We have 2x7.7 Gb paired end ~100bp reads.
With kmer=45 option RAY assembled it for ~2h10m on 16 core 32 Gb node.
Suspecting it's too fast we checked and assembled on 64core 512 Gb node. Surprisingly it was longer, ~2h20m.
Command
mpirun -n 16 ~/apps/Ray-2.3.1/Ray -k 45 -amos -p ~/fw.fq ~/rev.fq -o ...
What's interesting, Outputnumbers for assemblies are almost the same (N50, maxcontig etc).
So the first question why do we have increased time for 64 cores? As I read somewhere MPI is not always more productive with large number of cores (processes) due to increased messaging between processes. Can this be an issue?
resources used.
For 64 cores:
cput=148:50:45,mem=24.7Gb, vmem=56.4Gb
For 16 cores:
cput=34:28:06, mem=14.6Gb,vmem=18.2Gb
Also scaffolding, it is the main difference in time usage.
It took 57 min for 64 and 27 min for 16 cores. (Before scaffolding, 64 core is actually a little bit faster)
Sequence loading. It took 9 min more for 64 cores.
Every rank in 64 cores loads 4 times less reads than each of 16 core. (that is obvious)
But memory used for reads for every 64 cores rank is only 2 times less (which is not so obvious). 2.Why is it so?
Again I am newbie here...to my understanding vmem -it is a memory of data exchange between hard and RAM.
So can we 'explain' 64 cores increased vmem by increased memory given for the reads at 64 core ranks? (increased in terms: we do not use 4 times less mem fo reads only 2 times less at 64 cores comparing to 16cores)
We have 2x7.7 Gb paired end ~100bp reads. With kmer=45 option RAY assembled it for ~2h10m on 16 core 32 Gb node. Suspecting it's too fast we checked and assembled on 64core 512 Gb node. Surprisingly it was longer, ~2h20m. Command mpirun -n 16 ~/apps/Ray-2.3.1/Ray -k 45 -amos -p ~/fw.fq ~/rev.fq -o ...
What's interesting, Outputnumbers for assemblies are almost the same (N50, maxcontig etc).
resources used. For 64 cores: cput=148:50:45,mem=24.7Gb, vmem=56.4Gb For 16 cores: cput=34:28:06, mem=14.6Gb,vmem=18.2Gb
Also scaffolding, it is the main difference in time usage. It took 57 min for 64 and 27 min for 16 cores. (Before scaffolding, 64 core is actually a little bit faster)
Sequence loading. It took 9 min more for 64 cores. Every rank in 64 cores loads 4 times less reads than each of 16 core. (that is obvious) But memory used for reads for every 64 cores rank is only 2 times less (which is not so obvious). 2.Why is it so?
Again I am newbie here...to my understanding vmem -it is a memory of data exchange between hard and RAM. So can we 'explain' 64 cores increased vmem by increased memory given for the reads at 64 core ranks? (increased in terms: we do not use 4 times less mem fo reads only 2 times less at 64 cores comparing to 16cores)
Thank you. Anastasiia