Hiccups error

[Kush B.]

Hi Guys,

I tried to run Hiccups and I always get this error, any idea why?

Reading file: inter_30.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-linux-x86_64" with base name "JCudaDriver"

Operating system name: Linux

Architecture         : amd64

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-linux-x86_64.so'

        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:415)

        at juicebox.tools.clt.juicer.HiCCUPS.run(HiCCUPS.java:360)

        at juicebox.tools.HiCTools.main(HiCTools.java:83)

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

java.lang.UnsatisfiedLinkError: /groups/cbdm-db/kb124/juicer-master_test/AWS/scripts/lib64/libJCudaDriver-linux-x86_64.so: libcuda.so.1: cannot open shared object file: No such file or directory

        at java.lang.ClassLoader$NativeLibrary.load(Native Method)

        at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1937)

        at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1855)

        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:415)

        at juicebox.tools.clt.juicer.HiCCUPS.run(HiCCUPS.java:360)

        at juicebox.tools.HiCTools.main(HiCTools.java:83)

        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:415)

        at juicebox.tools.clt.juicer.HiCCUPS.run(HiCCUPS.java:360)

        at juicebox.tools.HiCTools.main(HiCTools.java:83)

Thank you!

KB

[Muhammad Saad Shamim]

Can you provide us with the exact command you are running?

It looks like the natives library folder is not being passed in (native libs for jcuda).

See https://github.com/theaidenlab/juicebox/blob/master/native_launcher/juicebox.sh

Have you confirmed that CUDA 7 or 7.5 is installed?

- Muhammad Saad Shamim

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[Kush B.]

I load Cuda through module load function-

module load dev/java/jdk1.8 

module load dev/cuda/7.5.18 

Also, have modified juicebox file like this-

java -Duser.home=/groups/cbdm-db/kb124/Java -Djava.io.tmpdir=/groups/cbdm-db/kb124/Java/tmp -Djava.awt.headless=true -Djava.library.path=`dirname $0`/lib64  -Xms512m -Xmx2048m -jar `dirname $0`/juicebox_tools.7.5.jar $*

Have put JCuda native libraries for version 7.5 in lib64 folder.

- Muhammad Saad Shamim

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[Kush B.]

Sorry, juicebox is modified like this-

java -Duser.home=/groups/cbdm-db/kb124/Java -Djava.io.tmpdir=/groups/cbdm-db/kb124/Java/tmp -Djava.awt.headless=true -Djava.library.path=`dirname $0`/lib64 -Xmx32000m -Xms8000m -jar `dirname $0`/juicebox_tools.7.5.jar $*

And, command line-

/groups/cbdm-db/kb124/juicer-master_test/AWS/scripts/juicebox hiccups --ignore_sparsity inter_30.hic inter.30_loops.txt

[Muhammad Saad Shamim]

Can you confirm that libJCudaDriver-linux-x86_64.so is in the lib64 folder? (that's the file it can't find per error message)

Also try hardcoding -Djava.library.path=/path/to/lib64 for your machine.

- Muhammad Saad Shamim

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[Kush B.]

Yes, libJCudaDriver-linux-x86_64.so is lib64 folder.

Hardcoding doesn't help either.

- Muhammad Saad Shamim

[Neva Durand]

It's looking for "/lib/libJCudaDriver-linux-x86_64.so"

Maybe create a softlinked folder called lib/ that links to lib64/

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[Kush B.]

Sorry, how do I softlink it? 

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[Kush B.]

So, I tried to softlink, not sure its the right way-

ln -s /groups/cbdm-db/kb124/juicer-master_test/AWS/scripts/lib64/libJCudaDriver-linux-x86_64.so /lib/libJCudaDriver-linux-x86_64.so

but go this issue-

ln: creating symbolic link `/lib/libJCudaDriver-linux-x86_64.so': Permission denied

[Zhibo M.]

Hi Kush,

Did you have the problem solved at the end? I am having the exact same problem like yours.
Thanks,

Zhibo

[Neva Durand]

This will depend on your CUDA version and also your exact chip (x86 versus Power 8 e.g.).  

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