[CCPPETMR/CCPPETMR_VM] upgrade to Ubuntu 18.04 LTS (#94)
Kris Thielemans
It makes sense to upgrade from 16.04 LTS. Gadgetron is/will be using this as reference and needs more recent boost etc.
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Edoardo Pasca
Edoardo Pasca
Following this issue I will try the newest gadgetron.
Edoardo Pasca
install cmake >= 3.9 as for CCPPETMR/SIRF-SuperBuild#144
Edoardo Pasca
What about python version? Shall I upgrade to 3?
Kris Thielemans
There might be consequences for spyder and jupyter. Would have to be checked.
Kris Thielemans
Trying the new VM. I got a message "Machine will suspend soon due to inactivity". Not a major problem of ourse, but a bit strange to have a VM suspend. This might help
Kris Thielemans
Running one of the jupyter notebook. Error
import matplotlib.pyplot as plt
produces
ImportError: No module named functools_lru_cache
Some possibly related comments on this here with a manual work-around at the bottom:
sudo cp /usr/lib/python2.7/dist-packages/backports/functools_lru_cache.py /usr/local/lib/python2.7/dist-packages/backports/
That makes the import go one step further, but exists at
/usr/lib/python2.7/dist-packages/matplotlib/__init__.py in <module>()
121 # cbook must import matplotlib only within function
122 # definitions, so it is safe to import from it here.
--> 123 from . import cbook
124 from matplotlib.cbook import (
125 _backports, mplDeprecation, dedent, get_label, sanitize_sequence)
ImportError: cannot import name cbook
The first google result talks about various conflicts with ipython etc.
Funnily enough, after the above cp I don't have the cbook problem on the command line with python nor ipython. Not sure what python we're running from jupyter notebooks. (It says python2).
How did jupyter get installed anyway? I don't see it in our scripts.
This looks a bit like a rabbithole...
Kris Thielemans
How did jupyter get installed anyway? I don't see it in our scripts.
Sorry. it's in the vagrantfile of course.
Edoardo Pasca
BTW, shall we build for python 3 rather than python 2.7?
Kris Thielemans
I think the problem might be that we're using apt-get to install matplotlib, but pip install jupyter. Probably better to use pip for all python packages.
I haven't been able to try if this works or not, as I can't get an internet connection on the VM. Possibly because my VN is 5.2.12 (too old?). Note that after update_VGA.sh, I have a failure to install some vbox service.
Kris Thielemans
I think going for python3 might be better, but do think that pip install would in any case be best. I guess would have to be pip3 then.
doesn't look good though.
Kris Thielemans
By the way, upgrading to VB 5.2.20 and update_VGA.sh doesn't resolve the problem with the vbox service nor the network connection.
Kris Thielemans
installed VB 5.2.18, reimported, still problem with the vboxadd-service and no network connection. oh well
Kris Thielemans
By the way, the mouse also moves really slowly for me on this VM (it's much faster on other VMs). Most likely something wrong with the VGA.
Kris Thielemans
I've created my own VM via vagrant (after upgrading that to 2.2.2).
I have problem that vagrant starts a VM which says that no bootable media are found.
This seems to happen sometimes. I first thought it was due to the new VDI lines, but am now not sure.
I have VGA problems
I have to remove VGA complete as per #77
sudo apt-get install build-essential module-assistant
sudo /opt/VBoxGuestAdditions-*/uninstall.sh
sudo apt-get purge virtualb*
sudo reboot
and reinstall the VGA. Possibly because you have to re-install the vagrant-vbguest plug-in after reinstalling vagrant, but I think it still didn't work after I did that.
Python matplot lib complains
from . import tkagg # Paint image to Tk photo blitter extension.
1: File "/usr/local/lib/python2.7/dist-packages/matplotlib/backends/tkagg.py", line 5, in <module>
1: from six.moves import tkinter as Tk
1: File "/usr/lib/python2.7/dist-packages/six.py", line 203, in load_module
1: mod = mod._resolve()
1: File "/usr/lib/python2.7/dist-packages/six.py", line 115, in _resolve
1: return _import_module(self.mod)
1: File "/usr/lib/python2.7/dist-packages/six.py", line 82, in _import_module
1: __import__(name)
1: File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 42, in <module>
1: raise ImportError, str(msg) + ', please install the python-tk package'
1: ImportError: No module named _tkinter, please install the python-tk package
a bit weird this. Possibly caused by still using Python 2.7. matplotlib should really default to something else...
The good news is that running things in spyder all works!
Edoardo Pasca
currently vagrant up hangs waiting for user input with a scrambled output
default: Unpacking software-properties-common (0.96.24.32.7) over (0.96.24.32.4) ...
default: Package configuration┌──────────────────┤ Configuring keyboard-configuration ├──────────────────┐│
The layout of keyboards varies per country, with some countries having ││
multiple common layouts. Please select the country of origin for the││
keyboard of this computer.││││
Country of origin for the keyboard:││││
Dutch↑││Dzongkha▒││English (Australian)▮││English (Cameroon)▒││English (Ghana)▒││
English (Nigeria)▒││English (South Africa)▒││English (UK)▒││English (US) � ↓││││││<Ok><Cancel>│││
└──────────────────────────────────────────────────────────────────────────┘
packing sosreport (3.6-1ubuntu0.18.04.2) over (3.5-1ubuntu3.18.04.1) ...
default: Preparing to unpack .../81-tmux_2.6-3ubuntu0.1_amd64.deb ...
default: Unpacking tmux (2.6-3ubuntu0.1) over (2.6-3) ...
default: Preparing to unpack .../82-cloud-initramfs-copymods_0.40ubuntu1.1_all.deb ...
default: Unpacking cloud-initramfs-copymods (0.40ubuntu1.1) over (0.40ubuntu1) ...
default: Preparing to unpack .../83-cloud-initramfs-dyn-netconf_0.40ubuntu1.1_all.deb ...
default: Unpacking cloud-initramfs-dyn-netconf (0.40ubuntu1.1) over (0.40ubuntu1) ...
default: Preparing to unpack .../84-libtirpc1_0.2.5-1.2ubuntu0.1_amd64.deb ...
default: Unpacking libtirpc1:amd64 (0.2.5-1.2ubuntu0.1) over (0.2.5-1.2) ...
default: Preparing to unpack .../85-open-vm-tools_2%3a10.3.0-0ubuntu1~18.04.3_amd64.deb ...
default: Unpacking open-vm-tools (2:10.3.0-0ubuntu1~18.04.3) over (2:10.2.0-3ubuntu3) ...
default: Preparing to unpack .../86-overlayroot_0.40ubuntu1.1_all.deb ...
default: Unpacking overlayroot (0.40ubuntu1.1) over (0.40ubuntu1) ...
default: Setting up libquadmath0:amd64 (8.2.0-1ubuntu2~18.04) ...
default: Setting up python-apt-common (1.6.3) ...
default: Setting up libgomp1:amd64 (8.2.0-1ubuntu2~18.04) ...
default: Setting up libatomic1:amd64 (8.2.0-1ubuntu2~18.04) ...
default: Setting up libpython3.6-stdlib:amd64 (3.6.7-1~18.04) ...
default: Setting up libisc169:amd64 (1:9.11.3+dfsg-1ubuntu1.3) ...
default: Setting up libapt-inst2.0:amd64 (1.6.8) ...
default: Setting up libnss-systemd:amd64 (237-3ubuntu10.11) ...
default: Setting up git-man (1:2.17.1-1ubuntu0.4) ...
default: Setting up keyboard-configuration (1.178ubuntu2.7) ...
default:
Edoardo Pasca
probably similar to #21
Edoardo Pasca
fails to find system Boost at the minute...
Casper da Costa-Luis
Python matplot lib complains
you need to apt-get install python-dev python-tk
https://github.com/CCPPETMR/SIRF-SuperBuild/blob/master/docker/build_python-ubuntu.sh#L2-L5
Edoardo Pasca
Closed #94.