Problems with Installation/Testing of CP2 on linux cluster

Dear Support,

I am trying to install CP2 for one of our PhD students @ Northwestern University’s HPC Cluster (it.northwestern.edu/research … hpc/quest/). It is a general purpose cluster with Intel Nehalem processors(partly), and RHEL 5.3 and kernel 2.6.18. I used an updated Makefile provided to the student (0.1.4 updated on 2011/01/16) to do the auto install of all the prereqs with gcc-4.2.3 and java/jre1.6.0_20. I subsequently updated my $PATH and $LD_LIBRARY_PATH to reflect the CP2, Python installs.

[quote]# CP2, python-2.5 and many other CP2 prerequisites
export PATH="{HOME}/usr/CellProfiler2/bin:{PATH}“
export LD_LIBRARY_PATH=”${HOME}/usr/CellProfiler2/lib:HOME/usr/CellProfiler2/lib64:{LD_LIBRARY_PATH}“
export PYTHONPATH=”{HOME}/usr/CellProfiler2/lib/python2.5/site-packages:{PYTHONPATH}"
# java-1.6 for 64bit
export JAVA_HOME=/software/java/jre1.6.0_20
export PATH="JAVA_HOME/bin:{PATH}“
export LD_LIBRARY_PATH=”{JAVA_HOME}/lib/amd64:{JAVA_HOME}/lib/amd64/server:${LD_LIBRARY_PATH}"
[/quote]

When I run the test “python CellProfiler.py” however I am getting a few errors. I apologize for the nature of this long post, but I would be grateful for any insight as to what’s happening.

[quote]python CellProfiler.py
running build_ext
skipping ‘_cpmorphology2.c’ Cython extension (up-to-date)
skipping ‘_watershed.c’ Cython extension (up-to-date)
cythoning _propagate.pyx to _propagate.c

Error compiling Cython file:


cdef unsigned int ivalue
if little_endian_flag==1:
ivalue = pValue[1]
else:
ivalue = pValue[0]
if ivalue & 0x80000000:
^

/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/_propagate.pyx:57:14: Truth-testing Python object not allowed without gil

Error compiling Cython file:


cdef unsigned int ivalue
if little_endian_flag==1:
ivalue = pValue[1]
else:
ivalue = pValue[0]
if ivalue & 0x80000000:
^

/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/_propagate.pyx:57:14: Operation not allowed without gil

Error compiling Cython file:


cdef unsigned int ivalue
if little_endian_flag==1:
ivalue = pValue[1]
else:
ivalue = pValue[0]
if ivalue & 0x80000000:
^

/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/_propagate.pyx:57:14: Converting to Python object not allowed without gil

Error compiling Cython file:


ivalue1=pValue[1]
ivalue2=pValue[0]
else:
ivalue1=pValue[0]
ivalue2=pValue[1]
if ivalue1 & 0x80000000:
^

/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/_propagate.pyx:82:15: Truth-testing Python object not allowed without gil

Error compiling Cython file:


ivalue1=pValue[1]
ivalue2=pValue[0]
else:
ivalue1=pValue[0]
ivalue2=pValue[1]
if ivalue1 & 0x80000000:
^

/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/_propagate.pyx:82:15: Operation not allowed without gil

Error compiling Cython file:


ivalue1=pValue[1]
ivalue2=pValue[0]
else:
ivalue1=pValue[0]
ivalue2=pValue[1]
if ivalue1 & 0x80000000:
^

/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/_propagate.pyx:82:15: Converting to Python object not allowed without gil
building ‘_propagate’ extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc -I/home/psi391/usr/CellProfiler2/lib/python2.5/site-packages/numpy/core/include -I/home/psi391/usr/CellProfiler2/include/python2.5 -c _propagate.c -o build/temp.linux-x86_64-2.5/_propagate.o -O3
_propagate.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.
error: command ‘gcc’ failed with exit status 1
Using jdk_home = None
Using jdk_home = None
running build_ext
skipping ‘javabridge.c’ Cython extension (up-to-date)
building ‘javabridge’ extension
gcc -pthread -shared build/temp.linux-x86_64-2.5/javabridge.o -L/software/java/jre1.6.0_20/jre/lib/amd64/server -ljvm -o javabridge.so
/usr/bin/ld: cannot find -ljvm
collect2: ld returned 1 exit status
error: command ‘gcc’ failed with exit status 1
running build_ext
skipping ‘LAP.c’ Cython extension (up-to-date)
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/align.py”, line 32, in
from cellprofiler.cpmath.filter import stretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/applythreshold.py”, line 24, in
from cellprofiler.modules.identify import Identify, O_BACKGROUND, O_ENTROPY
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/correctilluminationcalculate.py”, line 40, in
from cellprofiler.cpmath.filter import median_filter, convex_hull_transform
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/loadimages.py”, line 60, in
import bioformats.formatreader as formatreader
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/bioformats/init.py”, line 19, in
import cellprofiler.utilities.jutil as jutil
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/utilities/jutil.py”, line 159, in
import javabridge
ImportError: No module named javabridge
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/createwebpage.py”, line 28, in
from cellprofiler.modules.loadimages import C_FILE_NAME, C_PATH_NAME
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/loadimages.py”, line 99, in
import identify as I
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/crop.py”, line 45, in
from cellprofiler.cpmath.filter import stretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/displaydataonimage.py”, line 35, in
from cellprofiler.modules.identify import M_LOCATION_CENTER_X, M_LOCATION_CENTER_Y
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/editobjectsmanually.py”, line 47, in
import identify as I
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/enhanceedges.py”, line 30, in
from cellprofiler.cpmath.filter import laplacian_of_gaussian
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/enhanceorsuppressfeatures.py”, line 26, in
from cellprofiler.cpmath.filter import enhance_dark_holes, circular_hough
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/expandorshrinkobjects.py”, line 53, in
from cellprofiler.modules.identify import add_object_count_measurements
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/exporttodatabase.py”, line 75, in
import MySQLdb
File “build/bdist.linux-x86_64/egg/MySQLdb/init.py”, line 19, in
File “build/bdist.linux-x86_64/egg/_mysql.py”, line 7, in
File “build/bdist.linux-x86_64/egg/_mysql.py”, line 6, in bootstrap
ImportError: libmysqlclient_r.so.16: cannot open shared object file: No such file or directory
WARNING: MySQL could not be loaded.
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/exporttodatabase.py”, line 87, in
from identify import M_NUMBER_OBJECT_NUMBER
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/filterobjects.py”, line 42, in
from cellprofiler.modules.identify import FF_PARENT, FF_CHILDREN_COUNT
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identifydeadworms.py”, line 38, in
import identify as I
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identifyobjectsingrid.py”, line 61, in
from cellprofiler.modules.identify import add_object_count_measurements
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identifyobjectsmanually.py”, line 24, in
import identify as I
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identifyprimaryobjects.py”, line 132, in
import identify as cpmi
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identifysecondaryobjects.py”, line 81, in
import identify as cpmi
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identifytertiaryobjects.py”, line 61, in
import identify as cpmi
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/loadimages.py”, line 60, in
import bioformats.formatreader as formatreader
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/bioformats/init.py”, line 19, in
import cellprofiler.utilities.jutil as jutil
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/utilities/jutil.py”, line 159, in
import javabridge
ImportError: No module named javabridge
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/loadimages.py”, line 99, in
import identify as I
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/loadimages.py”, line 60, in
import bioformats.formatreader as formatreader
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/bioformats/init.py”, line 19, in
import cellprofiler.utilities.jutil as jutil
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/utilities/jutil.py”, line 159, in
import javabridge
ImportError: No module named javabridge
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/loadsingleimage.py”, line 50, in
from loadimages import LoadImagesImageProvider, C_SCALING, C_FILE_NAME
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/loadimages.py”, line 99, in
import identify as I
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/loaddata.py”, line 131, in
import identify as I
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/maskobjects.py”, line 25, in
import identify as I
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/measureimagequality.py”, line 74, in
import cellprofiler.cpmath.threshold as cpthresh
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/measureobjectintensity.py”, line 69, in
from cellprofiler.cpmath.filter import stretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/measureobjectradialdistribution.py”, line 62, in
from cellprofiler.cpmath.propagate import propagate
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/propagate.py”, line 50, in
import _propagate
ImportError: No module named _propagate
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/measureneurons.py”, line 48, in
import cellprofiler.cpmath.propagate as propagate
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/propagate.py”, line 50, in
import _propagate
ImportError: No module named _propagate
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/measuretexture.py”, line 119, in
from cellprofiler.cpmath.filter import gabor, stretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/relateobjects.py”, line 56, in
from cellprofiler.modules.identify import C_PARENT, C_CHILDREN
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/reassignobjectnumbers.py”, line 51, in
from cellprofiler.modules.identify import get_object_measurement_columns
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/rescaleintensity.py”, line 33, in
from cellprofiler.cpmath.filter import stretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/run_imagej.py”, line 21, in
import bioformats
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/bioformats/init.py”, line 19, in
import cellprofiler.utilities.jutil as jutil
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/utilities/jutil.py”, line 159, in
import javabridge
ImportError: No module named javabridge
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/saveimages.py”, line 40, in
from bioformats.formatreader import *
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/bioformats/init.py”, line 19, in
import cellprofiler.utilities.jutil as jutil
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/utilities/jutil.py”, line 159, in
import javabridge
ImportError: No module named javabridge
Failed to load bioformats. SaveImages will not be able to save movies.

Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/loadimages.py”, line 60, in
import bioformats.formatreader as formatreader
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/bioformats/init.py”, line 19, in
import cellprofiler.utilities.jutil as jutil
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/utilities/jutil.py”, line 159, in
import javabridge
ImportError: No module named javabridge
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/saveimages.py”, line 71, in
from cellprofiler.modules.loadimages import C_FILE_NAME, C_PATH_NAME
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/loadimages.py”, line 99, in
import identify as I
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/smooth.py”, line 30, in
from cellprofiler.cpmath.filter import median_filter, bilateral_filter, circular_average_filter
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/straightenworms.py”, line 46, in
from untangleworms import C_WORM, F_CONTROL_POINT_X, F_CONTROL_POINT_Y
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/untangleworms.py”, line 37, in
import identify as I
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/trackobjects.py”, line 93, in
import cellprofiler.cpmath.filter as cpfilter
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/init.py”, line 296, in add_module
m = import(mod, globals(), locals(), ‘all’], 0)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/untangleworms.py”, line 37, in
import identify as I
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
None
could not load these modules (‘cellprofiler.modules.align’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.applythreshold’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.correctilluminationcalculate’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.createwebpage’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.crop’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.displaydataonimage’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.editobjectsmanually’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.enhanceedges’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.enhanceorsuppressfeatures’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.expandorshrinkobjects’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.exporttodatabase’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.filterobjects’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.identifydeadworms’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.identifyobjectsingrid’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.identifyobjectsmanually’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.identifyprimaryobjects’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.identifysecondaryobjects’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.identifytertiaryobjects’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.loadimages’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.loadsingleimage’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.loaddata’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.maskobjects’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.measureimagequality’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.measureobjectintensity’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.measureobjectradialdistribution’, ImportError(‘No module named _propagate’,)), (‘cellprofiler.modules.measureneurons’, ImportError(‘No module named _propagate’,)), (‘cellprofiler.modules.measuretexture’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.relateobjects’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.reassignobjectnumbers’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.rescaleintensity’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.run_imagej’, ImportError(‘No module named javabridge’,)), (‘cellprofiler.modules.saveimages’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.smooth’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.straightenworms’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.trackobjects’, ImportError(‘No module named _filter’,)), (‘cellprofiler.modules.untangleworms’, ImportError(‘No module named _filter’,))]
Traceback (most recent call last):
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/loadimages.py”, line 60, in
import bioformats.formatreader as formatreader
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/bioformats/init.py”, line 19, in
import cellprofiler.utilities.jutil as jutil
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/utilities/jutil.py”, line 159, in
import javabridge
ImportError: No module named javabridge
Traceback (most recent call last):
File “CellProfiler.py”, line 224, in
show_splashbox = True)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cellprofilerapp.py”, line 16, in init
super(CellProfilerApp, self).init(*args, **kwargs)
File “/home/psi391/usr/CellProfiler2/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 7978, in init
self._BootstrapApp()
File “/home/psi391/usr/CellProfiler2/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 7552, in _BootstrapApp
return core.PyApp__BootstrapApp(*args, **kwargs)
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cellprofilerapp.py”, line 41, in OnInit
from cellprofiler.gui.cpframe import CPFrame
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/gui/cpframe.py”, line 31, in
from cellprofiler.gui.directoryview import DirectoryView
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/gui/directoryview.py”, line 28, in
from cellprofiler.modules.loadimages import LoadImagesImageProvider, is_image
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/loadimages.py”, line 99, in
import identify as I
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/modules/identify.py”, line 29, in
from cellprofiler.cpmath.threshold import TM_MANUAL, TM_MEASUREMENT, TM_METHODS, get_threshold
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/threshold.py”, line 28, in
from cellprofiler.cpmath.filter import stretch, unstretch
File “/hpc/home/psi391/usr/CellProfiler2/CellProfiler/cellprofiler/cpmath/filter.py”, line 19, in
import _filter
ImportError: No module named _filter
[/quote]

Thanks in advance,

Pradeep

Hi all & thanks Pradeep,
There was a problem with cellprofiler/cpmath/_propagate.pyx that was only apparent when using Cython 0.14. It’s fixed in SVN revision 10890. If you do an SVN update or otherwise check out the source, the problem should be solved.

–Lee