[ImageJ-devel] OpenCL plugin
Rick Lentz
rwlentz at wisc.edu
Sat Jan 15 11:59:13 CST 2011
Hi Pol,
Thank you for trying the draft Getting Started with ImageJ OpenCL plugins
tutorial. I made a few updates based on your feedback. Specifically, I
changed sobel.cl to use floats vs doubles (this should take care of the
error you ran into). I also corrected the line error to line 169 for the
update to the common.mk file.
I am not sure about the ./oclParticles error. I have a similar error
when running GL based apps - but my error is specific to tunneling X over
SSH. I am not sure if you are tunneling or not. Looks like a group at
Cambridge has a solid solution for GL over a SSH tunnel (see attached).
Michael Bien (author of JOCL) has filed a ticket for JOCL regarding
working around a bug identified in the Apple implementation of
OpenCL<https://jogamp.org/bugzilla/show_bug.cgi?id=458>.
Either the Windows 32/64 or Linux 32/64 implementations should work for
you. Let me know if you have any issues moving forward with your OpenCL /
CUDA ImageJ plugin.
Sincerely,
Rick Lentz
On Fri, Jan 14, 2011 at 3:19 AM, Pol kennel <pol.kennel at gmail.com> wrote:
> Rick,
>
> Your tutorial is so clear I dont understand why I get again an error with
> sobel example, but I dont want to abuse of your helpfulness.
>
> I really do exactly the same as your tutorial (except line 137 of
> common.mk that don't refers to a NVCCFLAGS so a replace line 169 and
> compil was ok).
>
> SobelExample error :
>
>
> com.jogamp.opencl.CLException$CLInvalidBinaryException:
> CLDevice [id: 139780449736272 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]
> at com.jogamp.opencl.CLException.newException(CLException.java:78)
> at com.jogamp.opencl.CLProgram.build(CLProgram.java:363)
> at com.jogamp.opencl.CLProgram.build(CLProgram.java:245)
> at demos.SobelFilterExample.init(SobelFilterExample.java:66)
> at demos.SobelFilterExample.runTest(SobelFilterExample.java:240)
> at demos.SobelFilterExample.main(SobelFilterExample.java:193)
>
> I also noted that some examples in
> /NVIDIA_GPU_Computing_SDK/OpenCL/bin/linux/release/ crash like
> ./oclParticles with error :
> X Error of failed request: BadWindow (invalid Window parameter)
> Major opcode of failed request: 138 (NV-GLX)
> Minor opcode of failed request: 4 ()
> Resource id in failed request: 0x4e00002
> Serial number of failed request: 49
> Current serial number in output stream: 49
>
> ./oclBandWidthTest is ok.
>
> If you have an idea, please let me know. Have a nice day.
>
> Regards,
> Pol
>
> 2011/1/14 Pol kennel <pol.kennel at gmail.com>
>
> Hi Rick,
>>
>> You perfectly understood what I need, this will lead to apply "heavy"
>> texture features extraction on large image aiming segmentation (the method
>> will be published soon).
>> I hope to have time in future to create a clear plugin for IJ that could
>> be shared with users and contribuate to IJ community :) So thanks for your
>> help, I'll try your last tutorial today, with hopes to get started with
>> OpenCL quick... I have a last (at least) question : are we constrained to
>> write gpu code in Cl ? could we use directly java codes ?
>>
>> Best regards,
>> Pol
>>
>> 2011/1/13 Rick Lentz <rwlentz at wisc.edu>
>>
>> Hi Pol,
>>>
>>> I am thinking that the material under http://www.imagejdev.org/OpenCLwas 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 - but 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
>>>>
>>>>
>>>
>>>
>>>
>>>
>> --
>> Pol Kennel
>>
>>
>
>
> --
> Pol Kennel
>
>
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