On Fri, Mar 21, 2014 at 5:42 AM, Nilaksha Neththikumara <nilakshafreezon@gmail.com> wrote:
Thank you very much. I was able to download blast locally and configure the loc. file so now it is up and running. :) But another problem encountered when I'm trying to align a fasta file with 4mb, giving an error called
blastn(708,0xa03ca1a8) malloc: *** mach_vm_map(size=1048576) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Bus error: 10
I referred a bit and the only solution i could come across was that it is some kind of an error encountered when overloading the memory of a single thread.
It does sounds like a memory (RAM) problem, yes. However in general using more threads will not save memory (it may even need more).
So I quit galaxy, jumped into the terminal and performed the same task with num_threads =16 (my mac pro got two quad cores with virtual dual cores : 2*4*2 =16) So far good.
Stange. Perhaps you had some other memory hungry tasks running before at the same time as the failed BLAST?
When examining the code in galaxy it was using a value called ${GALAXY_SLOTS:-4} to the num_thread argument yet I'm sure it only utilised a single core. Can I configure it to use all the 16 cores? Any advice please?
Bjoern answered that; This would have defaulted to 4 threads if the GALAXY_SLOTS setting wasn't setup.
PS: Since my new questions are out of track with my first question (blast+ wrapper with remote searching) do I need to start a new thread? Sorry if I'm doing anything wrong here. I'm just very new and novice. (got my appointment in the beginning of March right after my graduation , no body is familiar with bioinformatics here in Sri Lanka, so I'm struggling to make my move alone with the help of you all over the world )
Yes, next time you have a completely new question, start a new thread. Also try reading the forums at seqanswers.com and Q&A at biostars.org Regards, Peter