henriqueslab / nanoj-srrf Goto Github PK

I'm having trouble getting NanoJ SRRF to process my files. It doesn't seem to be able to start OpenCL and throws an error. It doesn't switch over to Java and the CPU though. It just stops. A bit frustrating because the initial (CPU-based) results were very promising before I updated everything and started trying to get the GPU to work.

Here is an example of the (not so informative) error:

sep 01, 2018 6:19:05 EM com.amd.aparapi.internal.kernel.KernelRunner executeOpenCL
WARNING: ### CL exec seems to have failed. Trying to revert to Java ###

The data is a small (cropped) 100 frame 16 bit stack from a Yokogawa spinning disk confocal. It is as close as I can make it to the sample data:
https://bitbucket.org/rhenriqueslab/nanoj-srrf/downloads/Anti-Tubulin-Alexa647%20Ultra-high%20density%20data.tif.zip
The sample data works - my data does not. I have attached a cropped but otherwise unmodified file. This particular example fades badly, but that shouldn't have anything to do with the error.

I would be most grateful for any suggestions as I have done everything I can think of.
Thanks!
AL

Sys info:
Win10 64 bit build 17134
Nvidia GeForce GTX 970 - most recent drivers 399.07, DirectX 12
Java - most recent release, version 8 update 181 (build 1.8.0_181-b13)
Fiji/ImageJ - most recent update 1.52e
NanoJ - most recent release, 2.0RC1
SRRF - most recent release 1.13stable1

Mandelbrot OpenCL test:
NVIDIA Corporation_GPU
Identity of device used: - NVIDIA Corporation_GPU
global:589824 local:(derived)1024
Execution mode=GPU
Executed at 535.0FPS
Best Device: - NVIDIA Corporation_GPU

Benchmark results:
ImageJ 512 512 610 3 3 57.908
NanoJ-JTP 512 512 610 3 3 51.583
NanoJ-GPU 512 512 610 3 3 132.019
ImageJ 512 512 610 3 3 59.008
NanoJ-JTP 512 512 610 3 3 53.319
NanoJ-GPU 512 512 610 3 3 184.720
ImageJ 512 512 615 3 3 58.598
NanoJ-JTP 512 512 615 3 3 65.116
NanoJ-GPU 512 512 615 3 3 181.586
small_stack.zip

Fiji crashes when I attempt to run peak localization in NanoJ Core.

The following link to 'tutorials on how to install, run and compile NanoJ-SRRF' as provided in 'readme' is not working. Gives a 404 error " That link has no power here!!". Is this resource available elswhere? Any help will be most appreciated.

https://bitbucket.org/rhenriqueslab/nanoj-srrf/wiki/Getting%20set%20up%20with%20SRRF

Thank You

Hi to HenriquesLab,

I recently watched a webinar about AI in microscopy, and saw your work with SRRF.
Amazed with the results, I wanted to see for myself how does it work with my data.

But, unfortunately as the subject says, Fiji crashes instantly upon starting the plugin.

I am sending you the error report.

This happens with latest Fiji version with Imagej 1.53f51 and Java 1.8.0_172(64-bit) runtime on Windows 10.

Hope you can address this and make it working again ; )

Best
Marko

hs_err_pid29672.log

Hello, Could you share with us the source code for running SRRF simulations? We want to replicate the simulation results in Figure 2 and Supplementary Note 2. Then, we are hoping to run the simulation pipeline on 2D coordinate arrays. Thanks for this great tool!

Apologies in advance, my coding experience is virtually nonexistent, but I can no longer get SRRF to run.

The error:

EM com.amd.aparapi.internal.kernel.KernelRunner executeOpenCL
WARNING: ### CL exec seems to have failed. Trying to revert to Java ###

The last time I used SRRF, I was able to blaze through a .nji file in under 30 seconds, but now it's claiming to require an hour at 0 FPS. Based on my reading, it sounds like the program is no longer able to utilize my GPU? This is frustrating because this plug-in was giving us great data with zero issues prior to now!

Since I last used it about a month ago, I believe there have been updates to FIJI, Java, and my NVIDIA drivers. As a habit I updated these all automatically, but now I can't find old files to roll back to and prove it's the new drivers causing issues. Regarding the NVIDIA drivers, I have tried both the gaming and studio drivers to no avail.

My computer info:

Operating System: Windows 10 Home 64-bit
Card name: NVIDIA GeForce GTX 1060
Card driver: 441.20 (11/12/2019)
Java Version: 8 Update 231
FIJI Version: 1.52r
SRRF Version: 1.14 Stable 1

Any ideas? This really is an amazing plug-in that our lab would hate to not be able to use.

Edit: Update

I have also checked OpenCL in ImageJ and tested that OpenCL is able to detect my graphics card as successfully test it with Mandelbrot. So ImageJ and OpenCL can recognize my graphics card but for some reason SRRF can no longer use OpenCL?

NanoJ crashes Fiji when I try to process a sample or even access the OpenCL settings. I have this issue on both my laptop (Lenovo T460, Windows 10) and my desktop:
--------------- S Y S T E M ---------------

OS: Windows 10.0 , 64 bit Build 17763 (10.0.17763.379)

CPU:total 12 (initial active 12) (12 cores per cpu, 1 threads per core) family 23 model 8 stepping 2, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul, mmxext, 3dnowpref, lzcnt, sse4a, tsc, tscinvbit, tscinv, bmi1

Memory: 4k page, physical 16730068k(9182640k free), swap 19770980k(5874876k free)

vm_info: Java HotSpot(TM) 64-Bit Server VM (25.172-b11) for windows-amd64 JRE (1.8.0_172-b11), built on Mar 28 2018 21:21:52 by "java_re" with MS VC++ 10.0 (VS2010)
Crash report below:

hs_err_pid17792.log

All drivers are up to date, as is Windows 10.

This page says "Step 1: Open Fiji, go to the ‘Help’ menu and then ‘Update Fiji’". I believe this (correct) menu item is now labelled "Update ..." and there is another (wrong) menu item called "Update ImageJ", which I was accidentally clicking.