e-SRRF exception memory

[EsleyGit]

Hi, I have the following exception:

(Fiji Is Just) ImageJ 2.3.0/1.53q; Java 1.8.0_172 [64-bit]; Linux 5.13.0-39-generic; 1225MB of 2332MB (52%)

java.lang.NoClassDefFoundError: com/jogamp/opencl/CLException
at nanoj.liveSRRF.gui.LiveSRRF_optimised_.run(LiveSRRF_optimised_.java:155)
at ij.IJ.runUserPlugIn(IJ.java:243)
at ij.IJ.runPlugIn(IJ.java:204)
at ij.Executer.runCommand(Executer.java:152)
at ij.Executer.run(Executer.java:70)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.ClassNotFoundException: com.jogamp.opencl.CLException
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 6 more

Can somebody explain me what is the problem and how solve it?
Thank you a lot.

[ammendes]

A quick look at the eSRRF code points to a possible issue loading OpenCL. Are you sure you have a working installation?

[EsleyGit]

Hi Alfonso. How do I check the OpenCL instalallation? El lun, 2 may 2022 a la(s) 19:07, Afonso Mendes ***@***.***) escribió:

…

A quick look at the eSRRF code points to a possible issue loading OpenCL. Are you sure you have a working installation? — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AM7M3W2KA5DAPP5CYPUQOOLVIBU3RANCNFSM5TN2NSKQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[ammendes]

I believe you are running Linux. If so, can you open a new terminal and write "clinfo" without the quotes, then press Enter.
Let me know the output of that.

[EsleyGit]

Yes, you are right, I have linux. I made a screenshot. El mar, 3 may 2022 a la(s) 05:39, Afonso Mendes ***@***.***) escribió:

…

I believe you are running Linux. If so, can you open a new terminal and write "clinfo" without the quotes, then press Enter. Let me know the output of that. — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AM7M3W5US2YUFH53RL6PBYLVID67ZANCNFSM5TN2NSKQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[EsleyGit]

Hi, I run on another computer with linux. The result is: Number of platforms 0 El mar, 3 may 2022 a la(s) 07:42, Esley Torres ***@***.***) escribió:

…

Yes, you are right, I have linux. I made a screenshot. El mar, 3 may 2022 a la(s) 05:39, Afonso Mendes ***@***.***) escribió: > I believe you are running Linux. If so, can you open a new terminal and > write "clinfo" without the quotes, then press Enter. > Let me know the output of that. > > — > Reply to this email directly, view it on GitHub > <#3 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AM7M3W5US2YUFH53RL6PBYLVID67ZANCNFSM5TN2NSKQ> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> >

[ammendes]

You did not share the screenshot, I think.

For the "Number of platforms 0" error you might want to check this thread: https://stackoverflow.com/questions/54567402/clinfo-shows-number-of-platforms-0

Seems like some issue with your graphics drivers. Do you have an Nvidia or AMD GPU?

[EsleyGit]

I do not have a GPU. Can I still run e-SRRF? El mar, 3 may 2022 a la(s) 09:00, Afonso Mendes ***@***.***) escribió:

…

You did not share the screenshot, I think. For the "Number of platforms 0" error you might want to check this thread: https://stackoverflow.com/questions/54567402/clinfo-shows-number-of-platforms-0 Seems like some issue with your graphics drivers. Do you have an Nvidia or AMD GPU? — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AM7M3WY3D6S4VNJELUITTEDVIEWODANCNFSM5TN2NSKQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[ammendes]

I'm not sure, but in theory, yes. OpenCL should detect your CPU as a platform and allow it to be used. I've read multiple recent threads with this issue in Ubuntu and it seems related to your OpenCL SDK.

[EsleyGit]

So, how can I check the OpenCL SDK? El jue., 5 may. 2022 5:44, Afonso Mendes ***@***.***> escribió:

…

I'm not sure, but in theory, yes. OpenCL should detect your CPU as a platform and allow it to be used. I've read multiple recent threads with this issue in Ubuntu and it seems related to your OpenCL SDK. — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AM7M3W5XBVLZ3LSL6NLHTMDVIORBTANCNFSM5TN2NSKQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[HannahSHeil]

Hi @EsleyGit, you can find some instructions to set up openCL on linux correctly here: https://clij.github.io/clij2-docs/faq
I hope this helps.

[HannahSHeil]

Hi @EsleyGit, here you find some information on how to setup you CPU for OpenCL: https://www.intel.com/content/www/us/en/developer/articles/tool/opencl-drivers.html

[MorneArin]

Hi all, I have the same problem, may I ask for your advice how to fix it?

I have Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz 2.90 GHz with 32.0 GB RAM (31.3 GB usable)
My graphics card is NVIDIA GeForce RTX 2070 (driver details say that opencl32 and opencl64 are installed, see screenshot)
I tried to run eSRRF parameters sweep with the raw image (*.czi), tiff (attached as 8 Brady HFFs 7x SRRF C=0.zip), and CLIJ-converted tiff (the one you see on another screenshot).
The error is the same, tho:

(Fiji Is Just) ImageJ 2.9.0/1.53t; Java 1.8.0_322 [64-bit]; Windows 10 10.0; 213MB of 23963MB (<1%)
 
java.lang.NoClassDefFoundError: com/jogamp/opencl/CLMemory
	at nanoj.liveSRRF.gui.ParametersSweep_.run(ParametersSweep_.java:105)
	at ij.IJ.runUserPlugIn(IJ.java:237)
	at ij.IJ.runPlugIn(IJ.java:203)
	at ij.Executer.runCommand(Executer.java:152)
	at ij.Executer.run(Executer.java:70)
	at java.lang.Thread.run(Thread.java:750)
Caused by: java.lang.ClassNotFoundException: com.jogamp.opencl.CLMemory
	at java.net.URLClassLoader.findClass(URLClassLoader.java:387)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:419)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:352)
	... 6 more

Thanks in advance!

[HannahSHeil]

Hi, this could be also the incompatibility issue with CLIJ (see also #2). Could you please try with a Fiji without CLIJ?

[alexeybondar]

Hi, this could be also the incompatibility issue with CLIJ (see also #2). Could you please try with a Fiji without CLIJ?

Hi -
I'm facing a similar issue both on a Windows machine with AMD Radeon R9 200 / HD 7900 and a MacBook Pro with Intel Iris Plus Graphics 655. I don't have CLIJ on any of these machines. Both throw an apparent OpenCL problem at me. Have you figured out a reason for that and, ideally, a fix? I've tried looking at it briefly but it's beyond my capacity to figure out what exactly is wrong.

Thank you!

The error itself:
Windows:
(Fiji Is Just) ImageJ 2.14.0/1.54f; Java 1.8.0_322 [64-bit]; Windows 10 10.0; 227MB of 49043MB (<1%)

java.lang.NoClassDefFoundError: com/jogamp/opencl/CLMemory
at nanoj.liveSRRF.gui.ParametersSweep_.run(ParametersSweep_.java:105)
at ij.IJ.runUserPlugIn(IJ.java:244)
at ij.IJ.runPlugIn(IJ.java:210)
at ij.Executer.runCommand(Executer.java:152)
at ij.Executer.run(Executer.java:70)
at java.lang.Thread.run(Thread.java:750)
Caused by: java.lang.ClassNotFoundException: com.jogamp.opencl.CLMemory
at java.net.URLClassLoader.findClass(URLClassLoader.java:387)
at java.lang.ClassLoader.loadClass(ClassLoader.java:419)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:352)
... 6 more

Mac:
(Fiji Is Just) ImageJ 2.14.0/1.54f; Java 1.8.0_172 [64-bit]; Mac OS X 10.16; 150MB of 7902MB (1%)

java.lang.NoClassDefFoundError: com/jogamp/opencl/CLException
at nanoj.liveSRRF.gui.ParametersSweep_.run(ParametersSweep_.java:105)
at ij.IJ.runUserPlugIn(IJ.java:244)
at ij.IJ.runPlugIn(IJ.java:210)
at ij.Executer.runCommand(Executer.java:152)
at ij.Executer.run(Executer.java:70)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.ClassNotFoundException: com.jogamp.opencl.CLException
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 6 more

[HannahSHeil]

Hi, it is hard to pinpoint what exactly is going wrong with openCL. Usually updating everything (Fiji, openCL and JRE) has been a fix for some users.
On your windows machine it seems to be a memory issue, while on the MAC it is openCL itself that is not running.