Problem with installing GranOO on cluster

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Problem with installing GranOO on cluster

dxvn818
Hello,

I have problem with installing GranOO on cluster related to VTK. I have downloaded VTK-8.2.0 source code and built. On cluster there are following directories:
       granoo
       VTK-8.2.0

When I compile GranOO, it still shows the following error:


I try setting VTK environment in the CMakeList.txt in /granoo/tags/2.0/CMake/CMakeList.txt as:

      SET(VTK_DIR "/home/dxvn818/VTK-8.2.0" CACHE PATH "VTK directory override" FORCE)

but it does not work.

Could you please give me a guide to fix it ?

Thank you,
Vinh
Do Xuan Vinh Nguyen
PhD Student,
School of Mechanical, Materials, Mechatronic and Biomedical Engineering,
Faculty of Engineering and Information Sciences,
University of Wollongong, New South Wales, Australia
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Re: Problem with installing GranOO on cluster

Cédric Hubert
Administrator
Hi Vinh,

Try to help CMake finding it this way:
&> cmake /path/to/GranOO -DCMAKE_PREFIX_PATH="/home/dxvn818/VTK-8.2.0"

Your VTK install directory is supposed to contain the /lib, /include, etc. directories.

Cédric

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Re: Problem with installing GranOO on cluster

dxvn818
Hi Cédric,

It works. Thank you very much.

Vinh
Do Xuan Vinh Nguyen
PhD Student,
School of Mechanical, Materials, Mechatronic and Biomedical Engineering,
Faculty of Engineering and Information Sciences,
University of Wollongong, New South Wales, Australia
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Re: Problem with installing GranOO on cluster

dxvn818
In reply to this post by Cédric Hubert
Hello Cédric,

When I tried to submita simple test job on cluster which is attached in this post, although I built successfully program, it shows the following error related to libboost:

/home/dxvn818/granoo/workspace/Tensile_DE/build/tension.exe: error while loading shared libraries: libboost_chrono.so.1.62.0: cannot open shared object file: No such file or directory

I have no experience on running job on cluster while the cluster admin is busy now. Do you know what 's wrong with it ?

Thank you,

Vinh

job.sh
Do Xuan Vinh Nguyen
PhD Student,
School of Mechanical, Materials, Mechatronic and Biomedical Engineering,
Faculty of Engineering and Information Sciences,
University of Wollongong, New South Wales, Australia
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Re: Problem with installing GranOO on cluster

Damien André
Administrator
Hello,
There is some problems with your dynamic library files. I am not able to solve your problem. You probably must talk with your  server admin to solve this issue. It does not concern granoo.... this is  a "sys admin" problem !
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Re: Problem with installing GranOO on cluster

Cédric Hubert
Administrator
In reply to this post by dxvn818
Hi Vinh,

That's not specific to a cluster. It's just that the libraries are not installed in a default path, or even installed in your home directory, or somewhere else.

Locate the libboost_chrono.so.1.62.0 library.
Once found, if the library path is "/path/to/user/libraries/libboost_chrono.so.1.62.0", add the following line in your job.sh script:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/user/libraries

If not, I guess you need the help of the cluster administrator...
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Re: Problem with installing GranOO on cluster

dxvn818
Hello Damien and Cédric,

Thanks for your reply. After adding the library path as Cédric suggested, it still shows the same error.I have contacted server admin for help.

Vinh
Do Xuan Vinh Nguyen
PhD Student,
School of Mechanical, Materials, Mechatronic and Biomedical Engineering,
Faculty of Engineering and Information Sciences,
University of Wollongong, New South Wales, Australia
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Re: Problem with installing GranOO on cluster

dxvn818
Hello,

I would like to ask if granoo-cooker tool, which is used to generate discrete domain, can only run in single core ?

Vinh
Do Xuan Vinh Nguyen
PhD Student,
School of Mechanical, Materials, Mechatronic and Biomedical Engineering,
Faculty of Engineering and Information Sciences,
University of Wollongong, New South Wales, Australia
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Re: Problem with installing GranOO on cluster

Damien André
Administrator
Yes, it runs only on one core  :(
Sorry.
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Re: Problem with installing GranOO on cluster

Mr.Happy
Hi,

So the granoo-cooker tool can only run on one core. What about main algorithm of Granoo (the DEM part), can it run on multiple cores?

Thanks!
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Re: Problem with installing GranOO on cluster

Damien André
Administrator
GranOO can be ran as multithread. For example, if you you set :

<GranOO Version="2.0" .... ThreadNumber="4"> 
Some plugins will be ran in //

To get the list of multithreaded plugins, you can read the plugin documentation.
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Re: Problem with installing GranOO on cluster

Mr.Happy
I set ThreadNumber="10", but i did not notice any difference in the simulation. Any advice?
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Re: Problem with installing GranOO on cluster

Damien André
Administrator
Hello,
Only few numbers of plugins are multithreaded. As i wrote before :
Damien André wrote
To get the list of multithreaded plugins, you can read the plugin documentation.