FAQ

• wat

故障检修过程

故障检修平行问题

有时ipyrad在HPC系统中会出现平行运算的一些问题。首先会在运算节点上得到交互式壳（这里是带有 qsub -I 的YMMV），读者需要指定队列和特别的来源

qsub -I

ipcluster start —-n 4 —-daemonize

然后输入 ipython 打开ipython的会话。

import ipyparallel as ipp

rc = ipp.Client()
rc[:]

结果应当长这样：..parsed-literal:

Out[1]: <DirectView [0, 1, 2, 3]>

import ipyparallel as ipp

rc = ipp.Client(profile=“default”)
rc[:]

import ipyrad as ip

##
data = ip.load_json(“dir/path.json”)

print data._ipcluster

data = ip.Assembly(‘test’)

data.set_params(“raw_fastq_path”, “path_to_data/\*.gz”)
data.set_params(“barcodes_path”, “path_to_barcode.txt”)

data.run(“1”)

print data.stats
print data._ipcluster

{‘profile’: ‘default’, ‘engines’: ‘Local’, ‘quiet’: 0, ‘cluster_id’: ‘’, ‘timeout’: 120, ‘cores’: 48}

data.write_params(‘params-test.txt’)

不要忘了完成时终止ipcluster嗷嗷~~