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  • is is possible to run SOAP3 with a Cuda 4.1 toolkit?

    I've recently had to re-setup a misplaced configuration of CUDA on our Tesla based Ubuntu server.

    Given we have an Ubuntu 10.04.4 LTS system I've downloaded the latest stable Cuda Toolkit. That is the release 4.1.

    Then a colleague invited me to install SOAP3 and the installation process went smoothly.

    Then I left the machine to my colleague. So he started preparing the working enviroment and the let me know that:

    Code:
    $ /opt/soap3_0.01beta/2bwt-builder /biodata/arab/TAIR9_chr_all.fas
    works ok, the second command, instead, as an issue.

    Code:
    $ /opt/soap3_0.01beta/BGS-Build TAIR9_chr_all.fas.index
    
    /opt/soap3_0.01beta/BGS-Build: error while loading shared libraries: libcudart.so.3: cannot open shared object file: No such file or directory
    Indeed in /usr/local/cuda/lib there is only libcudart.so.4

    SOAP3 website explicitly says: "SOAP3 was developed under the 64-bit linux platform and the CUDA Driver version 3.2."

    So I hoped making a simbolic link would work but this gave a worst result.
    Tried to write down an email to the SOAP3 staff address provided but their mailserver gave me an error
    Failure to deliver the message to the recipient or group
    Restrict delivery to this address can not pass your e-mail.

    Googling has given me nothing to work on.
    Do you have any ideas other than removing CUDA 4.1 and try to get working the 3.2 release ?

    TIA
    SysAdmin & ICT consultant
    http://about.me/nicola.losito

  • #2
    seems a difficult question.

    it's also difficult to get in touch with the SOAP Genomics guys in China, we've sent them 4 emails and all came back with errors. Any idea at least on how to get in touch with them?

    thanks
    SysAdmin & ICT consultant
    http://about.me/nicola.losito

    Comment


    • #3
      I am getting the same error with the BGS-Build command, using SOAP-dp that I downloaded and installed today. ... except that it is seeking libcudart.so.4. however, the file does exist in the user/local/cuda/lib directory with filetype 'link to shared library'.

      I am new to Linux so I'm not sure why it can't find the file that is there, unless the soap3 is looking in the wrong place?

      Did you ever find a solution?
      thanks!

      Comment


      • #4
        Excuse me ... your installation asks for the libcudart.so.4 even if it's present on your system?

        My problem was (it still is but I'm testing something else nowadays) that it needed the libcudart.so.3 ...
        SysAdmin & ICT consultant
        http://about.me/nicola.losito

        Comment


        • #5
          Originally posted by NicolaLosito View Post
          Excuse me ... your installation asks for the libcudart.so.4 even if it's present on your system?
          Yes. It seems like a path problem, but my libcudart.so.4 is in the same path that your v3 was.

          Comment

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