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  • bwa installation problem on ia64

    Hello,

    I am using bwa-0.5.8c and I got an installation failure Error 1. After successful compilation without -m4 in the CFLAGS line, I got an error message saying not enough memory allocated when running it. I have 136G memory. I'd like to know how to allocate more memory. If the 32bit installation restricted memmory usage to about 3GB. Then Can onyone tell me how to install it on ia64 machine? Thanks.

  • #2
    Can you dump your full compilation details somewhere?
    Also, are you positive you installed a 64bit OS on that hardware? What do
    you get when running?:

    Code:
    $ uname -a
    -drd

    Comment


    • #3
      Thanks drio. This is the ternimal display of my installation of bwa-0.5.8c on SGI Altix® 4700 System running SUSE(R) Linux Enterprise Server 10.3:

      make[1]: Entering directory `/vol1/home/tongyg/bwa-0.5.8c'
      make[1]: Nothing to be done for `lib'.
      make[1]: Leaving directory `/vol1/home/tongyg/bwa-0.5.8c'
      make[1]: Entering directory `/vol1/home/tongyg/bwa-0.5.8c/bwt_gen'
      make[1]: Nothing to be done for `lib'.
      make[1]: Leaving directory `/vol1/home/tongyg/bwa-0.5.8c/bwt_gen'
      gcc -g -Wall -O2 -m64 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen

      Comment


      • #4
        Quite an interesting machine you go there.
        My question still remains, are you sure you are running a full 64 bit OS? The hardware is 64bit for sure. Can you show me the output of?

        Code:
        $ uname -a
        $ file /bin/ls
        $ ldd /bin/ls
        -drd

        Comment


        • #5
          $ uname -a
          Linux linux 2.6.16.60-0.23.PTF.403865.0-default #1 SMP Thu May 15 06:38:31 UTC 2008 ia64 ia64 ia64 GNU/Linux

          $ file /bin/ls
          /bin/ls: ELF 64-bit LSB executable, IA-64 (Intel 64 bit architecture), version 1 (SYSV), for GNU/Linux 2.6.4, dynamically linked (uses shared libs), for GNU/Linux 2.6.4, stripped

          $ ldd /bin/ls
          linux-gate.so.1 => (0xa000000000000000)
          librt.so.1 => /lib/librt.so.1 (0x2000000000068000)
          libacl.so.1 => /lib/libacl.so.1 (0x2000000000088000)
          libc.so.6.1 => /lib/libc.so.6.1 (0x20000000000a8000)
          libpthread.so.0 => /lib/libpthread.so.0 (0x20000000002fc000)
          /lib/ld-linux-ia64.so.2 (0x2000000000000000)
          libattr.so.1 => /lib/libattr.so.1 (0x2000000000338000)

          Comment


          • #6
            Alright everything looks good, can you do ldd ./bwa (on your bwa binary just compiled?).
            If you do make clean and recompile again, do you get any warning message?
            If so, can you print it here?
            Are there any other users using the machine?
            -drd

            Comment


            • #7
              I do not know if bwa will work on ia64. ia64 is a monster to many programmers. It is big-endian which changes a lot of things.

              Comment


              • #8
                The 32bit mode installation seems work well on my ia64 SGI machine. The memory allocation problem was probably caused by the parameter bwtsw treating small database. Thanks.

                Comment

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