Loading ...
Sorry, an error occurred while loading the content.

Linux Version....

Expand Messages
  • apierce51
    Using gcc version 2.95.2 on a Turbolinux system, the code seems to compile fine, and 4 of the 5 test cases run too. testSequenceReaderFasta Seg faults in Test
    Message 1 of 2 , Jul 10, 2002
    • 0 Attachment
      Using gcc version 2.95.2 on a Turbolinux system, the code seems to
      compile fine, and 4 of the 5 test cases run too.
      testSequenceReaderFasta Seg faults in Test 17. I have not done enough
      investigation as to why this is happening though.

      On a RedHat 7.1 system with gcc 2.96, code compiles clean,
      testHashTableNoOverlap after running for awhile with the msg "Caught
      exception: bad_alloc", and testSequenceReaderFasta still Seg faults in
      test 17.

      And on yet another Linux system, this time Turbolinux with gcc 3.0.4,
      the code compiles clean, testHashTableNoOverlap ends with the msg
      "Killed" and testSequenceReaderFasta segfaults in test 17 after
      printing out c1, which is unlike the other 2 systems, which did not
      print c1.

      Andy Pierce
    • coxtonyj
      ... Hi Andy, Thanks for the detailed feedback. The bad_alloc exception is caused by the system running out of memory - testHashTableNoOverlap uses quite a lot.
      Message 2 of 2 , Jul 10, 2002
      • 0 Attachment
        --- In ssahausers@y..., "apierce51" <apierce@s...> wrote:
        > Using gcc version 2.95.2 on a Turbolinux system, the code seems to
        > compile fine, and 4 of the 5 test cases run too.
        > testSequenceReaderFasta Seg faults in Test 17. I have not done enough
        > investigation as to why this is happening though.
        >
        > On a RedHat 7.1 system with gcc 2.96, code compiles clean,
        > testHashTableNoOverlap after running for awhile with the msg "Caught
        > exception: bad_alloc", and testSequenceReaderFasta still Seg faults in
        > test 17.
        >
        > And on yet another Linux system, this time Turbolinux with gcc 3.0.4,
        > the code compiles clean, testHashTableNoOverlap ends with the msg
        > "Killed" and testSequenceReaderFasta segfaults in test 17 after
        > printing out c1, which is unlike the other 2 systems, which did not
        > print c1.
        >
        > Andy Pierce

        Hi Andy,

        Thanks for the detailed feedback.

        The bad_alloc exception is caused by the system running out of memory
        - testHashTableNoOverlap uses quite a lot.

        Most of these errors seem to be different systems ways of saying the
        assertion in line 1017 of testSequenceReaderFasta.cpp has failed. This
        fixes it on my system:

        In Global/GlobalDefinitions.cpp, insert after line 221 the line
        if((andMask==0)&&(i!=0)) andMask=~0;

        Unfortunately when I fix that I get another error in test 21.I
        wouldn't worry too much about this though. The code was originally
        written as a library and this test tests a feature that is not used in
        the command line executable. If you comment out this test the program
        runs to completion on my system.

        Hope that helps.

        Tony Cox
      Your message has been successfully submitted and would be delivered to recipients shortly.