CUDA natives error for HiCCUPS

[arasim...@gmail.com]

Hi, 

I am trying to run HICCUPS on my hic file on my laptop. I just installed CUDA from the webpage by downloading the dmg file and installing it according to the instructions (architecture: "x86_64", version ="10.12").

However, when I try to run the script with default options just to try, I get an error message (please see below).  It looks like I need to install the native libraries. However, I have no idea how to install the native libraries from the page you provided (http://www.jcuda.org/downloads/downloads.html), as there are many options and different ways to install them.  I am running it on a mac El Capitan v10.11.6.

Thanks!

Rasim

Error message:

laptop$ java -jar ~/juicer/juicer_tools_0.7.5.jar hiccups mysample.hic ./hiccups_results/ --ignore_sparsity

Reading file: mysample.hic

HiC file version: 8

No valid configurations specified, using default settings

Warning Hi-C map is too sparse to find many loops via HiCCUPS.

Default settings for 5kb, 10kb, and 25kb being used

Running HiCCUPS for resolution 5000

Exception in thread "main" java.lang.UnsatisfiedLinkError: Could not load the native library.

Error while loading native library "JCudaDriver-apple-x86_64" with base name "JCudaDriver"

Operating system name: Mac OS X

Architecture         : x86_64

Architecture bit size: 64

Stack trace from the attempt to load the library as a resource:

java.lang.NullPointerException: No resource found with name '/lib/libJCudaDriver-apple-x86_64.dylib'

at jcuda.LibUtils.loadLibraryResource(LibUtils.java:149)

at jcuda.LibUtils.loadLibrary(LibUtils.java:83)

at jcuda.driver.JCudaDriver.<clinit>(JCudaDriver.java:269)

at jcuda.utils.KernelLauncher.initialize(KernelLauncher.java:603)

at jcuda.utils.KernelLauncher.<init>(KernelLauncher.java:586)

at jcuda.utils.KernelLauncher.create(KernelLauncher.java:393)

at jcuda.utils.KernelLauncher.create(KernelLauncher.java:321)

at jcuda.utils.KernelLauncher.compile(KernelLauncher.java:270)

at juicebox.tools.utils.juicer.hiccups.GPUController.<init>(GPUController.java:55)

at juicebox.tools.clt.juicer.HiCCUPS.runHiccupsProcessing(HiCCUPS.java:416)

at juicebox.tools.clt.juicer.HiCCUPS.run(HiCCUPS.java:361)

at juicebox.tools.HiCTools.main(HiCTools.java:86)

Stack trace from the attempt to load the library as a file:

java.lang.UnsatisfiedLinkError: no JCudaDriver-apple-x86_64 in java.library.path

at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1867)

at java.lang.Runtime.loadLibrary0(Runtime.java:870)

at java.lang.System.loadLibrary(System.java:1122)

at jcuda.LibUtils.loadLibrary(LibUtils.java:94)

at jcuda.driver.JCudaDriver.<clinit>(JCudaDriver.java:269)

at jcuda.utils.KernelLauncher.initialize(KernelLauncher.java:603)

at jcuda.utils.KernelLauncher.<init>(KernelLauncher.java:586)

at jcuda.utils.KernelLauncher.create(KernelLauncher.java:393)

at jcuda.utils.KernelLauncher.create(KernelLauncher.java:321)

at jcuda.utils.KernelLauncher.compile(KernelLauncher.java:270)

at juicebox.tools.utils.juicer.hiccups.GPUController.<init>(GPUController.java:55)

at juicebox.tools.clt.juicer.HiCCUPS.runHiccupsProcessing(HiCCUPS.java:416)

at juicebox.tools.clt.juicer.HiCCUPS.run(HiCCUPS.java:361)

at juicebox.tools.HiCTools.main(HiCTools.java:86)

at jcuda.LibUtils.loadLibrary(LibUtils.java:128)

at jcuda.driver.JCudaDriver.<clinit>(JCudaDriver.java:269)

at jcuda.utils.KernelLauncher.initialize(KernelLauncher.java:603)

at jcuda.utils.KernelLauncher.<init>(KernelLauncher.java:586)

at jcuda.utils.KernelLauncher.create(KernelLauncher.java:393)

at jcuda.utils.KernelLauncher.create(KernelLauncher.java:321)

at jcuda.utils.KernelLauncher.compile(KernelLauncher.java:270)

at juicebox.tools.utils.juicer.hiccups.GPUController.<init>(GPUController.java:55)

at juicebox.tools.clt.juicer.HiCCUPS.runHiccupsProcessing(HiCCUPS.java:416)

at juicebox.tools.clt.juicer.HiCCUPS.run(HiCCUPS.java:361)

at juicebox.tools.HiCTools.main(HiCTools.java:86)"

[Neva Durand]

Hello,

Please try the latest jar - the natives libraries for Apple should be included in that and should work.  (Version 1.7.6).

https://github.com/theaidenlab/juicer/wiki/Download

Best

Neva

[Muhammad Saad Shamim]

We forgot to update this thread. 

Rasim figured out that his computer did not have an NVIDIA GPU, but rather an Intel Iris GPU.

And HiCCUPS requires CUDA, which requires NVIDIA GPUs.

- Muhammad Saad Shamim

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[Muhammad Shamim]

In the latest jar, we have added the ability to run a CPU version of HiCCUPS. 

You can read more about it here: https://github.com/aidenlab/juicer/wiki/CPU-HiCCUPS 

Please let us know if you have further questions.

Best,

- Muhammad S Shamim

On Tuesday, October 31, 2017 at 4:25:36 PM UTC-5, Muhammad Shamim wrote:

We forgot to update this thread. 

Rasim figured out that his computer did not have an NVIDIA GPU, but rather an Intel Iris GPU.

And HiCCUPS requires CUDA, which requires NVIDIA GPUs.

- Muhammad Saad Shamim