CP 2.0 not starting up

Hi,

I just installed CP 2.0 (using the Makefile.CP2, which is really helpful). Other than changing versions for few of the dependent packages, which don’t exist anymore, everything went pretty smooth.

After the installation, when I start CellProfiler by doing “python CellProfiler.py” from “$INSTALLPREFIX/CellProfiler/” folder, I get the following error.

[root@host CellProfiler]# python CellProfiler.py
WARNING:root:Distributed support disabled: please install nuageux
running build_ext
running build_ext
Traceback (most recent call last):
File “CellProfiler.py”, line 294, in
show_splashbox = (options.pipeline_filename is None))
File “/cm/shared/apps/CellProfiler/2.0/CellProfiler/cellprofiler/cellprofilerapp.py”, line 18, in init
super(CellProfilerApp, self).init(*args, **kwargs)
File “/cm/shared/apps/CellProfiler/2.0/lib/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 7978, in init
self._BootstrapApp()
File “/cm/shared/apps/CellProfiler/2.0/lib/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 7552, in _BootstrapApp
return core.PyApp__BootstrapApp(*args, **kwargs)
File “/cm/shared/apps/CellProfiler/2.0/CellProfiler/cellprofiler/cellprofilerapp.py”, line 29, in OnInit
splashbitmap = wx.EmptyBitmapRGBA(CellProfilerSplash.GetWidth(), CellProfilerSplash.GetHeight(), 255, 255, 255, 255)
File “/cm/shared/apps/CellProfiler/2.0/lib/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_gdi.py”, line 897, in EmptyBitmapRGBA
return gdi._EmptyBitmapRGBA(width, height, red, green, blue, alpha)
ValueError: Width and height must be greater than zero

More information:

[root@host CellProfiler]# echo $JAVA_HOME
/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/
[root@host CellProfiler]# echo $LD_LIBRARY_PATH
/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64//jre/lib/amd64:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64//jre/lib/amd64/server:/cm/shared/apps/CellProfiler/2.0/lib:/cm/shared/apps/CellProfiler/2.0/lib64:/cm/shared/apps/slurm/2.3.4/lib64/slurm
[root@host CellProfiler]# echo $PATH
/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64//bin:/cm/shared/apps/CellProfiler/2.0/bin:/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/cm/shared/apps/cmgui:/cm/local/apps/cmd/bin:/cm/local/apps/cmd/sbin:/cm/local/apps/cluster-tools/bin:/cm/shared/apps/slurm/2.3.4/bin:/cm/shared/apps/slurm/2.3.4/sbin:/root/bin
[root@host CellProfiler]# echo $PYTHONPATH
/cm/shared/apps/CellProfiler/2.0/lib/python2.6/site-packages
[root@host CellProfiler]# echo $HOST
$HOSTNAME $HOSTTYPE
[root@host CellProfiler]# echo $HOST
$HOSTNAME $HOSTTYPE
[root@host CellProfiler]# echo $HOSTTYPE
x86_64

Any idea what is going on?

Thanks,
Prakash

I figured this one out late last night after posting this thread. It is interesting what made it work.

I had to change just one line in $INSTALL/CellProfiler/cellprofiler/cellprofilerapp.py file

from
splashbitmap = wx.EmptyBitmapRGBA(CellProfilerSplash.GetWidth(), CellProfilerSplash.GetHeight(), 255, 255, 255, 255)
to
splashbitmap = wx.EmptyBitmapRGBA(CellProfilerSplash.GetWidth()+1, CellProfilerSplash.GetHeight()+1, 255, 255, 255, 255)

After that, the CP GUI started up just fine. Not sure why that is the case, but I got a hint from “https://groups.google.com/forum/?fromgroups=#!topic/android-developers/pTNy4cRo7wE” that GetWidth() and GetHeight() returns 0. That is what prompted me to add (+1) to those.

Any other details from CP developers would be appreciated.

Thanks.

Hi Prakash,

Thanks for taking the time to investigate this! This is the first I’ve seen this issue reported, and we have a fair number of folks who are running CP on Linux. Just to clarify, what version of wx are you running?

Regards,
-Mark

Hi,

wx - 2.8
wxPython - 2.8.11.0

Does that sound right?

Thanks.

hi hi

I recently got a task to try to install CP on our Linux Ubuntu 12.04 server ,64 bit … I followed as prakashvel , the Makefile.CP2 . This was needed as our boot/root partition has issues with disk space so i need to install CP on partition with a lot of HD space.

I also had to change and update the versions   of the  dependent packages inside of Makefile.CP2 , namely i did set ** pcre-8.21,  libpng-1.4.12,    zlib-1.2.7**.

(I would just go to their web/ftp pages and pick some version. )
Further i had to export HOSTTYPE=“x86_64” (for some reason Makefile.CP2 doesn’t see it while shell does) ,and instal GIT software.

Note for **libpng **i had to change ftp path as old one is not existing so i had set it to:
ftp://ftp.simplesystems.org/pub/libpng/ … libpng14….
I seem to downgraded libpng from libpng-1.5 to libpng-1.4.12 ( as -1.4.12 is only found in libpng14 ftp dir.)

At he moment I’m stuck with libs: pango-1.28.3 , pixman-0.20.2
these versions i did not change they were downloaded as original script Makefile.CP2 instructs .
In the log i see they are complaining.

Can you please check my log and give advice ?
Log is in the Gdrive, you have to download it since it ~ 4MB :
https://docs.google.com/file/d/0B4LuO2QQI4otMG1LdmNBYm9qV00/edit?usp=sharing

oh and , prakashvel can you send me your Makefile.CP2 ?
CP team maybe you can update the Makefile.CP2 file ?

ciao,
Branko

Hi all, sorry for the late response!
The short, official answer is we don’t yet support Ubuntu 12.04 64 bit. But don’t give up because we may soon!

A more immediate answer to your question is that you should just disable the splashbox at startup. The cleanest way to do that is to go into $(YOURCELLPROFILERPATH)/CellProfiler/cellprofiler/cellprofilerapp.py and add the following line:

after

(you can of course also delete this second line, if you’d like).

That’s just a quick fix, but probably won’t fix all of your problems (in my spare time I did a 64 bit Ubuntu build, but ran into some incompatibilities with vigra–newer versions of gcc, such as those you’d get from the Ubuntu repos, don’t play nicely with vigra, and I haven’t found a workaround that I like). So far, we are focusing our support on 64-bit Red Hat, so we might not have an inclusive solution for you for a little bit, but if you do get past the vigra bit (or somehow don’t see it…) let us know.

Good luck!

Samuel