Installation issues with the older and the newest cc3d linux versions


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0
24 days ago by
Dear reader,

I have encountered some installation issues with the older, and also the newest cc3d linux version(/s) [using win ubuntu 18].

Some additional info below:
File attached: installation_25718.txt (3.33 KB)

I wonder if somebody could (please):
a) post the newest cc3d linux binary and installation guide to internet (here or some other place, https://sourceforge.net/projects/cc3d/?), or
b) send (here/the other cc3d internet site) completely installed&dependency free linux version's files/folder,
which would presumably work as such when run on (win app) ubuntu file system (../compucell3d.sh +enter)?
c) have any other ideas, what(?)

Thanks!

Best regards,
Pauli
Community: CompuCell3D

4 Answers


0
19 days ago by
Hi,

I got the installation binary files, but still have some issues, namely:

I tried to run the program after cygwin (1) and ubuntu 18 (win) (2) installations, but...
(1)
pauli@Kansallinen ~/CC3D_v377
$ ./compucell3d.sh
CompuCell3D - version 3.7.7
./compucell3d.sh: rivi 40: /home/pauli/CC3D_v377/Python27/bin/python: cannot execute binary file: Exec format error

(2)

(fyi)
pauli@Kansallinen:~/CC3D_v377$ ls -l
total 20
...
-rwxr-xr-x 1 1481910 3007 1473 Feb 1 00:52 compucell3d.sh
...
-rwxr-xr-x 1 1481910 3007 846 Feb 5 18:30 optimization.sh
-rwxr-xr-x 1 1481910 3007 1477 Feb 5 18:29 paramScan.sh
drwxr-sr-x 1 1481910 3007 512 Feb 5 23:07 player5
...
-rwxr-xr-x 1 1481910 3007 1510 Feb 5 23:19 runScript.sh
-rwxr-xr-x 1 1481910 3007 618 Feb 1 00:53 twedit++.sh

THEN:
pauli@Kansallinen:~/CC3D_v377$ ./compucell3d.sh
./compucell3d.sh: 10: ./compucell3d.sh: Bad substitution
CompuCell3D - version 3.7.7
['/home/pauli/CC3D_v377/player5', '/home/pauli/CC3D_v377/Python27/lib/python27.zip', '/home/pauli/CC3D_v377/Python27/lib/python2.7', '/home/pauli/CC3D_v377/Python27/lib/python2.7/plat-linux2', '/home/pauli/CC3D_v377/Python27/lib/python2.7/lib-tk', '/home/pauli/CC3D_v377/Python27/lib/python2.7/lib-old', '/home/pauli/CC3D_v377/Python27/lib/python2.7/lib-dynload', '/home/pauli/.local/lib/python2.7/site-packages', '/home/pauli/CC3D_v377/Python27/lib/python2.7/site-packages']
QXcbConnection: Could not connect to display
Aborted (core dumped)

tried several pages for the display issue, but does not seem to work...
/e.g. https://superuser.com/questions/1075659/open-ubuntu-bashs-gui-applications-on-windows-10

Any ideas/suggestions how to solve?

0
16 days ago by
I will build binaries for kubuntu 18.04 64 bit later soon. In the mean time you may want to check easy-to-follow conda-based installation instructions

http://www.compucell3d.org/SrcBin/CompilingOnLinux2017

This could get you running on many types of linuxes really fast . Regardless we will post binaries for 18.04
0
16 days ago by
We uploaded ubuntu  18_04_64 binaries to the sourceforge website:

https://sourceforge.net/projects/cc3d/files/3.7.8/linux/ubuntu_18_04_64/

Take a look and see if they work for you. We tested them on clean install of ubuntu 18_04 64bit and they seem to work fine
Hi,
Thanks for the binaries again. So now
I experienced the same problem with the screen/gui, when opening the compucell3d.sh:

ptikka@Kansallinen:~/CC3D_GIT/378_auto$ ./compucell3d.sh -x
./compucell3d.sh: 10: ./compucell3d.sh: Bad substitution
CompuCell3D - version 3.7.6
['/home/ptikka/CC3D_GIT/378_auto/player5', '/home/ptikka/CC3D_GIT/378_auto/Python27/lib/python27.zip', '/home/ptikka/CC3D_GIT/378_auto/Python27/lib/python2.7', '/home/ptikka/CC3D_GIT/378_auto/Python27/lib/python2.7/plat-linux2', '/home/ptikka/CC3D_GIT/378_auto/Python27/lib/python2.7/lib-tk', '/home/ptikka/CC3D_GIT/378_auto/Python27/lib/python2.7/lib-old', '/home/ptikka/CC3D_GIT/378_auto/Python27/lib/python2.7/lib-dynload', '/home/ptikka/CC3D_GIT/378_auto/Python27/lib/python2.7/site-packages']
QXcbConnection: Could not connect to display 127.0.0.1:10.0

The best self-help that I found was here (below), but it did not work for me (see above):
https://stackoverflow.com/questions/44720732/php-ubuntu-qxcbconnection-could-not-connect-to-display-aborted
Aborted (core dumped)

Any Ideas how to solve this?
Next I test the conda_based installation.

BR.
Pauli


written 5 days ago by Pauli Tikka  
At this point I really think you should try compiling the code yourself. Part of a challenge here is that we are dealing with non-standard configuration. Are you on cluster of some sort or do you have root access to the machine you are trying to install too?

If you are in charge of the machine I would recommend using ubuntu 18_04_64 bit.

Another task you can perform now is to try running any of the pyqt5 demos . for example try downloading and running https://github.com/baoboa/pyqt5/tree/master/examples/mainwindows/mdi


For this to work you need to have functional copy of pyqt5 which is easy to install via conda , simply type
conda install pyqt​

Let me know if you can run any pyqt5 application. If , yes than we should try figuring out how to compile CC3D on your system. The conda-based installer should work

written 4 days ago by Maciek Swat  
Hi,

Thanks!

I tried both of the solutions:

1) ...In the mean time you may want to check easy-to-follow conda-based installation instructions
(http://www.compucell3d.org/SrcBin/CompilingOnLinux2017)

2) ...installed pyqt with: conda install -c conda-forge pyqt ,
and tried the compiling cc3d in my system; which is at the moment just my win PC with ubuntu 18.04 application from MSstore.
The idea was to later run my model simulations as a part of a swarm parameter estimation code of J. Sluka with my/his cluster computers that have linux cc3d paramscan.sh available.

---

But the results were (for 1,2):
1)
USING SYSTEM
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ptikka/cc3d_376_build
[ 5%] Built target muParserShared
[ 6%] Built target BasicUtilsShared
[ 9%] Built target cleaver
[ 11%] Built target AutomatonShared
[ 11%] Swig source
[ 12%] Swig source
:1: Error: Unable to find 'swig.swg'
:3: Error: Unable to find 'python.swg'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CC3DXML/CC3DXML.i:32: Error: Unable to find 'std_string.i'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CC3DXML/CC3DXML.i:35: Error: Unable to find 'std_map.i'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CC3DXML/CC3DXML.i:38: Error: Unable to find 'std_vector.i'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CC3DXML/CC3DXML.i:41: Error: Unable to find 'std_list.i'
core/pyinterface/CC3DXML/CMakeFiles/CC3DXML_swig_compilation.dir/build.make:61: recipe for target 'core/pyinterface/CC3DXML/CMakeFiles/_CC3DXML.dir/CC3DXMLPYTHON.stamp' failed
make[2]: *** [core/pyinterface/CC3DXML/CMakeFiles/_CC3DXML.dir/CC3DXMLPYTHON.stamp] Error 1
:make[2]: *** Deleting file 'core/pyinterface/CC3DXML/CMakeFiles/_CC3DXML.dir/CC3DXMLPYTHON.stamp'
1CMakeFiles/Makefile2:5451: recipe for target 'core/pyinterface/CC3DXML/CMakeFiles/CC3DXML_swig_compilation.dir/all' failed
:make[1]: *** [core/pyinterface/CC3DXML/CMakeFiles/CC3DXML_swig_compilation.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
Error: Unable to find 'swig.swg'
:3: Error: Unable to find 'python.swg'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CompuCellPython/CompuCell.i:16: Error: Unable to find 'typemaps.i'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CompuCellPython/CompuCell.i:54: Error: Unable to find 'windows.i'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CompuCellPython/CompuCell.i:124: Error: Unable to find 'stl.i'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CompuCellPython/CompuCell.i:129: Error: Unable to find 'std_string.i'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CompuCellPython/CompuCell.i:132: Error: Unable to find 'std_map.i'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CompuCellPython/CompuCell.i:135: Error: Unable to find 'std_set.i'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CompuCellPython/CompuCell.i:138: Error: Unable to find 'std_vector.i'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CompuCellPython/CompuCell.i:140: Error: Unable to find 'stl.i'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CompuCellPython/CompuCell.i:143: Error: Unable to find 'exception.i'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CompuCellPython/CompuCellExtraDeclarations.i:29: Error: Unable to find 'std_string.i'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CompuCellPython/CompuCellExtraDeclarations.i:32: Error: Unable to find 'std_map.i'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CompuCellPython/CompuCellExtraDeclarations.i:35: Error: Unable to find 'std_set.i'
/home/ptikka/CC3D_GIT3/CompuCell3D/core/pyinterface/CompuCellPython/CompuCellExtraDeclarations.i:40: Error: Unable to find 'std_vector.i'
core/pyinterface/CompuCellPython/CMakeFiles/CompuCell_swig_compilation.dir/build.make:61: recipe for target 'core/pyinterface/CompuCellPython/CMakeFiles/_CompuCell.dir/CompuCellPYTHON.stamp' failed
make[2]: *** [core/pyinterface/CompuCellPython/CMakeFiles/_CompuCell.dir/CompuCellPYTHON.stamp] Error 1
make[2]: *** Deleting file 'core/pyinterface/CompuCellPython/CMakeFiles/_CompuCell.dir/CompuCellPYTHON.stamp'
CMakeFiles/Makefile2:5502: recipe for target 'core/pyinterface/CompuCellPython/CMakeFiles/CompuCell_swig_compilation.dir/all' failed
make[1]: *** [core/pyinterface/CompuCellPython/CMakeFiles/CompuCell_swig_compilation.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

2) 'in conda'
(my_env22) ptikka@Kansallinen:~$ python mdi.py
QXcbConnection: Could not connect to display :0
Aborted (core dumped)

Ideas to solve?

BR,
Pauli
written 4 days ago by Pauli Tikka  
PS
the other thing that I tried was (the installation guide solution as in your cc3d homepage for ubuntu 18.04):

(my_env22) ptikka@Kansallinen:~$ sudo apt-get install g++ swig cmake-gui python-numpy python-pyqt5 python-pyqt5.qsci python-pyqt5.qtopengl python-pyqt5.qtsvg libvtk6-dev python-vtk6 python-dev libxml2-dev build-essential git
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'cmake-qt-gui' instead of 'cmake-gui'
build-essential is already the newest version (12.4ubuntu1).
g++ is already the newest version (4:7.3.0-3ubuntu2).
python-dev is already the newest version (2.7.15~rc1-1).
python-numpy is already the newest version (1:1.13.3-2ubuntu1).
cmake-qt-gui is already the newest version (3.10.2-1ubuntu2).
libvtk6-dev is already the newest version (6.3.0+dfsg1-11build1).
python-pyqt5 is already the newest version (5.10.1+dfsg-1ubuntu2).
python-pyqt5.qsci is already the newest version (2.10.2+dfsg-4).
python-pyqt5.qtopengl is already the newest version (5.10.1+dfsg-1ubuntu2).
python-pyqt5.qtsvg is already the newest version (5.10.1+dfsg-1ubuntu2).
python-vtk6 is already the newest version (6.3.0+dfsg1-11build1).
swig is already the newest version (3.0.12-1).
git is already the newest version (1:2.17.1-1ubuntu0.1).
The following additional packages will be installed:
libxml2
The following packages will be upgraded:
libxml2 libxml2-dev
2 upgraded, 0 newly installed, 0 to remove and 121 not upgraded.
Need to get 1420 kB of archives.
After this operation, 0 B of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxml2-dev amd64 2.9.4+dfsg1-6.1ubuntu1.2 [757 kB]
Get:2 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxml2 amd64 2.9.4+dfsg1-6.1ubuntu1.2 [663 kB]
Fetched 1420 kB in 1s (1211 kB/s)
(Reading database ... 103749 files and directories currently installed.)
Preparing to unpack .../libxml2-dev_2.9.4+dfsg1-6.1ubuntu1.2_amd64.deb ...
Unpacking libxml2-dev:amd64 (2.9.4+dfsg1-6.1ubuntu1.2) over (2.9.4+dfsg1-6.1ubuntu1) ...
Preparing to unpack .../libxml2_2.9.4+dfsg1-6.1ubuntu1.2_amd64.deb ...
Unpacking libxml2:amd64 (2.9.4+dfsg1-6.1ubuntu1.2) over (2.9.4+dfsg1-6.1ubuntu1) ...
Setting up libxml2:amd64 (2.9.4+dfsg1-6.1ubuntu1.2) ...
Setting up libxml2-dev:amd64 (2.9.4+dfsg1-6.1ubuntu1.2) ...
Processing triggers for libc-bin (2.27-3ubuntu1) ...
Processing triggers for man-db (2.8.3-2) ...
(my_env22) ptikka@Kansallinen:~$ pip install pyqtgraph
Collecting pyqtgraph
Downloading https://files.pythonhosted.org/packages/cd/ad/307e0280df5c19986c4206d138ec3a8954afc722cea991f4adb4a16337d9/pyqtgraph-0.10.0.tar.gz (1.5MB)
100% |████████████████████████████████| 1.6MB 1.6MB/s
Collecting numpy (from pyqtgraph)
Downloading https://files.pythonhosted.org/packages/85/51/ba4564ded90e093dbb6adfc3e21f99ae953d9ad56477e1b0d4a93bacf7d3/numpy-1.15.0-cp27-cp27mu-manylinux1_x86_64.whl (13.8MB)
100% |████████████████████████████████| 13.8MB 1.3MB/s
Building wheels for collected packages: pyqtgraph
Running setup.py bdist_wheel for pyqtgraph ... done
Stored in directory: /home/ptikka/.cache/pip/wheels/93/a2/de/184ecdefdb91d760706d02389015dfa3b96e927eb1c42ace37
Successfully built pyqtgraph
Installing collected packages: numpy, pyqtgraph
Successfully installed numpy-1.15.0 pyqtgraph-0.10.0
You are using pip version 10.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
(my_env22) ptikka@Kansallinen:~$ cd /home/m/CC3D_GIT4
-bash: cd: /home/m/CC3D_GIT4: No such file or directory
(my_env22) ptikka@Kansallinen:~$ cd /CC3D_GIT4
-bash: cd: /CC3D_GIT4: No such file or directory
(my_env22) ptikka@Kansallinen:~$ cd ~/CC3D_GIT4
(my_env22) ptikka@Kansallinen:~/CC3D_GIT4$ ls
(my_env22) ptikka@Kansallinen:~/CC3D_GIT4$ git clone https://github.com/CompuCell3D/CompuCell3D.git .
Cloning into '.'...
remote: Counting objects: 22653, done.
remote: Compressing objects: 100% (34/34), done.
remote: Total 22653 (delta 12), reused 26 (delta 9), pack-reused 22610
Receiving objects: 100% (22653/22653), 52.68 MiB | 3.28 MiB/s, done.
Resolving deltas: 100% (14719/14719), done.
Checking out files: 100% (9965/9965), done.
(my_env22) ptikka@Kansallinen:~/CC3D_GIT4$ cmake-gui
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-ptikka'
qt.qpa.screen: QXcbConnection: Could not connect to display :0
Could not connect to any X display.
written 4 days ago by Pauli Tikka  
So this is actually very important. Your system, for whatever reason, fails to open any qt application (cmake-gui is a qt application). If you are running on your personal machine you should instal ubuntu from https://www.ubuntu.com/download/desktop, not from MS Store. If this is a cluster you need to tell administrator to locate the problem that prevents you from running qt-based applications that are part of the operating system (such as cmake-gui). Let me know how this goes
written 3 days ago by Maciek Swat  

Hi,

I got the cc3d installation working with binaries (but not with the compiling method) by correcting my ubuntu 18.04 win app version as mentioned in:
https://tech-ish.com/2018/05/10/how-to-install-ubuntu-desktop-on-windows-10/

Example drive (see the photos):
ptikka@Kansallinen:~/CC3D_GIT/378_auto$ ./compucell3d.sh
./compucell3d.sh: 10: ./compucell3d.sh: Bad substitution
CompuCell3D - version 3.7.6
['/home/ptikka/CC3D_GIT/378_auto/player5', '/home/ptikka/CC3D_GIT/378_auto/P...


The compiled installation still produces:

ptikka@Kansallinen:~/CC3D_install$ ./compucell3d.sh
./compucell3d.sh: 10: ./compucell3d.sh: Bad substitution
CompuCell3D - version 3.7.7
['/home/ptikka/CC3D_install/player5', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-x86_64-linux-gnu', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/gtk-2.0']
Could not import roadrunner
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-ptikka'
compucell3d.pyw: type(argv)= <type 'list'>
compucell3d.pyw: argv= ['--currentDir=/home/ptikka/CC3D_install']
Could not create PLotManager. resorting to PLotManagerBase - plots will not work properly. Here is the exception:
No module named pyqtgraph
could not import pyqtgraph
/home/ptikka/CC3D_install/player5/Plugins/ViewManagerPlugins/PlotWindowInterface.py:16: RuntimeWarning: Could not find webcolors. Run "pip install webcolors" to fix this
warnings.warn('Could not find webcolors. Run "pip install webcolors" to fix this', RuntimeWarning)
Traceback (most recent call last):
File "/home/ptikka/CC3D_install/player5/compucell3d.pyw", line 258, in <module>
error_code = main(sys.argv[1:])
File "/home/ptikka/CC3D_install/player5/compucell3d.pyw", line 232, in main
mainWindow = UserInterface()
File "/home/ptikka/CC3D_install/player5/UI/UserInterface.py", line 93, in __init__
self.__createViewManager()
File "/home/ptikka/CC3D_install/player5/UI/UserInterface.py", line 483, in __createViewManager
self.viewmanager = SimpleTabView(self) # ViewManager.factory(self, self)
File "/home/ptikka/CC3D_install/player5/Plugins/ViewManagerPlugins/SimpleTabView.py", line 124, in __init__
from WidgetManager import WidgetManager
File "/home/ptikka/CC3D_install/player5/Plugins/ViewManagerPlugins/WidgetManager.py", line 2, in <module>
from PlotWindowInterface import PlotWindowInterface
File "/home/ptikka/CC3D_install/player5/Plugins/ViewManagerPlugins/PlotWindowInterface.py", line 18, in <module>
import pyqtgraph as pg
ImportError: No module named pyqtgraph

(I have installed pyqtgraph and the depencies as: http://www.compucell3d.org/SrcBin/LinuxCompile)

Anyway, so far so good. Thank you for your help!

BR, Pauli
written 3 days ago by Pauli Tikka  
So the issue is with swig that ships with conda. On ubuntu 18.04 swig struggles finding its core include files. The solution is to remove swig executable from conda environment created and install swig manually from sources.

So remove swig executable from <xxx>/miniconda2/envs/<your env>/swig

install swig from source (www.swig.org)

and add swig (compiled manually) to your path:
export PATH=<PATH TO SWIG>/bin:$PATH​
written 3 days ago by Maciek Swat  
0
16 days ago by
Hi,

Thank you for your answer! Should there be any issues I’ll let you know!

BR,
Pauli
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