Geoviewer tab - Segmentation fault still occuring

Installation
21

Hi @manousos

I am not sure how to locate the command you are refering to. I don’t seem to have any files called .profile.

I also installed VirtualBox today and Ubuntu 18.04. I followed the “Only once instructions” and everything seems to have installed. When I open flair I can click the geometry tab and now see interactive blank viewpanels. However, when I try to include a simple geometry it once again crashes with

Segmentation fault (core dumped)

Is there a better chance of success troubleshooting this installation with the VM and Ubuntu?

Thanks!
-Jason

22

Dear @Jason_O,

the .profile file is a file (hidden) in your home directory.
Could you please type:

less ~/.profile

and send me the output?

PS. I would keep the discussion of this thread only for the MacOs case,
since for the VirtualBox installation the cause of the problem might be total different.

23

Hi @manousos

The output for

less ~/.profile

is below

MacPorts Installer addition on 2020-08-19_at_16:53:27: adding an appropriate PATH variable for use with MacPorts.

export PATH=“/opt/local/bin:/opt/local/sbin:$PATH”

Finished adapting your PATH environment variable for use with MacPorts.

Setting PATH for Python 3.8

The original version is saved in .profile.pysave

PATH=“/Library/Frameworks/Python.framework/Versions/3.8/bin:${PATH}”

export PATH

/Users/J/.profile (END)

Many Thanks!
-Jason

24

Dear @Jason_O

Your .profile is exactly as it should be and as I expected.
The problem, from what I can guess,
is that during compilation the correct macport python version is not loaded.

Could you please, in a new terminal, type:

sudo port select --set python3 python37
which python3

If the output of the last will be:
opt/local/bin/python3
then, in the same terminal enter the folder where geoviewer was expanded and type:

make clean; make -j DEBUG=yes > newmakeproc.log; make install DESTDIR=PATH_FLAIR

and then try opening flair again and see if everything is ok.
In case of failure again, send us the output file newmakeproc.log

Thanos

25

Hi @manousos

After the first command (I changed python37 to python38) then

which python3

I get

/Library/Frameworks/Python.framework/Versions/3.8/bin/python3

Does this mean I have python in the wrong place?

Jason

26

Dear @Jason_O,

Could you try with 7 instead of 8?

Thanos

27

@manousos

Selecting ‘python37’ for ‘python3’ failed: The specified version ‘python37’ is not valid.

I previously uninstalled 37 when I was instructed to clean up my python installs

28

Then after

which python

get

/usr/bin/python

29

@Jason_O,

This is normal, since - for reason that we have to figure out -
the system insists on using a python version NOT installed via macports.
Did you try to install a python3 version by NOT using macports?
Especially using DMG installers from python.org?
because if yes this could explain the problem…

A possible solution will be:

sudo rm -Rf /Library/Frameworks/Python.framework/Versions/3.8

But please do this only if you know that you do not need this framework anymore.
(that would have been my guess :wink: )

and then try again:

sudo port select --set python3 python38

and the installation procedure as described before.

Thanos

30

@manousos

Yes I believe I used the DMG installer from python.org. Should I remove python from my machine and try to install it some other way?

Thanks!
-Jason

31

@Jason_O,

the answer is yes.
as described in the installation instructions,
you have to use the python3 version provided by macports.
sure, you can have different ones installed,
BUT flair requires python3 provided by macports (mainly for simplicity)

So please remove any python3 versions that exist under:
/Library/Frameworks/Python.framework/Versions/
i.e.:

sudo rm -Rf /Library/Frameworks/Python.framework/Versions/3.*

In addition, you should remove all the symbolic links in /usr/local/bin:

sudo rm /usr/local/bin/python3*

Then install the macport python3 version and all the dependencies required by flair and geoviewer typing:

sudo port install python38 gcc10 xorg-server xorg py38-tkinter pkgconfig py38-pillow py38-numpy py38-matplotlib +tkinter py38-scipy py38-pydicom py38-pip gnuplot ghostscript gdb xterm

Then open a new terminal and:

sudo port select --set python3 python38
which python3

Now the output of the above should be different than before and equal to:
/opt/local/bin/python3
If yes, then (and always under the same terminal tab) proceed as described before:

make clean; make -j DEBUG=yes > macportpython.log; make install DESTDIR=PATH_FLAIR

Thanos

32

@manousos

Thanos,
Thank you very much for all of the time and effort you and @luillo put into this. Everything appears to be working correctly!!!

Best,
-Jason