[ImageJ-devel] Fwd: OpenCL plugin
Rick Lentz
rwlentz at wisc.edu
Thu Jan 13 13:00:20 CST 2011
Hi Pol,
I am thinking that the material under http://www.imagejdev.org/OpenCL was
not going to be as useful for you as a getting started tutorial. I have
removed the publication related material from our website. I created a Getting
Started with OpenCL in ImageJ
Tutorial<https://docs.google.com/document/d/12aiL7urwcve7Mi-YyuOtAVlTZ5P6outcay75YiQlqyQ/edit?hl=en>
with
the goal of helping ImageJ users get started quickly with OpenCL.
Back to your issues, for the research publication I compiled the jogamp
files. For your application, I do not think you need to do this. The
compilation steps listed were specific to Ubuntu 9.10 and NVidia 3.1. If I
am understanding your ImageJ need correctly, I think you are looking to run
a few Java examples that help you get into writing OpenCL plugins for
ImageJ. I hope the attached draft copy of the tutorial will help you get
there quickly.
Please let me know if you any troubles with the tutorial - and have any
feedback regarding the tutorial.
Best Regards,
Rick Lentz
Hi Pol,
Can you do a fresh pull from our repository - You should not have to build
these unless you really want to.
You can download the needed components directly from:
http://jogamp.org/deployment/webstart/
I have also updated the ImageJ plugin demo source to include the most
recent Jogamp OpenCL binaries and native libs.
Sincerely,
Rick
On Thu, Jan 13, 2011 at 9:55 AM, Pol kennel <pol.kennel at gmail.com> wrote:
> In fact my *jocl* building also crash during Junit tests, with error
> stacks like :
>
> [junit] Testcase: createContextTest(com.jogamp.opencl.gl.CLGLTest): Caused
> an ERROR
> [junit] test timed out after 5000 milliseconds
> [junit] java.lang.Exception: test timed out after 5000 milliseconds
> [junit] at java.lang.Object.wait(Native Method)
> [junit] at java.lang.Object.wait(Object.java:485)
> [junit] at
> com.jogamp.opengl.impl.SharedResourceRunner.doAndWait(SharedResourceRunner.java:152)
> [junit] at
> com.jogamp.opengl.impl.SharedResourceRunner.getOrCreateShared(SharedResourceRunner.java:100)
> [junit] at
> com.jogamp.opengl.impl.x11.glx.X11GLXDrawableFactory.getOrCreateSharedContextImpl(X11GLXDrawableFactory.java:253)
> [junit] at
> javax.media.opengl.GLDrawableFactory.getOrCreateSharedContext(GLDrawableFactory.java:275)
> [junit] at
> javax.media.opengl.GLDrawableFactory.getIsSharedContextAvailable(GLDrawableFactory.java:250)
> [junit] at
> javax.media.opengl.GLProfile.initProfilesForDeviceImpl(GLProfile.java:1251)
> [junit] at
> javax.media.opengl.GLProfile.initProfilesForDevice(GLProfile.java:1224)
> [junit] at
> javax.media.opengl.GLProfile.initProfilesForDefaultDevices(GLProfile.java:1192)
> [junit] at javax.media.opengl.GLProfile.access$000(GLProfile.java:66)
> [junit] at javax.media.opengl.GLProfile$1.run(GLProfile.java:112)
> [junit] at java.security.AccessController.doPrivileged(Native Method)
> [junit] at
> javax.media.opengl.GLProfile.initSingleton(GLProfile.java:110)
> [junit] at com.jogamp.opencl.gl.CLGLTest.init(CLGLTest.java:70)
> [junit] at
> com.jogamp.opencl.gl.CLGLTest.createContextTest(CLGLTest.java:102)
>
> So there is another problem I don t identify...
>
> 2011/1/13 Pol kennel <pol.kennel at gmail.com>
>
> Hi Rick,
>>
>> Thank a lot for your detailed answers an to pay attention to my problems !
>>
>> I finally resolved my problem with the OpenGL lib with your previous mail
>> : a link was not set correctly to the libGL.so file. I now have the same
>> output with *ldd /usr/lib/libGL.so *command. So I build correctly C and
>> OpenCL project, demos work well.
>>
>> I also build correctly *gluegen*, *jogl*, *jocl* and *jocl-demos*projects (note that lines "git clone
>> http://github.com/sgothel/gluegen.git gluegen" and "git clone
>> http://github.com/sgothel/jogl-demos.git jogl-demos" are missing on the
>> http://www.imagejdev.org/setting-jocl-jogl-and-gluegen page of your
>> tutorial).
>>
>> However, I stoped in building *joal* and *jogl-demos. *You probably omit
>> to precise the building of the *joal *project (but it could be intended
>> ?) ; when building *joal* with *ant* in the */joal/make/* directory I get
>> an error :
>> "*/home/pol/joal/make/build.xml:369: taskdef class
>> com.sun.gluegen.ant.GlueGenTask cannot be found*
>> * using the classloader
>> AntClassLoader[/home/pol/gluegen/build/gluegen.jar:/home/pol/gluegen/build/antlr.jar:/home/pol/gluegen/make/lib/antlr.jar]
>> *"
>> (gluegen.jar and antlr.jar still in the right directory, is there
>> classpath to set for gluegen ?). In the *joal* readme file, I found that
>> OpenAL lib are need, so i downloaded libopenal-dev/openal1 packets from
>> synaptic, and follow instructions saying to copy gluegen.properties and
>> joal.properties and jogl.properties into home directory but don't know how
>> to set correctly properties into this files.
>> *joal* building stills crash.
>>
>> Regarding to *jogl-demos *when* *building with* ant *in *
>> ~/jogl-demos/make/* i get 27 errors like :
>> [javac] Compiling 169 source files to /home/pol/jogl-demos/build/classes
>> [javac] /home/pol/jogl-demos/src/demos/applets/GearsJOALApplet.java:11:
>> package com.jogamp.openal.util does not exist
>> [javac] import com.jogamp.openal.util.ALut;"
>> [...]
>> I suppose it s due to joal, OpenAL again....
>>
>> (How) Did you install it ?
>>
>>
>> On the other side, i have update the decon project from svn.
>> When running *SobelFilterExample.java *i get :
>>
>> *Retrieving test image... *
>> *Starting iteration... 0*
>> *Local work size dimensions are max array size of*
>> *unavailable functions: [clCreateEventFromGLsyncKHR,
>> clIcdGetPlatformIDsKHR]*
>> *Discovered NVIDIA CUDA*
>> *com.jogamp.opencl.CLException$CLInvalidBinaryException: *
>> *CLDevice [id: 140626625730048 name: GeForce GTS 240 type: GPU profile:
>> FULL_PROFILE] build log:*
>> *ptxas application ptx input, line 104; error : Instruction 'cvt'
>> requires SM 1.3 or higher, or map_f64_to_f32 directive*
>> *ptxas application ptx input, line 105; error : Instruction 'cvt'
>> requires SM 1.3 or higher, or map_f64_to_f32 directive*
>> *ptxas application ptx input, line 106; error : Instruction 'mul'
>> requires SM 1.3 or higher, or map_f64_to_f32 directive*
>> *ptxas application ptx input, line 107; error : Instruction 'mul'
>> requires SM 1.3 or higher, or map_f64_to_f32 directive*
>> *ptxas application ptx input, line 108; error : Instruction 'add'
>> requires SM 1.3 or higher, or map_f64_to_f32 directive*
>> *ptxas application ptx input, line 109; error : Instruction 'sqrt'
>> requires SM 1.3 or higher, or map_f64_to_f32 directive*
>> *ptxas application ptx input, line 110; error : Instruction 'cvt'
>> requires SM 1.3 or higher, or map_f64_to_f32 directive*
>> *ptxas fatal : Ptx assembly aborted due to errors*
>> *error : Ptx compilation failed: gpu='sm_11', device
>> code='cuModuleLoadDataEx_4'*
>> *: Considering profile 'compute_11' for gpu='sm_11' in
>> 'cuModuleLoadDataEx_4'*
>> *: Retrieving binary for 'cuModuleLoadDataEx_4', for gpu='sm_11', usage
>> mode=' '*
>> *: Considering profile 'compute_11' for gpu='sm_11' in
>> 'cuModuleLoadDataEx_4'*
>> *: Control flags for 'cuModuleLoadDataEx_4' disable search path*
>> *: Ptx binary found for 'cuModuleLoadDataEx_4', architecture='compute_11'
>> *
>> *: Ptx compilation for 'cuModuleLoadDataEx_4', for gpu='sm_11', ocg
>> options=' '*
>> *ptxas application ptx input, line 104; warning : Double is not
>> supported. Demoting to float*
>> *error: CL_INVALID_BINARY (man page:
>> http://www.khronos.org/opencl/sdk/1.1/docs/man/xhtml/errors.html)*
>> * at com.jogamp.opencl.CLException.newException(CLException.java:49)*
>> * at com.jogamp.opencl.CLProgram.build(CLProgram.java:335)*
>> * at com.jogamp.opencl.CLProgram.build(CLProgram.java:174)*
>> * at publication.SobelFilterExample.<init>(SobelFilterExample.java:66)*
>> * at publication.SobelFilterExample.runTest(SobelFilterExample.java:204)*
>> * at publication.SobelFilterExample.main(SobelFilterExample.java:155)*
>>
>> So I suppose it s due to miss installation of JOAL.
>>
>>
>> I'll be so thankful if you can get me out of this deadlock.... I can
>> already see the light far away :)
>>
>> Best regards,
>>
>>
>> Pol
>>
>>
>>
>> PS : I'm often connected on google chat so if you prefer answer me online
>> please let me know you gmail address.
>>
>>
>>
>> 2011/1/12 Rick Lentz <rwlentz at wisc.edu>
>>
>> Hi Pol,
>>>
>>> Regarding your first question it is likely that the linker is missing a
>>> reference to OpenGL. My instructions were for a prior major release of
>>> Ubuntu as well as a prior minor release of NVidia's CUDA SDK. I have
>>> updated the setup instructions to reflect the current versions as well as
>>> tested against 64bit Mac and Linux OSs.
>>>
>>> With regard to your specific problem, many of NVidia's examples include
>>> use of OpenGL. NVidia's documentation indicates that libgl.so is referenced
>>> via static link to appear to be located in /usr/lib/libgl.so (per
>>> http://developer.download.nvidia.com/compute/cuda/3_2_prod/drivers/docs/README_Linux.txtunder Chapter 5, Listing of Installed Components, 4th bullet). Chapter 5 of
>>> NVidia's documentation goes on to describe the linking process that happens
>>> when installing the developer drivers. Perhaps this linking did not happen
>>> when you installed the NVidia development drivers for Linux. Did you get an
>>> error during installation of the developer drivers reporting something in
>>> this regard? Chapter 5 concludes on how to check a Linux dynamic library
>>> using the command line tool ldd. In this case, ldd /usr/lib/libGL.so
>>>
>>> Here is the output I get when running ldd /usr/lib/libGL.so
>>>
>>> ldd /usr/lib/libGL.so
>>> linux-vdso.so.1 => (0x00007ffff33e6000)
>>> libnvidia-tls.so.260.19.14 => /usr/lib/tls/libnvidia-tls.so.260.19.14
>>> (0x00007fc82b46b000)
>>> libnvidia-glcore.so.260.19.14 => /usr/lib/libnvidia-glcore.so.260.19.14
>>> (0x00007fc82987f000)
>>> libX11.so.6 => /usr/lib/libX11.so.6 (0x00007fc829549000)
>>> libXext.so.6 => /usr/lib/libXext.so.6 (0x00007fc829337000)
>>> libc.so.6 => /lib/libc.so.6 (0x00007fc828f93000)
>>> libdl.so.2 => /lib/libdl.so.2 (0x00007fc828d8f000)
>>> libm.so.6 => /lib/libm.so.6 (0x00007fc828b0c000)
>>> libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00007fc8288ef000)
>>> /lib64/ld-linux-x86-64.so.2 (0x00007fc82b974000)
>>> libXau.so.6 => /usr/lib/libXau.so.6 (0x00007fc8286eb000)
>>> libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00007fc8284e5000)
>>>
>>>
>>> If the libGL.so file is present and linked property, you can double check
>>> for inclusion of libGL.so path by ensuring its path in your bash profile
>>> under the variable LD_LIBRARY_PATH. NVidia asks for the installer to add
>>> these additions in the Linux install documents. Here is the line in my
>>> .bashrc file that allows the linker to find libGL.so (specifically the
>>> ":/usr/lib" portion of this line):
>>>
>>> export
>>> LD_LIBRARY_PATH="/usr/lib:/usr/local/cuda/lib64:/usr/local/cuda/lib:/usr/lib32:/usr/local/lib"
>>>
>>> I also had issues compiling the most recent version of NVidia's C
>>> samples. I reflected a work around in the updated web documents (see the
>>> bottom of: http://www.imagejdev.org/setting-host-machine ).
>>>
>>> Please let me know if you have any more questions or difficulties with
>>> the ImageJ OpenCL plugin examples.
>>>
>>> Sincerely,
>>>
>>> Rick Lentz
>>>
>>>
>>> On Tue, Jan 11, 2011 at 4:20 AM, Pol kennel <pol.kennel at gmail.com>wrote:
>>>
>>>> Hello,
>>>>
>>>> I am a PhD student working on image segmentation by texture analysis
>>>> with an application on remote sensing images (Montpellier, France). So i
>>>> have to process very large images (e.g. 15000*8000).
>>>> All methods I developed are formed as plugin under ImageJ API that I
>>>> really like, but not yet applicable on this sort of image.
>>>> Recently, I tough to use finally my graphic card (Nvidia GTS240) which I
>>>> think will help me a lot in my process. So after several search on the web,
>>>> I found this <http://imagejdev.org/plugins/opencl-plugin> (OpenCL
>>>> plugin you wrote) great ! it's precisely what i need.
>>>>
>>>> So I decided to follow your tutorial to setup the environment but met
>>>> some problems... :
>>>>
>>>> 1. When launching makefile in "~/NVIDIA_GPU_Computing_SDK/C/ " and
>>>> "~/NVIDIA_GPU_Computing_SDK/OpenCL" I had following error "/usr/bin/ld:
>>>> cannot find -lGL". Plus, I dont have the same demo files, maybe because of
>>>> version ? (cudatoolkit_3.2.16_linux_64, gpucomputingsdk_3.2.16 and
>>>> devdriver_3.2_linux_64_260.19.26 on Ubuntu 10.10). On the other side demos I
>>>> have work perfectly (ooclDCT8x8, oclHistogram,...)
>>>> 2. *Main problem is that the repository you indicate to get the
>>>> example project (http://www.loci.wisc.edu/svn/decon) doesn't work...
>>>> *"
>>>> http://dev.loci.wisc.edu/svn/software/branches/maven/projects/opencl-decon"
>>>> repository works well. Is is the same ?
>>>>
>>>>
>>>> Thanks a lot if you find time to answer me (and sorry for my english).
>>>>
>>>> And thanks you for work you are doing on ImageJ.
>>>>
>>>> Best regards,
>>>> *
>>>> *
>>>> --
>>>> Pol Kennel
>>>>
>>>>
>>>
>>
>>
>> --
>> Pol Kennel
>>
>>
>
>
> --
> Pol Kennel
>
>
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