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sebhtml / ray

Ray -- Parallel genome assemblies for parallel DNA sequencing
http://denovoassembler.sf.net
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test seed merging code on NormalStool #204

Open sebhtml opened 10 years ago

sebhtml commented 10 years ago

/mnt/lustre03/corbeil/corbeil_group/nne-790-ab/projects/ANL

sebhtml commented 10 years ago

the new code in code/SpuriousSeedAnnihilator/ (code/SpuriousSeedAnnihilator/SeedMergingWorkflow.cpp ) has still some issues. it won't ship in 2.3.0

sebhtml commented 10 years ago

Works with MPI_IO=n on mp2

616d2a26cc1e39f59325a0e632af46262edaa12c

sebhtml commented 10 years ago

(without seed merging)

[boisver1@ip03-mp2 ANL]$ qsub NormalStool-9.sh 45367.mp2.m [boisver1@ip03-mp2 ANL]$ pwd /mnt/lustre03/corbeil/corbeil_group/nne-790-ab/projects/ANL

sebhtml commented 10 years ago

with -merge-seeds on

[boisver1@ip03-mp2 ANL]$ qsub NormalStool-10.sh 45369.mp2.m

sebhtml commented 10 years ago

Problem with Message.cpp 533 with routing

will rerun with core generation

[boisver1@ip03-mp2 ANL]$ qsub NormalStool-11.sh 45534.mp2.m

sebhtml commented 10 years ago

with routing:

[boisver1@ip03-mp2 ANL]$ pwd /mnt/lustre03/corbeil/corbeil_group/nne-790-ab/projects/ANL [boisver1@ip03-mp2 ANL]$ qsub NormalStool-12.sh 49061.mp2.m

sebhtml commented 10 years ago

new location (lustre03 is read-only and will be decommissioned.)

/mnt/scratch_mp2/corbeil/corbeil_group/nne-790-ab/projects/ANL

sebhtml commented 10 years ago

Rank 245 has 173 seeds >= 1000 nt.

but has 3500 seeds >= 1 nt.

a lot of them are just deadends...

sebhtml commented 10 years ago

[boisver1@ip03-mp2 ANL]$ qsub NormalStool-14.sh 26991.mp2.m

sebhtml commented 10 years ago

-14 hanged at the start, maybe because of hardware, who knows.

sebhtml commented 10 years ago

-15 failed because 3 checkpoint files are corrupted on mp2.

[boisver1@ip03-mp2 ANL]$ qsub NormalStool-16.sh
27065.mp2.m

sebhtml commented 10 years ago

with raw code (-13): Rank 1 has 3583 seeds to register. with new patch: xxx