Closed HangweiXi closed 5 years ago
I'm not sure how you configured your AWS Slurm, have you checked the Canu FAQ to make sure it supports all the required features (array jobs, hold, etc)? Essentially, it is saying the requested machines don't exist. Canu should be requesting 16gb and 8 cores in a single array job which is below what your Slurm claims exists. You can see the exact request command in correction/0-mercounts/meryl-count.jobSubmit-01.sh
. You'll have to figure out if there are other options you need to provide to Slurm to support array jobs. Since you've only got 1 node in your "cluster" anyway, you might as well run with useGrid=false.
Thanks for your reply! I find a way to active other nodes on the grid and Canu is working. I still have some question about it.
-- (tag)Threads
-- (tag)Memory |
-- (tag) | | algorithm
-- ------- ------ -------- -----------------------------
-- Grid: meryl 256 GB 32 CPUs (k-mer counting)
-- Grid: cormhap 31 GB 8 CPUs (overlap detection with mhap)
-- Grid: obtovl 16 GB 8 CPUs (overlap detection)
-- Grid: utgovl 16 GB 8 CPUs (overlap detection)
-- Grid: ovb 3 GB 1 CPU (overlap store bucketizer)
-- Grid: ovs 32 GB 1 CPU (overlap store sorting)
-- Grid: red 8 GB 4 CPUs (read error detection)
-- Grid: oea 4 GB 1 CPU (overlap error adjustment)
-- Grid: bat 256 GB 16 CPUs (contig construction)
-- Grid: gfa 16 GB 16 CPUs (GFA alignment and processing)
I can understand it should be the requirement of each step. My question is: Is it the requirement for a single job array in each step?
Thank you very much!
Hi
I'm trying to use Canu to assembly a plant genome on AWS. The command is
It successfully submit a job but finally crash
The
canu.out
The
meryl-count.jobSubmit-01.out
under correction/0-mercountsThank you