These are chat archives for dereneaton/ipyrad

29th
Jul 2017
Wind-ant
@Wind-ant
Jul 29 2017 01:28
When I run ipyrad in HPC, the report said that "No ipcluster instance found",should I add follow sentences-ipcluster start --n20 --engines=MPI --ip=* --daemonize?Then it looks like:
cd /GS01/home/chej2td/luozhihu/tibezhao
/GS01/software/bin/mpirun --mca btl openib,self \
ipcluster start --n20 --engines=MPI --ip=* --daemonize
sleep 60
ipyrad -p params-tibezhao_assembled.txt -s 123 -c 20 --MPI -d
ipcluster stop
any suggestion for my script will be pleasure
Deren Eaton
@dereneaton
Jul 29 2017 14:50
Hi @Wind-ant , we're still working on a better tutorial/documentation for the ipcluster setup.
If you start ipcluster then you do not need to use the --MPI flag with ipyrad. Just the following:
Wind-ant
@Wind-ant
Jul 29 2017 14:58
I had the same problem like @JStarrett ,my process was stucked in step3,no error report and no file generated, the directory clsut_0.85 is empty all the time,what should I do?
the step1 and step 2 is normal,
Wind-ant
@Wind-ant
Jul 29 2017 15:23
and when I wanna kill it,the system said:qdel: Server could not connect to MOM 112298.kop.cn,so I could only wait for the administrator to stop it.