Hello,
I think you are right.
srun is part of the SLURM. As I understand it, SLURM is something that
will use a a
type of MPI and launch the job for you.
But still, I am pretty sure that "-n 16" should be given to srun, not Ray.
If it is working already, I guess that srun is "stealing" the "-n 16"
from Ray in
your command line.
According to https://computing.llnl.gov/tutorials/*slurm*/*slurm*.pdf
srun --ntask=16 hostname
Le 2012-05-18 15:26, nikos ioannidis a écrit :
Hello, sorry for repeating myself
in the previous question you told me that the command
14 srun ~/Ray-1.7/Ray -n 16 -k 35 -minimumCoverage 40 \
15 -p ~/Staphylococcus_aureus/frag_
1.fastq ~/Staphylococcus_aureus/frag_2.fastq\
16 -p ~/Staphylococcus_aureus/shortjump_1.fastq
~/Staphylococcus_aureus/shortjump_2.fastq\
17 -o Staphy1635c40
is not running properly, but i'm running in a cluster and the mpi is
in my path, also the message i get at the end of the job is:
NCPUS JobName State Timelimit
Submit Eligible Start
End NodeList
----- --------- ---------- ----- ---------- ---------- ------------
------------------- ------------------- -------------------
------------------- ---------------
16 staphy163+ COMPLETED 01:10:00
2012-05-18T09:41:43 ..............
r02c3b7
and if i put for example -n 96 it's working, am i correct or i have
to put mpiexec at the begging ? But i thing that this won't work with
srun in the cluster i'm working.
Thank you.
---------- Forwarded message ----------
From: *nikos ioannidis* <[email protected] <mailto:[email protected]>>
Date: Fri, May 18, 2012 at 7:31 PM
Subject: minimun coverage set up question
To: [email protected]
<mailto:[email protected]>
hello,
i have set the minimum coverage at 40 with kmar size at 35 of a
bacteria and i get this output:
861 Rank 0: the minimum coverage is 40
862 Rank 0: the peak coverage is 8
863 Rank 0: Assembler panic: no peak observed in the k-mer coverage
distribution.
864 Rank 0: to deal with the sequencing error rate, try to lower the
k-mer length (-k)
865 Rank 15: sent 50519 messages, received 50520 messages.
866 Rank 14: sent 50583 messages, received 50584 messages.
867 Rank 13: sent 50504 messages, received 50505 messages.
868 Rank 12: sent 50565 messages, received 50566 messages.
869 Rank 11: sent 50318 messages, received 50319 messages.
870 Rank 10: sent 50318 messages, received 50319 messages.
871 Rank 9: sent 50328 messages, received 50329 messages.
872 Rank 8: sent 50590 messages, received 50591 messages.
873 Rank 7: sent 50494 messages, received 50495 messages.
874 Rank 6: sent 50421 messages, received 50422 messages.
875 Rank 5: sent 50401 messages, received 50402 messages.
876 Rank 4: sent 72261 messages, received 72262 messages.
877 Rank 3: sent 118348 messages, received 118349 messages.
878 Rank 2: sent 118723 messages, received 118724 messages.
879 Rank 1: sent 118452 messages, received 118453 messages.
880 Rank 0: sent 118589 messages, received 118573 messages.
how can i set the average coverage? Because all the papers i see have
examined at coverage of N50, N40 , N30
also by this output i want to ask you if i'm running in parallel, the
Rank symbolize the spesific CPU/ task??
i gave this commant:
14 srun ~/Ray-1.7/Ray -n 16 -k 35 -minimumCoverage 40 \
15 -p ~/Staphylococcus_aureus/frag_1.fastq
~/Staphylococcus_aureus/frag_2.fastq\
16 -p ~/Staphylococcus_aureus/shortjump_1.fastq
~/Staphylococcus_aureus/shortjump_2.fastq\
17 -o Staphy1635c40
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