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Installing bedtools, intel vs gcc compiler

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  • Installing bedtools, intel vs gcc compiler

    I'm installing Bedtools for myself on a HPC cluster, the Bedtools website indicates it uses the GCC compiler while the cluster I'm working on uses the Intel compiler by default and says GCC is not recommended (but is available) on the cluster. What is the best way to install Bedtools in this situation?
    1. If I use the default Intel compiler and leave the makefile with g++, it starts off fine then there's an error and it exits with "This Intel <math.h> is for use with only the Intel compilers".
    2. If I use the default Intel compiler and change the Bedtools makefile (I think I'm editing this correctly) "export CXX" line from "g++" to "icc", I get over 1000 warnings but Bedtools seems to install fine (the few Bedtools tests I ran worked).
    3. If I load the gcc 5.3.0 compiler and make Bedtools (using the original makefile with "export CXX = g++") I get about 15 warnings but it seems to install properly.
    4. If I load the gcc 5.3.0 compiler and change the Bedtools makefile "export CXX" line from "g++" to "icc", it exits almost immediately with an error ("icc: Command not found").


    #1 and 4 don't complete as I expected, #3 seems the best, should I use #3 or do something else? I can provide the errors/output from make if that would help.
    Last edited by biocomputer; 03-15-2016, 10:23 AM.

  • #2
    For #3 are those actual errors or "warnings"? If it is the latter then #3 may be fine.

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    • #3
      Ah those are warnings not errors, I corrected the original post.

      Here's the output from #3:

      https://dl.dropboxusercontent.com/u/...205.3.0%29.txt
      Last edited by biocomputer; 03-15-2016, 10:27 AM.

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      • #4
        The warning messages are probably not going to cause a problem.
        The "set but not used" messages are probably harmless.
        The 'signed/unsigned comparison" is probably not a big deal; unless the chromosome size is greater than 2,147,483,647 bases.

        You are unlikely to find one that big.

        This biostar thread https://www.biostars.org/p/12560/ says that there's a species of wheat that has a chromosome that's bigger.

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        • #5
          Re #2, compiling bedtools 2.25.0 with Intel's icpc (ICC) 15.0.0 20140723 I got only a handful of trivial warnings (see https://github.com/arq5x/bedtools2/pull/382). If your warnings are similar, I suspect an ICC-compiled bedtools is fine.

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