Problems for running hiccups in juicer for calling loops

[ya...@vt.edu]

Dear all,

 

I have met the problem when I ran hiccups of juicer for calling loops.

 

My cuda version is 7.5.18

 

My input data is as followings:

Jcuda lib: /home/yanhd/software/jcuda/cuda_lib/JCuda-All-0.7.5-bin-Linux-x86_64

 

Jcuda: /home/yanhd/software/cuda/juicer_tools.1.6.2_jcuda.0.7.5.jar

Input_hic: Homo_sapiens_assembly19.rawchrom.hic

Opt_file: hiccups_results

 

My command is:

java -Xms512m -Xmx2048m 

-Djava.library.path=/home/yanhd/software/jcuda/cuda_lib/JCuda-All-0.7.5-bin-Linux-x86_64

-jar /home/yanhd/software/cuda/juicer_tools.1.6.2_jcuda.0.7.5.jar 

hiccups ./Homo_sapiens_assembly19.rawchrom.hic hiccups_results

 

I think the version of cuda is met with version Jcuda lib and Jcuda jar, but the error below still show that “Error while loading native library "JCudaDriver-linux-x86_64"

 

 

Could you please help me to solve the problem? Thanks a lot!

 

Best wishes

Haidong

Virginia Tech

 

[Muhammad Saad Shamim]

Hey Haidong,

Hope you're doing well. 

Can you try using one of the newer jars bundled for jcuda 8? These are backward compatible with older CUDA versions and have the native libs installed internally. https://github.com/aidenlab/juicer/wiki/Download

Best,

- Muhammad Saad Shamim

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[ya...@vt.edu]

Hey Muhammad Saad Shamim

Thanks for replying! I used the latest version of jcuda 8: juicer_tools.1.8.9_jcuda.0.8.jar, without specifying the lib path because you said this jcuda8 has the native libs. 

However, the problem shows that I cannot find JCudaRuntime-0.8.0-linux-x86_64 as following shows:

In addition, my command is 

java -Xms512m -Xmx2048m -jar /home/yanhd/software/jcuda/juicer_tools.1.8.9_jcuda.0.8.jar hiccups ./Homo_sapiens_assembly19.rawchrom.hic hiccups_results

Unable to assess map sparsity; continuing with HiCCUPS

Exception in thread "main" java.lang.UnsatisfiedLinkError: Error while loading native library "JCudaRuntime-0.8.0-linux-x86_64"

Operating system name: Linux

Architecture         : amd64

Architecture bit size: 64

---(start of nested stack traces)---

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

java.lang.UnsatisfiedLinkError: no JCudaRuntime-0.8.0-linux-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:143)

        at jcuda.runtime.JCuda.initialize(JCuda.java:406)

        at jcuda.runtime.JCuda.<clinit>(JCuda.java:390)

        at jcuda.driver.JCudaDriver.<clinit>(JCudaDriver.java:277)

        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:415)

Thanks 

Best wishes

haidong

[Muhammad Shamim]

Can you try the juicer_tools.jar for versions 1.7.5 and 1.7.6? If those don't work, it's possible that jcuda may need to be compiled into its jar on your hardware. We use the jcuda jars bundled by jcuda.org, with the exception of the ppc version (which had to be compiled on local hardware).