Cell Profiler 2.1.0 crashes

Hi I recently upgraded to Cell Profiler 2.1.0, but I am not able to run any pipeline. My computer crashes every time. I am running 64 bit Windows 7 Professional with 32 GB RAM, Intel i7 with 8 cores. I tried to uninstall - reinstall Cell profiler, decrease number of workers down to 4, but nothing helps. Do you have some idea what could be wrong. I attach the pipeline I am currently using. Thanks a lot for your help. Cheers,
Milan
140129CPAnalysis.cpproj (135 KB)

Hi Milan,

I have a few questions:[ul][li]You mention that CellProfiler crashes in each instance, but not whether there is any error message when it does. Does an error dialog appear when it occurs? [list][]If so, could you press the “Copy to clipboard” button and post the contents to this thread? [/li][li]If there’s no error dialog (e.g., CellProfiler suddenly dies and the program terminates altogether), that helpful to know too.[/li][/ul][/:m][li]In any case, does the crash occur on the same set of images (i.e, same well and site)? If so, could you post the offending image channels? [/li][/list:u]
Thanks,
-Mark

Hi Mark,

there is no error message. Suddenly the computer freeze. It does happen in different sets of images and also for different pipelines.
I am now re-formatting my computer. I had two disks in RAID1, but apparently not in standard way. So I will try to install Cell Profiler
later on and will see if the problem remains or not.
Thanks a lot for your help.
Cheers,
Milan

Hi Mark,

So the problem was caused by RAID1 HDD settings. I removed it, re-installed and everything is working properly now.
Cheers,
Milan

Hi!

Since I did not find any threads about Windows 8.1, but indeed I wanted to use Cell Profiler 2.1, this topic would the most appropriate for my question. I’m currently using 2.0 and 2.1 versions also, because it is not easy to transfer already optimized pipelines form 2.0-to-2.1, but…

Recently I’ve tried to install Cellprofiler 2.1 onto my home computer. It has Windows 8.1 64bit version. On my laptop (2-cores, Windows 7, Enterprise, 32bit) I’ve created a pipeline which I wanted to run faster on a 4-core computer (postponed thanks for the multi-thread support in the new version).

Interestingly the installation goes flawlessly. However, when I wanted to open the program itself after a few window flashing (illastic core, and main logo) nothing happens. I was trying to make a screenshot about the phenomenon, but even that attempt I could not afford (weird). So, the main effect is that nothing happens following a double click on the desktop icon (the program is starting for a few seconds and after that all the windows are disappearing). No error messages, no nothing (even the event viewer is silent in the operation system).

Thanks for your help!

Would you be able to open a command prompt and try to run CellProfiler? You can follow the instructions here (pcsupport.about.com/od/windows-8 … dows-8.htm), switch to your installation directory for CellProfiler, most likely by typing (note the quotes):cd "c:\program files\cellprofiler" and then run CellProfiler by typing:cellprofiler >> output.txtThis will dump messages to a text file “output.txt” in the cellprofiler folder. You can then post the contents to this forum thread. If this file is empty, you can still take a screenshot of the terminal window, or copy it’s contents, and post then that (actually, it’s probably best to do both).

Regards,
-Mark


Hi Mark!

Many thanks for the fast answer. I did what you requested and in the output.txt the following text appeared:

“Load ilastik Core
stopping worker thread 0
stopping worker thread 1
stopping worker thread 2
stopping worker thread 3
stopping worker thread 4”

Nothing useful, but…

When I started cellprofiler from command-prompt at least two important error messages appeared. Both of the are java related, one is even ascii-related. Since I could not save these messages i made a printscreen about it. Weirdly the command prompt resolution is somehow remained close to 640x480, so sorry for the resolution of the image. I try to upload it to here.

Thanks for your help!

Hi,
Could you check this forum thread and see if it solves your problem? The problem appears to be identical.

Note that the proposed solutions are two-fold (one involves modifying the registry, the other with creating an account without non-standard characters), so try both if needed. For that user, the second did the trick.
-Mark

Also, were you using CellProfiler 2.1 on Windows 8 before upgrading to 8.1, or did you go straight to using CP on Win 8.1?
-Mark

Hi! I’ve never tried it except under windeows 7 32bit.

But…

I’ve finally managed to rename all user folder dependencies on my computer (trust me, it was not easy) and now I have a another error message. I paste it here:

C:\Windows>cd …

C:>cd program files

C:\Program Files>cd cellprofiler

C:\Program Files\CellProfiler>cellprofiler

A fatal error has been detected by the Java Runtime Environment:

EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x00007ff892d6caa2, pid=2544, t

id=2340

JRE version: 6.0_18-b07

Java VM: Java HotSpot™ 64-Bit Server VM (16.0-b13 mixed mode windows-amd64

)

Problematic frame:

C [ntdll.dll+0x9caa2]

An error report file with more information is saved as:

C:\Program Files\CellProfiler\hs_err_pid2544.log

If you would like to submit a bug report, please visit:

java.sun.com/webapps/bugreport/crash.jsp

C:\Program Files\CellProfiler>

Any idea? Should I reinstall Java as well?

I’d give it a try, though CP comes with Java bundled, so it shouldn’t matter. But if you do re-install and you still get a similar message, could you post the .log file that gets saved to the CellProfiler folder?
-Mark

Hi Mark!

Wasn’t helped. Here is the error message:

Load ilastik Core
stopping worker thread 0
stopping worker thread 1
stopping worker thread 2
stopping worker thread 3
stopping worker thread 4

A fatal error has been detected by the Java Runtime Environment:

EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x00007ff892d6caa2, pid=4476, tid=1020

JRE version: 6.0_18-b07

Java VM: Java HotSpot™ 64-Bit Server VM (16.0-b13 mixed mode windows-amd64 )

Problematic frame:

C [ntdll.dll+0x9caa2]

An error report file with more information is saved as:

C:\Program Files\CellProfiler\hs_err_pid4476.log

If you would like to submit a bug report, please visit:

java.sun.com/webapps/bugreport/crash.jsp

And I paste the content of the error.log-file: hs_err_pid4476.log

A fatal error has been detected by the Java Runtime Environment:

EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x00007ff892d6caa2, pid=4476, tid=1020

JRE version: 6.0_18-b07

Java VM: Java HotSpot™ 64-Bit Server VM (16.0-b13 mixed mode windows-amd64 )

Problematic frame:

C [ntdll.dll+0x9caa2]

If you would like to submit a bug report, please visit:

java.sun.com/webapps/bugreport/crash.jsp

--------------- T H R E A D ---------------

Current thread (0x000000000d42f000): JavaThread “Thread-0” daemon [_thread_in_Java, id=1020, stack(0x0000000000040000,0x0000000000140000)]

siginfo: ExceptionCode=0xc0000005, reading address 0xffffffffffffffff

Registers:
EAX=0x000000000012e001, EBX=0x0000000000000002, ECX=0x0000000000139058, EDX=0x0000000000138f68
ESP=0x0000000000138ef8, EBP=0x00007ff867f3f170, ESI=0x0000000000000023, EDI=0x0000000000000003
EIP=0x00007ff892d6caa2, EFLAGS=0x0000000000010202

Top of Stack: (sp=0x0000000000138ef8)
0x0000000000138ef8: 0000000000000202 00007ff892d19ad7
0x0000000000138f08: 00007ff867b86eae 0000000000000063
0x0000000000138f18: 0000000000000003 0000000000000008
0x0000000000138f28: 00007ff8923a1d36 000000000dee0d90
0x0000000000138f38: 0000000000139818 0000000000000063
0x0000000000138f48: 0000000000000510 0000000000000007
0x0000000000138f58: 00007ff8923a1d36 0000000000000510
0x0000000000138f68: 0000000000140000 0000000000000000
0x0000000000138f78: 000000000012e000 0000000000000510
0x0000000000138f88: 000000006dc45466 0000000000000003
0x0000000000138f98: 0000000000000007 000000001e560a98
0x0000000000138fa8: 0000000000000050 0000000000000023
0x0000000000138fb8: 000000006d9c9986 000000000d413610
0x0000000000138fc8: 0000000000000002 000000000e2b4a30
0x0000000000138fd8: 000000000e2faaf0 00007ff867f3f170
0x0000000000138fe8: 00000000001391d0 0000000000139200

Instructions: (pc=0x00007ff892d6caa2)
0x00007ff892d6ca92: d9 b9 00 01 00 00 c7 81 02 01 00 00 00 00 00 00
0x00007ff892d6caa2: 0f 29 b1 00 02 00 00 0f 29 b9 10 02 00 00 44 0f

Stack: [0x0000000000040000,0x0000000000140000], sp=0x0000000000138ef8, free space=3e30000000000000000k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C [ntdll.dll+0x9caa2]

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
v blob 0x00000000094b703f
j java.util.jar.Attributes.putValue(Ljava/lang/String;Ljava/lang/String;)Ljava/lang/String;+13
j java.util.jar.Attributes.read(Ljava/util/jar/Manifest$FastInputStream;**
0x000000000d422800 JavaThread “Low Memory Detector” daemon [_thread_blocked, id=4664, stack(0x000000000d9a0000,0x000000000daa0000)]
0x000000000d41e800 JavaThread “CompilerThread1” daemon [_thread_blocked, id=2460, stack(0x000000000d8a0000,0x000000000d9a0000)]
0x000000000d418800 JavaThread “CompilerThread0” daemon [_thread_blocked, id=5444, stack(0x000000000d7a0000,0x000000000d8a0000)]
0x000000000d415800 JavaThread “Attach Listener” daemon [_thread_blocked, id=5092, stack(0x000000000d6a0000,0x000000000d7a0000)]
0x000000000d410800 JavaThread “Signal Dispatcher” daemon [_thread_blocked, id=2596, stack(0x000000000d5a0000,0x000000000d6a0000)]
0x000000000943d000 JavaThread “Finalizer” daemon [_thread_blocked, id=1676, stack(0x000000000d2a0000,0x000000000d3a0000)]
0x0000000009439000 JavaThread “Reference Handler” daemon [_thread_blocked, id=5852, stack(0x000000000d1a0000,0x000000000d2a0000)]
0x0000000009356800 JavaThread “main” [_thread_in_native, id=5420, stack(0x0000000009250000,0x0000000009350000)]

Other Threads:
0x000000000942d000 VMThread [stack: 0x000000000d0a0000,0x000000000d1a0000] [id=1804]
0x000000000d427800 WatcherThread [stack: 0x000000000daa0000,0x000000000dba0000] [id=2664]

VM state:not at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread: None

Heap
PSYoungGen total 19136K, used 4952K 0x0000000038c50000, 0x000000003a1a0000, 0x00000000436f0000)
eden space 16448K, 30% used 0x0000000038c50000,0x0000000039126178,0x0000000039c60000)
from space 2688K, 0% used 0x0000000039f00000,0x0000000039f00000,0x000000003a1a0000)
to space 2688K, 0% used 0x0000000039c60000,0x0000000039c60000,0x0000000039f00000)
PSOldGen total 43712K, used 0K 0x00000000236f0000, 0x00000000261a0000, 0x0000000038c50000)
object space 43712K, 0% used 0x00000000236f0000,0x00000000236f0000,0x00000000261a0000)
PSPermGen total 21248K, used 3001K 0x000000001e2f0000, 0x000000001f7b0000, 0x00000000236f0000)
object space 21248K, 14% used 0x000000001e2f0000,0x000000001e5de438,0x000000001f7b0000)

Dynamic libraries:
0x0000000140000000 - 0x0000000140017000 C:\Program Files\CellProfiler\CellProfiler.exe
0x00007ff892cd0000 - 0x00007ff892e7a000 C:\Windows\SYSTEM32\ntdll.dll
0x00007ff892b30000 - 0x00007ff892c6a000 C:\Windows\system32\KERNEL32.DLL
0x00007ff890110000 - 0x00007ff89021f000 C:\Windows\system32\KERNELBASE.dll
0x00007ff88ec70000 - 0x00007ff88ecf8000 C:\Windows\system32\apphelp.dll
0x00007ff867b80000 - 0x00007ff867fff000 C:\Windows\AppPatch\AppPatch64\AcLayers.DLL
0x00007ff8923a0000 - 0x00007ff892447000 C:\Windows\system32\msvcrt.dll
0x00007ff890b60000 - 0x00007ff890cd1000 C:\Windows\system32\USER32.dll
0x00007ff892340000 - 0x00007ff892391000 C:\Windows\system32\SHLWAPI.dll
0x00007ff88d730000 - 0x00007ff88d733000 C:\Windows\SYSTEM32\sfc.dll
0x00007ff889110000 - 0x00007ff88918b000 C:\Windows\SYSTEM32\WINSPOOL.DRV
0x00007ff892750000 - 0x00007ff892895000 C:\Windows\system32\GDI32.dll
0x00007ff8928a0000 - 0x00007ff892a76000 C:\Windows\SYSTEM32\combase.dll
0x00007ff8925f0000 - 0x00007ff892726000 C:\Windows\system32\RPCRT4.dll
0x00007ff88a8b0000 - 0x00007ff88a8c0000 C:\Windows\SYSTEM32\sfc_os.DLL
0x00007ff8865f0000 - 0x00007ff886601000 C:\Windows\SYSTEM32\SortWindows61.dll
0x00007ff892c90000 - 0x00007ff892cc4000 C:\Windows\system32\IMM32.DLL
0x00007ff890a20000 - 0x00007ff890b59000 C:\Windows\system32\MSCTF.dll
0x0000000075bc0000 - 0x0000000075c63000 C:\Windows\WinSxS\amd64_microsoft.vc90.crt_1fc8b3b9a1e18e3b_9.0.30729.8387_none_08e793bfa83a89b5\MSVCR90.dll
0x000000001e000000 - 0x000000001e2e9000 C:\Program Files\CellProfiler\PYTHON27.DLL
0x00007ff8905b0000 - 0x00007ff890655000 C:\Windows\system32\ADVAPI32.dll
0x00007ff890f20000 - 0x00007ff892337000 C:\Windows\system32\SHELL32.dll
0x00007ff890550000 - 0x00007ff8905a7000 C:\Windows\SYSTEM32\sechost.dll
0x0000000180000000 - 0x0000000180015000 C:\Program Files\CellProfiler\h5py.h5.pyd
0x00000000021a0000 - 0x00000000023a2000 C:\Program Files\CellProfiler\hdf5dll.dll
0x00007ff885e80000 - 0x00007ff885e98000 C:\Program Files\CellProfiler\zlib1.dll
0x00007ff883cb0000 - 0x00007ff883cc7000 C:\Program Files\CellProfiler\sz.dll
0x0000000001eb0000 - 0x0000000001ec6000 C:\Program Files\CellProfiler\h5py.h5e.pyd
0x0000000000500000 - 0x000000000050c000 C:\Program Files\CellProfiler\h5py._conv.pyd
0x0000000000530000 - 0x000000000053d000 C:\Program Files\CellProfiler\h5py.h5r.pyd
0x0000000001ed0000 - 0x0000000001ee0000 C:\Program Files\CellProfiler\h5py.h5s.pyd
0x0000000001ee0000 - 0x0000000001f69000 C:\Program Files\CellProfiler\numpy.core.multiarray.pyd
0x00000000027b0000 - 0x0000000002807000 C:\Program Files\CellProfiler\numpy.core.umath.pyd
0x0000000001f70000 - 0x0000000001f89000 C:\Program Files\CellProfiler\numpy.core._sort.pyd
0x0000000002810000 - 0x0000000002c51000 C:\Program Files\CellProfiler\numpy.core._dotblas.pyd
0x0000000010000000 - 0x00000000100c1000 C:\Program Files\CellProfiler\libiomp5md.dll
0x0000000002c80000 - 0x0000000002cad000 C:\Program Files\CellProfiler\numpy.core.scalarmath.pyd
0x0000000002cb0000 - 0x0000000002cb8000 C:\Program Files\CellProfiler\numpy.lib._compiled_base.pyd
0x0000000003620000 - 0x0000000003f1b000 C:\Program Files\CellProfiler\numpy.linalg.lapack_lite.pyd
0x0000000002cc0000 - 0x0000000002cd4000 C:\Program Files\CellProfiler\numpy.fft.fftpack_lite.pyd
0x0000000004ef0000 - 0x0000000004f4a000 C:\Program Files\CellProfiler\numpy.random.mtrand.pyd
0x00007ff88f9d0000 - 0x00007ff88f9ee000 C:\Windows\SYSTEM32\CRYPTSP.dll
0x00007ff88f5a0000 - 0x00007ff88f5d5000 C:\Windows\system32\rsaenh.dll
0x00007ff88fc00000 - 0x00007ff88fc26000 C:\Windows\SYSTEM32\bcrypt.dll
0x00007ff88ff80000 - 0x00007ff88ff8a000 C:\Windows\SYSTEM32\CRYPTBASE.dll
0x00007ff88ff20000 - 0x00007ff88ff80000 C:\Windows\SYSTEM32\bcryptPrimitives.dll
0x000000001d1a0000 - 0x000000001d1bf000 C:\Program Files\CellProfiler_ctypes.pyd
0x00007ff890840000 - 0x00007ff8909b8000 C:\Windows\system32\ole32.dll
0x00007ff8924b0000 - 0x00007ff892567000 C:\Windows\system32\OLEAUT32.dll
0x0000000005230000 - 0x000000000523c000 C:\Program Files\CellProfiler\h5py.utils.pyd
0x0000000005240000 - 0x000000000524c000 C:\Program Files\CellProfiler\h5py.h5i.pyd
0x0000000005250000 - 0x0000000005260000 C:\Program Files\CellProfiler\h5py.h5f.pyd
0x0000000005260000 - 0x000000000527c000 C:\Program Files\CellProfiler\h5py.h5p.pyd
0x0000000005280000 - 0x00000000052b1000 C:\Program Files\CellProfiler\h5py.h5t.pyd
0x00000000052c0000 - 0x00000000052d0000 C:\Program Files\CellProfiler\h5py.h5d.pyd
0x00000000052d0000 - 0x00000000052d8000 C:\Program Files\CellProfiler\h5py._proxy.pyd
0x00000000052e0000 - 0x00000000052f3000 C:\Program Files\CellProfiler\h5py.h5g.pyd
0x0000000005300000 - 0x0000000005310000 C:\Program Files\CellProfiler\h5py.h5l.pyd
0x0000000005310000 - 0x0000000005323000 C:\Program Files\CellProfiler\h5py.h5a.pyd
0x0000000005330000 - 0x0000000005339000 C:\Program Files\CellProfiler\h5py.h5fd.pyd
0x0000000005340000 - 0x0000000005354000 C:\Program Files\CellProfiler\h5py.h5o.pyd
0x0000000005360000 - 0x0000000005369000 C:\Program Files\CellProfiler\h5py.h5z.pyd
0x0000000005370000 - 0x000000000537e000 C:\Program Files\CellProfiler_socket.pyd
0x00007ff8909c0000 - 0x00007ff890a18000 C:\Windows\system32\WS2_32.dll
0x00007ff892730000 - 0x00007ff892739000 C:\Windows\system32\NSI.dll
0x0000000005380000 - 0x00000000054a3000 C:\Program Files\CellProfiler_ssl.pyd
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0x00000000058b0000 - 0x00000000058b7000 C:\Program Files\CellProfiler\zmq.utils.initthreads.pyd
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0x00000000058f0000 - 0x00000000058fb000 C:\Program Files\CellProfiler\zmq.core.error.pyd
0x0000000005910000 - 0x0000000005922000 C:\Program Files\CellProfiler\zmq.core.message.pyd
0x0000000005940000 - 0x000000000594d000 C:\Program Files\CellProfiler\zmq.core.context.pyd
0x0000000005960000 - 0x000000000597f000 C:\Program Files\CellProfiler\zmq.core.socket.pyd
0x0000000005990000 - 0x000000000599b000 C:\Program Files\CellProfiler_jsonlib.pyd
0x00000000059a0000 - 0x00000000059b0000 C:\Program Files\CellProfiler\zmq.core.poll.pyd
0x00000000059c0000 - 0x00000000059ca000 C:\Program Files\CellProfiler\zmq.core.stopwatch.pyd
0x00000000059e0000 - 0x00000000059ea000 C:\Program Files\CellProfiler\zmq.core.version.pyd
0x0000000005a00000 - 0x0000000005a0a000 C:\Program Files\CellProfiler\zmq.core.device.pyd
0x0000000005a20000 - 0x0000000005a2b000 C:\Program Files\CellProfiler_multiprocessing.pyd
0x0000000005a30000 - 0x0000000005a3d000 C:\Program Files\CellProfiler\zmq.devices.monitoredqueue.pyd
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0x0000000005d00000 - 0x0000000005d29000 C:\Program Files\CellProfiler\wxbase28u_net_vc.dll
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0x000000006d800000 - 0x000000006d80e000 C:\Program Files\CellProfiler\jre\bin\verify.dll
0x000000006d450000 - 0x000000006d477000 C:\Program Files\CellProfiler\jre\bin\java.dll
0x000000006d3b0000 - 0x000000006d3ba000 C:\Program Files\CellProfiler\jre\bin\hpi.dll
0x00007ff892740000 - 0x00007ff892747000 C:\Windows\system32\PSAPI.DLL
0x000000006d850000 - 0x000000006d862000 C:\Program Files\CellProfiler\jre\bin\zip.dll

VM Arguments:
jvm_args: -Dloci.bioformats.loaded=true -Xmx512m -Dplugins.dir=C:\Users\Balazs\AppData\Roaming\CellProfiler\ijplugins -Djava.util.prefs.PreferencesFactory=org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory
java_command:
Launcher Type: generic

Environment Variables:
PATH=C:\Program Files\CellProfiler\library.zip\numpy;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0;C:\Program Files (x86)\ATI Technologies\ATI.ACE\Core-Static;C:\Program Files\CellProfiler\jre\bin\server;C:\Program Files\CellProfiler\jre\bin
USERNAME=Balazs
OS=Windows_NT
PROCESSOR_IDENTIFIER=Intel64 Family 6 Model 23 Stepping 10, GenuineIntel

--------------- S Y S T E M ---------------

OS: Windows 7 Build 7600

CPU:total 4 (4 cores per cpu, 1 threads per core) family 6 model 23 stepping 10, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1

Memory: 4k page, physical 4192488k(2169964k free), swap 6289912k(3333248k free)

vm_info: Java HotSpot™ 64-Bit Server VM (16.0-b13) for windows-amd64 JRE (1.6.0_18-b07), built on Dec 17 2009 13:24:11 by “java_re” with MS VC++ 8.0 (VS2005)

time: Fri May 02 10:03:08 2014
elapsed time: 3 seconds

Thank you!**

Was this error produced using Win 8.1? I ask since I see at the bottom of the log contents a line saying the the OS is “Windows 7 Build 7600”.
-Mark

Also, our lead software engineer suggests the following:

Yes it is windows 8.1. Rather strange, that windows 7 is written in the log…OK! I’ll try what you have advised.