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[Edoardo Pasca]

probably needs CCPPETMR/SIRF-SuperBuild#220

The VM gets created correctly on the ubuntu18.04 branch of the SuperBuild

[Edoardo Pasca]

@paskino pushed 2 commits.

• 95cfaf4 build ubuntu18.04 branch of superbuild
• 7fec580 Merge branch 'ubuntu18.04' of https://github.com/CCPPETMR/CCPPETMR_VM into ubuntu18.04

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[Edoardo Pasca]

@paskino pushed 3 commits.

• 15d685a removed conflict message
• 4498f4b changed VM name
• fe620f5 uses SuperBuild master

[Edoardo Pasca]

@paskino pushed 1 commit.

• 906c3fa removed -V command

[Edoardo Pasca]

@paskino pushed 1 commit.

• ce6ea7f checks if user and homedir is already created

[Edoardo Pasca]

@paskino pushed 1 commit.

• dc5a998 bugfix

[Edoardo Pasca]

@paskino pushed 1 commit.

• 2f0aa63 bugfix~~

[Edoardo Pasca]

@paskino pushed 1 commit.

• c9d0898 fix test dir existence

[Kris Thielemans]

@KrisThielemans commented on this pull request.

Also will need to change SIRF_VM_VERSION in `UPDATE.sh

---

In scripts/bootstrap_ubuntu.sh:

> +# Could add custom logos here: /etc/gdm3/greeter.dconf-defaults 
+
+userHOME=/home/$SIRFUSERNAME
+
+if [ ! -d $userHOME/devel ]; then
+  mkdir $userHOME/devel 
+fi
+cd $userHOME/devel
+
+if [ ! -d $userHOME/devel/CCPPETMR_VM ]; then
+  git clone https://github.com/CCPPETMR/CCPPETMR_VM.git
+  cd CCPPETMR_VM
+  git checkout ubuntu18.04
+else
+  cd CCPPETMR_VM
+  git checkout ubuntu18.04

will need to change

---

In scripts/bootstrap_ubuntu.sh:

> +
+  # To remove the Ubuntu user from VM:
+#sudo deluser --remove-home ubuntu
+# Could add custom logos here: /etc/gdm3/greeter.dconf-defaults 
+
+userHOME=/home/$SIRFUSERNAME
+
+if [ ! -d $userHOME/devel ]; then
+  mkdir $userHOME/devel 
+fi
+cd $userHOME/devel
+
+if [ ! -d $userHOME/devel/CCPPETMR_VM ]; then
+  git clone https://github.com/CCPPETMR/CCPPETMR_VM.git
+  cd CCPPETMR_VM
+  git checkout ubuntu18.04

will need to change

---

In scripts/bootstrap_ubuntu.sh:

> +  git pull
+fi
+
+
+
+bash $userHOME/devel/CCPPETMR_VM/scripts/INSTALL_prerequisites_with_apt-get.sh
+bash $userHOME/devel/CCPPETMR_VM/scripts/INSTALL_CMake.sh /usr/local
+bash $userHOME/devel/CCPPETMR_VM/scripts/INSTALL_python_packages.sh
+
+# port 8888 is forwarded to 8888 so the user can use the host browser
+# Therefore no browser is installed on the VM
+python -m pip install jupyter
+python -m pip install spyder
+
+chown -R $SIRFUSERNAME:users $userHOME
+# the ubuntu18.04 branch latest commit

delete

---

In vagrant/Vagrantfile:

>         ]
-	vb.name = "SIRF_1.1.1"
+	vb.name = "SIRFCIL_2.0_18.04"

remove CIL

---

In CHANGES.md:

> @@ -1,5 +1,13 @@
 # ChangeLog
 
+## 2.0rc1
+- upgraded to Ubuntu 18.04
+- add port forwarding (8888 -> 8888 for jupyter)

and gadgetron?

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[Edoardo Pasca]

@paskino pushed 1 commit.

• 0be5275 install spyder and jupyter in pip script

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[Edoardo Pasca]

@paskino pushed 1 commit.

• 6a92d1b force spyder 3.2

[Kris Thielemans]

will need to update CHANGES.md

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[Edoardo Pasca]

@paskino pushed 1 commit.

• 9f77c76 manual configure jupyter

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[Edoardo Pasca]

@paskino pushed 1 commit.

• 3c04559 info on manual step to configure ip for jupyter

[Edoardo Pasca]

@paskino pushed 5 commits.

• 9e39448 add info on jupyter config
• 98069ce removed reference to specific branches
• d2ed794 updated VM name
• eabb9f5 add new version
• df0c4b2 Merge remote-tracking branch 'origin/master' into ubuntu18.04

[Edoardo Pasca]

@paskino commented on this pull request.

---

In CHANGES.md:

> @@ -1,5 +1,13 @@
 # ChangeLog
 
+## 2.0rc1
+- upgraded to Ubuntu 18.04
+- add port forwarding (8888 -> 8888 for jupyter)

Do we have to document it also here?

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[Edoardo Pasca]

@paskino pushed 1 commit.

• 4236308 update doc

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[Edoardo Pasca]

@paskino commented on this pull request.

---

In CHANGES.md:

> @@ -1,5 +1,13 @@
 # ChangeLog
 
+## 2.0rc1
+- upgraded to Ubuntu 18.04
+- add port forwarding (8888 -> 8888 for jupyter)

done it

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[Edoardo Pasca]

@paskino pushed 1 commit.

• 86de274 clean up

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[Edoardo Pasca]

Merged #104 into master.

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