juicer_tools hiccups error - 'GLIBC_2.14' not found

[Saneth]

Dear 3D Genomics members

I'm trying to run juicer_tools.1.8.9_jcuda.0.8.jar hiccups using GSE63525_IMR90_combined_30.hic file and received the error message - "java.lang.UnsatisfiedLinkError: /tmp/libJCudaRuntime-0.8.0-linux-x86_64.so: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/libJCudaRuntime-0.8.0-linux-x86_64.so)". 

I copied the complete error message after the main text of this email.

I checked my cuda, gcc and java versions and detail information is listed after the complete error message .

I would like to know whether the juicer_tools users or developers have encountered this error message. 

Most importantly I'd be extremely thankful if you can help me to fix this issue and generate the HiCCUP looplist file.

Thank you very much in advance.

Best regards

Pubudu

Command: 

java -jar juicer_tools.1.8.9_jcuda.0.8.jar hiccups -m 500 -r 1000000 -f 0.1 -p 2 -i 5 -d 20000 -c 1 ../GSE63525_IMR90_combined_30.hic IMR90_combined_30_chr1_loops

Error message: 

Reading file: ../GSE63525_IMR90_combined_30.hic

Using the following configurations for HiCCUPS:

Config res: 1000000 peak: 2 window: 5 fdr: 10% radius: 20000

Running HiCCUPS for resolution 1000000

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)

at juicebox.tools.clt.juicer.HiCCUPS.run(HiCCUPS.java:359)

at juicebox.tools.HiCTools.main(HiCTools.java:96)

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

java.lang.UnsatisfiedLinkError: /tmp/libJCudaRuntime-0.8.0-linux-x86_64.so: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/libJCudaRuntime-0.8.0-linux-x86_64.so)

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

at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1941)

at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1824)

at java.lang.Runtime.load0(Runtime.java:809)

at java.lang.System.load(System.java:1086)

at jcuda.LibUtils.loadLibraryResource(LibUtils.java:260)

at jcuda.LibUtils.loadLibrary(LibUtils.java:158)

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)

at juicebox.tools.clt.juicer.HiCCUPS.run(HiCCUPS.java:359)

at juicebox.tools.HiCTools.main(HiCTools.java:96)

---(end of nested stack traces)---

at jcuda.LibUtils.loadLibrary(LibUtils.java:193)

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)

at juicebox.tools.clt.juicer.HiCCUPS.run(HiCCUPS.java:359)

at juicebox.tools.HiCTools.main(HiCTools.java:96)

 

 

GPU: spci | grep -i nvidia

03:00.0 3D controller: NVIDIA Corporation GK110GL [Tesla K20Xm] (rev a1)

84:00.0 3D controller: NVIDIA Corporation GK110GL [Tesla K20Xm] (rev a1)

 

Linux distribution: uname -m && cat /etc/*release 

x86_64

CentOS release 6.10 (Final)

LSB_VERSION=base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch

CentOS release 6.10 (Final)

Rocks release 6.2 (SideWinder)

CentOS release 6.10 (Final)

 

GCC: gcc --version

gcc (GCC) 4.7.2

Linux kernal: uname -r

2.6.32-754.6.3.el6.x86_64

Cuda version:

 

cat /proc/driver/nvidia/version

NVRM version: NVIDIA UNIX x86_64 Kernel Module  384.111  Tue Dec 19 23:51:45 PST 2017

GCC version:  gcc version 4.4.7 20120313 (Red Hat 4.4.7-23) (GCC) 

 

nvcc -V

nvcc: NVIDIA (R) Cuda compiler driver

Copyright (c) 2005-2016 NVIDIA Corporation

Built on Sun_Sep__4_22:14:01_CDT_2016

Cuda compilation tools, release 8.0, V8.0.44

 

 

 

 

 

 

[Saneth]

Dear all

For what it's worth, I thought to submit the workaround that solved the error I've described in this thread.

The stable version available in the juicertools download page is not compiled in CentOs. Therefore, I downloaded the source code from the GitHub repo and compiled it in my server... and that solved the issue I had earlier.

Best

[Iftekhar]

Hi Saneth, 

I am having the exact same problem while running hiccups. Are you able to share the details of how you compiled the juicertools in your server?  am using a SLURM cluster at my institute. 

thank you,

- Iftekhar

[Muhammad Shamim]

Hi Iftekhar,

Would you be able to confirm if the latest jar gives you the same error?

https://github.com/aidenlab/juicer/wiki/Download#version-11301