HiCCUPS CUDA Version Issue

[Archit Ghosh]

Hi,

I was trying to run HiCCUPS on our cluster and received the following error... "UnsatisfiedLinkError: Error while loading native library JCudaDriver-0.8.0-linux-x86_64." I believe the newest version of HiCCUPS (v 1.14.08) still uses CUDA 8.0. Our cluster has OS RHEL7.4, GPU NVIDIA V100 and cuda driver 10 (rpm: cuda version cuda-driver-410.79-417). We have 2 cuda toolkits available: cuda10.0/toolkit/10.0.130 & cuda92/toolkit/9.2.88. I'm not sure if this software has a limitation dependency on the cuda version. 

I was wondering if your team has developed software on cuda 10 and has distribution? Any help would be greatly appreciated.

Thanks!

Archit

[Archit Ghosh]

Hi 3D genomics team,

I'm following up on this inquiry. I was wondering if you knew what I should do or if I'm missing something.

Thanks!

Archit

[Emel Kökrek]

Hi Archit,

I am working on a similar problem for a while now.

Ubuntu 18.04.4

Cuda-10.2

Java 11.0.6

JCuda 10.2

Your problem seems to be due to version incompatibility btw Cuda and JCuda. You can build JCuda for Cuda 10.2 or other versions. follow this link 

This might solve your problem. It didn't solve mine, yet.

However; HiCCUPS can't work with JCuda somehow. I receive an error like:

jcuda.CudaException: Could not prepare PTX for source file '/tmp/temp_JCuda_8033715261610944223.cu'

Caused by: java.io.IOException: Cannot run program "nvcc": error=2, No such file or directory

Caused by: java.io.IOException: error=2, No such file or directory

GPU/CUDA Installation Not Detected


Then I tried to build juicerbox myself for java 11 using the instructions here.

But I received warnings and couldn't build it.

5 Ocak 2020 Pazar 00:23:01 UTC+3 tarihinde Archit Ghosh yazdı:

[Muhammad Saad Shamim]

Hi Emel and Archit, 

You would need to recompile the juicer_tools jar from the github.com/aidenlab/juicebox (not juicer) repository.

You can download it with IntelliJ, replace the JCuda jar with a later version, and then build the jar to work with JCuda 10.

We haven't tested such changes, and aren't sure if you might encounter compatibility issues with JCuda 10.

Best,

- Muhammad Saad Shamim

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[Emel Kökrek]

Hi Muhammad,

actually I downloaded the files from juicebox repository, the link you wrote. (sorry for the typo in the previous message)

then followed these instructions below other than intelliJ instructions because I dont know how to use intelliJ.

But I receive a "build failed" error. As it can be seen in the screenshot in the previous message.

So, would the building problem be solved if I use intelliJ setup instead of these instructions?

Thank you in advance

14 Şubat 2020 Cuma 18:02:18 UTC+3 tarihinde Muhammad Saad Shamim yazdı:

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[Owen Chapman]

Hi all,

I just successfully built Juicebox using JCuda 10.0.0.  My repro below.

## Dependencies

- git clone the Juicebox repo

- JCuda .jar files corresponding to your version of CUDA. You can check your cuda version using nvcc --version

  (JCuda downloads page). It helps to follow their tutorial to check that JCuda is working before going any further.

- ant

- JDK 1.8

- commons.math3

## Add .jar dependencies

- Update Juicebox/lib/jcuda with your version of the JCuda jar and native jar.

- I also put commons.math3 in Juicebox/lib.

## Config to your new dependencies

- In juicebox.properties: change jdk.home.1.8 to point to your local JDK. Full path, no shortcuts.

- In build.xml, under <!-- Project Libraries -->, add the math3 jar: 

    <path id="library.math3.classpath">

        <pathelement location="${basedir}/lib/commons-math3-3.6.1/commons-math3-3.6.1.jar"/>

    </path>

- In build.xml, under <!-- Module Juicebox -->, add math3 to each of the 4 classpaths:

    <path id="juicebox.module.production.classpath">

        ... 

        <path refid="library.math3.classpath"/>

    </path>

- In build.xml, update all <zipfileset/> tags with your version of JCuda. For good measure, I also deleted the zipfileset tags corresponding to JCuda versions I wasn't using.

            <zipfileset src="${basedir}/lib/jcuda/jcuda-10.0.0.jar"/>

            <zipfileset src="${basedir}/lib/jcuda/jcuda-natives-10.0.0-linux-x86_64.jar"/>

## Compile

Run ant in the Juicebox directory.

[Emel Kökrek]

Thank you Owen,

I guess my problem is JDK 11 ...

I will try to follow yours.

Thanks again

25 Şubat 2020 Salı 06:05:14 UTC+3 tarihinde Owen Chapman yazdı:

[Neva Durand]

Thanks Owen - could you do a pull request and we can incorporate some of these?

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Neva Cherniavsky Durand, Ph.D.

Pronouns: she, her, hers

Assistant Professor, Aiden Lab

www.aidenlab.org