Friday, 15 July 2011

Performance of Ray @ Assemblathon 2

Ray is one of the assemblers that I watch closely but sadly lack the time to experiment with. Here's the candid email from Sebastien to the Ray mailing list on Ray's performance on the test data

For those who follow Assemblathon 2, my last run on my testbed (Illumina data from BGI and from Illumina UK for the Bird/Parrot):

(all mate-pairs failed detection because of the many peaks in each library, I will modify Ray to consider that)



Total number of unfiltered Illumina TruSeq v3 sequences: Total:
3 072 136 294, that is ~3 G sequences !


512 compute cores (64 computers * 8 cores/computer = 512)


Typical communication profile for one compute core:


[1,0]:Rank 0: sent 249841326 messages, received 249840303 messages.


Yes, each core sends an average of 250 M messages during the 18 hours !




Peak memory usage per core: 2.2 GiB


Peak memory usage (distributed in a peer-to-peer fashion): 1100 GiB


The peak occurs around 3 hours and goes down to 1.1 GiB per node immediately because the pool of defragmentation groups for k-mers occuring once is freed.



The compute cluster I use has 3 GiB per compute core. So using 2048 compute cores would give me 6144 GiB of distributed memory.




Number of contigs: 550764

Total length of contigs: 1672750795
Number of contigs >= 500 nt: 501312
Total length of contigs >= 500 nt: 1656776315
Number of scaffolds: 510607
Total length of scaffolds: 1681345451
Number of scaffolds >= 500 nt: 463741
Total length of scaffolds >= 500: 1666464367

k-mer length: 31

Lowest coverage observed: 1
MinimumCoverage: 42
PeakCoverage: 171
RepeatCoverage: 300
Number of k-mers with at least MinimumCoverage: 2453479388 k-mers
Estimated genome length: 1226739694 nucleotides
Percentage of vertices with coverage 1: 83.7771 %
DistributionFile: parrot-Testbed-A2-k31-

20110712.CoverageDistribution.txt

[1,0]: Sequence partitioning: 1 hours, 54 minutes, 47 seconds

[1,0]: K-mer counting: 5 hours, 47 minutes, 20 seconds
[1,0]: Coverage distribution analysis: 30 seconds
[1,0]: Graph construction: 2 hours, 52 minutes, 27 seconds
[1,0]: Edge purge: 57 minutes, 55 seconds
[1,0]: Selection of optimal read markers: 1 hours, 38 minutes, 13 seconds
[1,0]: Detection of assembly seeds: 16 minutes, 7 seconds
[1,0]: Estimation of outer distances for paired reads: 6 minutes, 26 seconds
[1,0]: Bidirectional extension of seeds: 3 hours, 18 minutes, 6 seconds
[1,0]: Merging of redundant contigs: 15 minutes, 45 seconds
[1,0]: Generation of contigs: 1 minutes, 41 seconds
[1,0]: Scaffolding of contigs: 54 minutes, 3 seconds
[1,0]: Total: 18 hours, 3 minutes, 50 seconds


10 largest scaffolds:


257646

266905
268737
272828
281502
294105
294106
296978
333171
397201


# average latency in microseconds (10^-6 seconds) when requesting a reply for a message of 4000 bytes

# Message passing interface rank Name Latency in microseconds
0 r107-n24 138
1 r107-n24 140
2 r107-n24 140
3 r107-n24 140
4 r107-n24 141
5 r107-n24 141
6 r107-n24 140
7 r107-n24 140
8 r107-n25 140
9 r107-n25 139
10 r107-n25 138
11 r107-n25 139
  S├ębastien

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