Hello Nicolas, On Sat, 2010-01-30 at 16:27 +0100, Nicolas Tourasse wrote: > I got a "std::bad_alloc" exception when trying to align 67 bacterial > genome sequences of 5 Mbp each. The error occurs at the 1st alignment > step after reading the sequences and creating the sorted mer lists. The > command line and the end of the output are shown below. > It is likely to be a problem with memory allocation related to a C++ > "new" statement. I would think it's a problem with a program statement, > because I'm running mauveAligner on a supercomputer with 16GB RAM CPUs > and the crash occurs when 4GB are used, so it's probably not a problem > of available RAM on the computer. Maybe the allocation statement makes > the program ask for more memory than it should use. In fact, the program > works fine when I align only 20 of the genomes. > > Would you be able to help me with this problem?
Yes indeed, std::bad_alloc is a c++ error that occurs when memory allocation fails with the new function. Although your supercomputer has plenty of memory, I have a strong suspicion that you might be using a 32-bit version of mauveAligner, which can not allocate more than 4GB of memory due to 32-bit address space limitations. Mauve releases contain both 32-bit and 64-bit builds. In the Linux release the 64-bit builds of mauveAligner and progressiveMauve reside in the linux-x64 subdirectory within the main release archive. It's possible to check whether a program is 32-bit or 64-bit using the 'file' command, e.g.: file mauveAligner In windows the 64-bit binaries are in a win64/ subdirectory. On Mac OS X the 32-bit and 64-bit versions are bundled together into a single "fat" binary, so Mac users shouldn't ever experience this issue. If that doesn't solve it then something has run seriously amok, and it would be great if you could provide more information (off-list) about your genome sequences. Cheers, -Aaron ------------------------------------------------------------------------------ The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
