Hi Gabriel, On Fri, 2013-11-08 at 07:10 +1100, Gabriel Andres Gallina Nizzo wrote: > Hello. I'm running progressive mauve in 54 genomes of ~3mb. I have > BioLinux 7, CPU Athlon X6 and 8GB RAM. So far so good but it's running > for 72 hours and fin the last 24 hours it's at the same point > according to the Mauve console. This is correct or is there something > wrong? Going to end at some point or should I stop? > Other questions: how much memory should be assigned (parameter-Xmx) in > this task? It is possible to make use of all the CPU core? According > to the system monitor, Mauve uses only one of the 6 available. > Thank you very much in advance for your reply > > It is not unusual for progressiveMauve to run for several days when aligning > 50 genomes. The running time grows at least cubically in the number of genomes, and also depends on the amount of apparent rearrangement in those genomes. If your 50 genomes are draft genomes in hundreds of scaffolds, it would help to order those scaffolds relative to a reference prior to doing the multiple alignment since that will reduce the number of apparent rearrangements.
To answer your other questions, the -Xmx parameter controls the memory available for the Java GUI, but the command-line aligner is a C++ program and will use as much memory as it needs. If it needs more than the 8GB on your system then the program will likely stall as the OS starts paging memory to/from the disk. If you use top or some other process monitor you can check how much CPU time progressiveMauve is using. If it's < 50% and the process vm size is >7GB then it's likely that the aligner has exhausted available memory on your system and your hard drive will probably burst into flames before the alignment finishes. Better to seek a machine with more RAM if that's the case. As for the number of cores, progressiveMauve currently runs single-threaded. Although there are many parts of the algorithm that could be amenable to parallelization the part which is most time-consuming is not trivially parallel. Hope that helps, -Aaron -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
