LSF LOAD_INDEX

LOAD_INDEX配置说明涉及动态负载指数的调度和暂停条件。当loadSched条件满足时,作业才会被调度到主机;若无RESUME_COND指定,恢复作业也需满足此条件。如果loadStop条件达成,主机上的作业会被暂停。该设置允许使用简单逻辑AND/OR定义条件,并且未设置阈值的负载指数不会影响作业调度。当主机上仅有批处理作业运行且系统处于交互式空闲状态时,LSF不会暂停作业。示例中展示了如何配置内存和交换空间的阈值以生成调度和暂停条件。

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LOAD_INDEX

Specifies scheduling and suspending thresholds for the specified dynamic load index.

Syntax

load_index=loadSched[/loadStop]
Specify io, it, ls, mem, pg, r15s, r1m, r15m, swp, tmp, ut, or a non-shared custom external load index. Specify multiple lines to configure thresholds for multiple load indices.

Specify io, it, ls, mem, pg, r15s, r1m, r15m, swp, tmp, ut, or a non-shared custom external load index as a column. Specify multiple columns to configure thresholds for multiple load indices.

Description

The loadSched condition must be satisfied before a job is dispatched to the host. If a RESUME_COND is not specified, the loadSched condition must also be satisfied before a suspended job can be resumed.

If the loadStop condition is satisfied, a job on the host is suspended.

The loadSched and loadStop thresholds permit the specification of conditions using simple AND/OR logic. Any load index that does not have a configured threshold has no effect on job scheduling.

LSF does not suspend a job if the job is the only batch job running on the host and the machine is interactively idle (it>0).

The r15s, r1m, and r15m CPU run queue length conditions are compared to the effective queue length as reported by lsload -E, which is normalized for multiprocessor hosts. Thresholds for these parameters should be set at appropriate levels for single processor hosts.

Example

MEM=100/10

SWAP=200/30

These two lines translate into a loadSched condition of
mem>=100 && swap>=200

and a loadStop condition of
mem < 10 || swap < 30

Default

Not defined

``` #!/bin/sh #BSUB -J MUMmer_Batch[1-145] # 作业名称,使用数组作业[1-145] #BSUB -n 10 # 请求20个CPU核心(供nucmer使用) #BSUB -R "span[hosts=1]" # 限制任务在单个节点运行 #BSUB -o MUMmer.%J.%I.out # 输出日志(%J=作业ID,%I=数组索引) #BSUB -e MUMmer.%J.%I.err # 错误日志 #BSUB -q normal # 提交到normal队列 module load MUMmer/4.0.0beta2 # 定义路径和参考基因组 input="/public/home/yding24/pangenome/PanRice" ref="${input}/MH63RS3.fasta" # 参考基因组路径(修正文件名) query_dir="${input}" # 查询基因组目录 output_dir="${input}/genomeFilter" # 输出目录 # 创建输出目录 mkdir -p "${output_dir}" # 读取查询基因组标识列表(假设144.accs.txt包含145行) query_ids=( $(cut -f1 "${input}/144.accs.txt") ) index=$LSB_JOBINDEX # 数组作业索引(1-145) i="${query_ids[$index-1]}" # 获取当前任务的基因组标识 # 执行比对流程 echo "Processing genome: $i (Index: $index)" # Step 1: nucmer比对 bsub -K -J "nuc_${i}" -n 20 -R "span[hosts=1]" \ -o "${output_dir}/nuc.${i}.out" -e "${output_dir}/nuc.${i}.err" \ "nucmer -l 50 -c 100 -g 30 -t 20 \ -p ${output_dir}/MH63_RP_${i} \ ${ref} ${query_dir}/${i}.fasta" # Step 2: delta-filter(依赖nucmer完成) bsub -K -J "delta_${i}" -n 1 -w "done(nuc_${i})" \ -o "${output_dir}/delta.${i}.out" -e "${output_dir}/delta.${i}.err" \ "delta-filter -g -r -q -i 90 -l 50 \ ${output_dir}/MH63_RP_${i}.delta > ${output_dir}/MH63_RP_${i}.filtered.delta" # Step 3: show-coords(依赖delta-filter完成) bsub -K -J "coords_${i}" -n 1 -w "done(delta_${i})" \ -o "${output_dir}/coords.${i}.out" -e "${output_dir}/coords.${i}.err" \ "show-coords -T ${output_dir}/MH63_RP_${i}.filtered.delta > ${output_dir}/MH63_RP_${i}.filtered.coords"```第二个作业依赖于第一个输出文件,第三个作业依赖于第二个输出文件,如何更改代码
03-30
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