Blast Program Memory Usage

[vinaydu]

Dear Members,

I have compiled and installed blastall and using the same in cent os ver 6.0.

When I am running this, it consumes very less amount of physical memory and blast is also taking very long.

free -g command showed that I have 725 Gbs of ram is installed

ps aux| grep "blastall" gives me the the process id using which I enquired that how much memory blastall is using.

top psID

this gives me that blastall is using only 11gb of ram.

I am using -a option to define the number of processors which is 48.

What could be reason that blastall is not utilizing the available memory?

[vinaydu]

Please reply members. My blast job is taking very long. Please help..

[amitbik]

Try to run your blast with mpirun. In some cases it workedout for me.

mpirun [option] command

[vinaydu]

Thanks amit. Let me try it. I will post the result...

[GenoMax]

Please reply members. My blast job is taking very long. Please help..

Please provide some additional information about the size of the query/database you are blasting against. What version of blast are you using? Are you running it on a cluster or a really large server (700+ G memory free seems suspect, since single servers with that much memory are not common).

[vinaydu]

@Genomax,

I am BLASTing against nr database which presently is ~15Gb.

I am using blastall.

I am running it on a large server, which has this much (750Gb) physical memory.

Please advise...

[sphil]

how many sequences are in your input set?

[vinaydu]

Hi sphil,

I have 9706 sequences in a file.

grep ">" fastafile | wc -l

Actually the intial fasta file was very big and hence I need to split it in smaller sizes.
Now even after spliting BLAST is reluctantly slow.

Further for some of the fasta files it terminates (bash message) hence i thought I should split it. But even after spliting for some files it is terminate and BAST is very slow. I am forcing xml output.

Any suggestions!!!!

[sphil]

Can you be more specific on "it is slow"? Does it take days, weeks or just a few hours?

[vinaydu]

Hi Sphil,

Yeah it takes 2-3 days to BLAST a fasta file containing 10K sequences and generating xml output. I have been blasting these files for last 10-12 days.. Still not complete.

Further my apprehension is that when the memory is available, why BLAST is not using it.

[sphil]

What comes into my mind is that every of your 10k sequences might end up aligning to a huge amount of sequences in the NR database. Therefore the output file is also very large (maybe compare...). What that means, imagine if every sequence hits in between 50 to 100 times. You end up blasting like 50k to 1000k sequences which really takes quite a bit amount of time. Try to set the "report max hits" flags...

[vinaydu]

Thanks sphil for showing the interest.

It is true that the output files generated are of the size of ~3.5 Gbs.

But I am more concerned about the physical memory utilization. BLAST is running fine. Only thing is that this process is not utilizing all the memory.

[sphil]

Why should it use all memory? It can only handle as many reads at the same time as you have CPU-kernels on hand. This should then somehow correlate with the memory used....

[vinaydu]

I am using 48 cpus using -a option for blast all. So you are indicating that this is fine?

[GenoMax]

Any well written program will use memory as needed. Having extra memory does not help per se (unless you start using a part of the RAM as a virtual drive to hold data, see below).

You never made it clear if this is a cluster or a single server. If you really have 768 GB of RAM on a single server and you are the only user actively using this system you could think about creating a virtual disk (if you do not have admin access you will need to ask the admins to see if they would be willing) and copy your db index into that space for the fastest possible access.

If you are using "blastall" that seems to indicate that you are not using a newer version of blast suite. Is that the case? Depending on which blast search (n/p) you are running you should optimize search parameters according to what it is you are trying to get from this search. Blast command line manual is a must read reference: http://www.ncbi.nlm.nih.gov/books/NBK1763/