Question: Abyss hangs when reading data
gravatar for quentin.santana
4.1 years ago by
quentin.santana0 wrote:

I'm using ABYSS 2.0.2 on a small genome (~45Mb). It was compiled with max k = 160. Currently, when reading the paired end files it will hang. This seems to be random, as each time I run abyss it will hang at a different number of reads being read. I don't have this problem if ABYSS is configured with max k = 128

eg. 0: Read 9900000 reads. 0: Hash load: 1755991 / 268435456 = 0.00654 using 224 MB 3: Read 8000000 reads. 3: Hash load: 1757569 / 268435456 = 0.00655 using 225 MB

I have set the eager limit for openmpi as directed in Abyss assembly runs forever

export mpirun="mpirun --mca btl_sm_eager_limit 16000 --mca btl_openib_eager_limit 16000"

or even disabled the shared memory using

export mpirun="mpirun --mca btl ^sm --mca btl_openib_eager_limit 16000"

Openmpi 1.10.4 is installed on the system

Any ideas what could be going on?

Thanks in advance

abyss assembly • 1.1k views
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