This page shows you how to run a regular bash script as a pipeline. The runAsPipeline script, accessible through the rcbio/1.2 module, converts an input bash script to a pipeline that easily submits jobs to the Slurm scheduler for you.
Features of the new pipeline:
Submit each step as a cluster job using sbatch.
Automatically arrange dependencies among jobs.
Email notifications are sent when each job fails or succeeds.
If a job fails, all its downstream jobs automatically are killed.
When re-running the pipeline on the same data folder, if there are any unfinished jobs, the user is asked to kill them or not.
When re-running the pipeline on the same data folder, the user is asked to confirm to re-run or not if a step was done successfully earlier.
Please read below for an example.
If you need help connecting to O2, please review the Using Slurm Basic and the How to Login to O2 wiki pages.
From Windows, use the graphical PuTTY program to connect to o2.hms.harvard.edu and make sure the port is set to the default value of 22.
From a Mac Terminal, use the ssh command, inserting your eCommons ID instead of user123:
ssh user123@o2.hms.harvard.edu |
For example, for user abc123, the working directory will be
srun --pty -p interactive -t 0-12:0:0 --mem 2000MB -c 1 /bin/bash mkdir /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline cd /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline |
# This will setup the path and environmental variables for the pipeline module load rcbio/1.2 |
echo -e "John Paul\nMike Smith\nNick Will\nJulia Johnson\nTom Jones" > universityA.txt cp universityA.txt universityB.txt |
# this command shows the content of file universityA.txt cat universityA.txt # Below is the content of universityA.txt John Paul Mike Smith Nick Will Julia Johnson Tom Jones |
# this command shows the content of file universityB.txt cat universityB.txt # below is the content of universityB.txt John Paul Mike Smith Nick Will Julia Johnson Tom Jones |
cp /n/app/rcbio/1.2/bin/bashScriptV1.sh .
# Below is the content of bashScriptV1.sh
cat bashScriptV1.sh
#!/bin/sh
for i in A B; do
u=university$i.txt
grep -H John $u >> John.txt; grep -H Mike $u >> Mike.txt
grep -H Nick $u >> Nick.txt; grep -H Julia $u >> Julia.txt
done
cat John.txt Mike.txt Nick.txt Julia.txt > all.txt |
How does this bash script work?
There is a loop that goes through the two university text files (for loop in line 6 above) to search for John and Mike (line 10 above), and then searches for Nick and Julia (line 12 above). After all searching is finished (line 13 above), then the results are merged into a single text file (line 15 above) . This means that the merge step (line 15 above) has to wait until the earlier two steps (line 10 and 12 above) are finished. However, the runAsPipeline workflow builder can't read this script directly. We will need to create a modified bash script that adds parts that explicitly tell the workflow builder the order in which the jobs need to run, among other things.
cp /n/app/rcbio/1.2/bin/bashScriptV2.sh .
cat bashScriptV2.sh
# Below is the conten of bashScriptV2.sh
#!/bin/sh
for i in A B; do
u=university$i.txt
#@1,0,find1,u,sbatch -p short -c 1 -t 50:0
grep -H John $u >> John.txt; grep -H Mike $u >> Mike.txt
#@2,0,find2,u,sbatch -p short -c 1 -t 50:0
grep -H Nick $u >> Nick.txt; grep -H Julia $u >> Julia.txt
done
#@3,1.2,merge
cat John.txt Mike.txt Nick.txt Julia.txt > all.txt |
Notice that there are a few things added to the script here:
Step 1 is denoted by #@1,0,find1,u,sbatch -p short -c 1 -t 50:0 (line 10 above), which means this is step 1 that depends on no other step, is named find1, and file $u needs to be copied to the /tmp directory. The sbatch command tells the pipeline runner the sbatch command to run this step.
Step 2 is denoted by #@2,0,find2,u (line 13 above), which means this is step2 that depends on no other step, is named find2, and file $u needs to be copy to /tmp directory. The sbatch command tells the pipeline runner the sbatch command to run this step.
Step 3 is denoted by #@3,1.2,merge, (line 18), which means that this is step3 that depends on step1 and step2, and the step is named merge. Notice, there is no sbatch here, so the pipeline runner will use default sbatch command from command line (see below).
Notice the format of step annotation is #@stepID,dependIDs,stepName,reference,sbatchOptions. Reference is optional, which allows the pipeline runner to copy data (file or folder) to local /tmp folder on the computing node to speed up the software. sbatchOptions is also optional, and when it is missing, the pipeline runner will use the default sbatch command given from command line (see below).
Here are two more examples:
#@4,1.3,map,,sbatch -p short -c 1 -t 50:0 Means step4 depends on step1 and step3, named map, no reference data to copy, with sbatch -p short -c 1 -t 50:0
#@3,1.2,align,db1.db2 Means step3 depends on step1 and step2, named align, $db1 and $db2 as reference data to be copied to /tmp , with default sbatch command (see below).
runAsPipeline bashScriptV2.sh "sbatch -p short -t 10:0 -c 1" useTmp |
This command will generate new bash script named slurmPipeLine.201801100946.sh in flag folder (201801100946 is the timestamp that runAsPipeline was invoked at). Then test run it, meaning does not really submit jobs, but only create a fake job id, 123 for each step. If you were to append run at the end of the command, the pipeline would actually be submitted to the Slurm scheduler.
Ideally, with 'useTmp', the software should run faster using local /tmp disk space for database/reference than the network storage. For this small query, the difference is small, or even slower if you use local /tmp. If you don't need /tmp, you can use noTmp.
With useTmp, the pipeline runner copy related data to /tmp and all file paths will be automatically updated to reflect a file's location in /tmp when using the useTmp option.
Note that only step 2 used -t 50:0, and all other steps used the default -t 10:0. The default walltime limit was set in the runAsPipeline command, and the walltime parameter for step 2 was set in the bash_script_v2.sh script.
runAsPipeline bashScriptV2.sh "sbatch -p short -t 10:0 -c 1" useTmp # Below is the output: converting bashScriptV2.sh to flag/slurmPipeLine.201801161424.sh find loopStart: for i in A B; do find job marker: #@1,0,find1,u: find job: grep -H John $u >> John.txt; grep -H Mike $u >> Mike.txt find job marker: #@2,0,find2,u,sbatch -p short -c 1 -t 50:0 sbatch options: sbatch -p short -c 1 -t 50:0 find job: grep -H Nick $u >> Nick.txt; grep -H Julia $u >> Julia.txt find loopend: done find job marker: #@3,1.2,merge: find job: cat John.txt Mike.txt Nick.txt Julia.txt > all.txt flag/slurmPipeLine.201801161424.sh .sh is ready to run. Starting to run ... Running flag/slurmPipeLine.201801161424.sh bashScriptV2.sh --------------------------------------------------------- step: 1, depends on: 0, job name: find1, flag: find1.A reference: .u depend on no job sbatch -p short -t 10:0 -c 1 --nodes=1 -J 1.0.find1.A -o /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/1.0.find1.A.out -e /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/1.0.find1.A.out /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/1.0.find1.A.sh # Submitted batch job 123 step: 2, depends on: 0, job name: find2, flag: find2.A reference: .u depend on no job sbatch -p short -c 1 -t 50:0 --nodes=1 -J 2.0.find2.A -o /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/2.0.find2.A.out -e /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/2.0.find2.A.out /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/2.0.find2.A.sh # Submitted batch job 123 step: 1, depends on: 0, job name: find1, flag: find1.B reference: .u depend on no job sbatch -p short -t 10:0 -c 1 --nodes=1 -J 1.0.find1.B -o /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/1.0.find1.B.out -e /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/1.0.find1.B.out /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/1.0.find1.B.sh # Submitted batch job 123 step: 2, depends on: 0, job name: find2, flag: find2.B reference: .u depend on no job sbatch -p short -c 1 -t 50:0 --nodes=1 -J 2.0.find2.B -o /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/2.0.find2.B.out -e /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/2.0.find2.B.out /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/2.0.find2.B.sh # Submitted batch job 123 step: 3, depends on: 1.2, job name: merge, flag: merge reference: depend on multiple jobs sbatch -p short -t 10:0 -c 1 --nodes=1 --dependency=afterok:123:123:123:123 -J 3.1.2.merge -o /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/3.1.2.merge.out -e /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/3.1.2.merge.out /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/3.1.2.merge.sh # Submitted batch job 123 all submitted jobs: job_id depend_on job_flag 123 null 1.0.find1.A 123 null 2.0.find2.A 123 null 1.0.find1.B 123 null 2.0.find2.B 123 ..123.123..123.123 3.1.2.merge --------------------------------------------------------- |
Thus far in the example, we have not actually submitted any jobs to the scheduler. To submit the pipeline, you will need to append the run parameter to the command. If run is not specified, test mode will be used, which does not submit jobs and gives theplaceholder of 123 for jobids in the command's output.
runAsPipeline bashScriptV2.sh "sbatch -p short -t 10:0 -c 1" useTmp run # Below is the output converting bashScriptV2.sh to flag/slurmPipeLine.201801101002.run.sh find loopStart: #loopStart,i find job marker: for i in A B; do find job: grep -H John $u >> John.txt; grep -H Mike $u >> Mike.txt find job marker: #@2,0,find2,u,sbatch -p short -c 1 -t 50:0 sbatch options: sbatch -p short -c 1 -t 50:0 find job: grep -H Nick $u >> Nick.txt; grep -H Julia $u >> Julia.txt find loopend: done find job marker: #@3,1.2,merge: find job: cat John.txt Mike.txt Nick.txt Julia.txt > all.txt flag/slurmPipeLine.201801101002.run.sh is ready to run. Starting to run ... Running flag/slurmPipeLine.201801101002.run.sh --------------------------------------------------------- step: 1, depends on: 0, job name: find1, flag: find1.A reference: .u depend on no job sbatch -p short -t 10:0 -c 1 --kill-on-invalid-dep=yes --nodes=1 -J 1.0.find1.A -o /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/1.0.find1.A.out -e /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/1.0.find1.A.out /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/1.0.find1.A.sh # Submitted batch job 8091045 step: 2, depends on: 0, job name: find2, flag: find2.A reference: .u depend on no job sbatch -p short -c 1 -t 50:0 --kill-on-invalid-dep=yes --nodes=1 -J 2.0.find2.A -o /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/2.0.find2.A.out -e /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/2.0.find2.A.out /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/2.0.find2.A.sh # Submitted batch job 8091046 step: 1, depends on: 0, job name: find1, flag: find1.B reference: .u depend on no job sbatch -p short -t 10:0 -c 1 --kill-on-invalid-dep=yes --nodes=1 -J 1.0.find1.B -o /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/1.0.find1.B.out -e /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/1.0.find1.B.out /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/1.0.find1.B.sh # Submitted batch job 8091047 step: 2, depends on: 0, job name: find2, flag: find2.B reference: .u depend on no job sbatch -p short -c 1 -t 50:0 --kill-on-invalid-dep=yes --nodes=1 -J 2.0.find2.B -o /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/2.0.find2.B.out -e /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/2.0.find2.B.out /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/2.0.find2.B.sh # Submitted batch job 8091048 step: 3, depends on: 1.2, job name: merge, flag: merge reference: depend on multiple jobs sbatch -p short -t 10:0 -c 1 --kill-on-invalid-dep=yes --nodes=1 --dependency=afterok:8091045:8091047:8091046:8091048 -J 3.1.2.merge -o /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/3.1.2.merge.out -e /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/3.1.2.merge.out /n/scratch/users/a/abc123/testRunBashScriptAsSlurmPipeline/flag/3.1.2.merge.sh # Submitted batch job 8091049 all submitted jobs: job_id depend_on job_flag 8091045 null 1.0.find1.A 8091046 null 2.0.find2.A 8091047 null 1.0.find1.B 8091048 null 2.0.find2.B 8091049 ..8091045.8091047..8091046.8091048 3.1.2.merge --------------------------------------------------------- |
You can use the command:
squeue -u $USER |
To see the job status (running, pending, etc.). You also get two emails for each step, one at the start of the step, one at the end of the step.
You can use the command:
ls -l flag |
This command list all the logs created by the pipeline runner. *.sh files are the slurm scripts for each step, *.out files are output files for each step, *.success files means job successfully finished for each step and *.failed means job failed for each steps.
You also get two emails for each step, one at the start of the step, one at the end of the step.
You can use the command to cancel running and pending jobs:
cancelAllJobs flag/alljobs.jid |
You can rerun this command in the same folder
runAsPipeline bashScriptV2.sh "sbatch -p short -t 10:0 -c 1" useTmp run |
This command will check if the earlier run is finished or not. If not, ask user to kill the running jobs or not, then ask user to rerun the successfully finished steps or not. Click 'y', it will rerun, directly press 'enter' key, it will not rerun.
cd proper/directory module load rcbio/1.2 and all/related/modules #submit job with proper partition, time, number of cores and memory sbatch --requeue --mail-type=ALL -p short -t 2:0:0 -c 2 --mem 2G /working/directory/flag/stepID.loopID.stepName.sh Or: runSingleJob "module load bowtie/1.2.2; bowtie -x /n/groups/shared_databases/bowtie_indexes/hg19 -p 2 -1 read1.fq -2 read2.fq --sam > out.bam" "sbatch -p short -t 1:0:0 -c 2 -mem 8G" |
For details about the second option: Get more informative slurm email notification and logs through rcbio/1.2
If you have a bash script with multiple steps and you wish to run it as Slurm pipeline, modify your old script and add the notation to mark the start and end of any loops, and the start of any step for which you want to submit as an sbatch job. Then you can use runAsPipeline with your modified bash script, as detailed above.
In case you wonder how it works, here is a simple example to explain:
For each step per loop, the pipeline runner creates a file looks like this (here it is named flag.sh):
#!/bin/bash
srun -n 1 bash -c "{ echo I am running...; hostname; otherCommands; } && touch flag.success"
sleep 5
export SLURM_TIME_FORMAT=relative
echo Job done. Summary:
sacct --format=JobID,Submit,Start,End,State,Partition,ReqTRES%30,CPUTime,MaxRSS,NodeList%30 --units=M -j $SLURM_JOBID
sendJobFinishEmail.sh flag
[ -f flag.success ] && exit 0 || exit 1 |
Then submit with:
sbatch -p short -t 10:0 -o flag.out -e flag.out flag.sh |
sendJobFinishEmail.sh is in /n/app/rcbio/1.2/bin/
Let us know if you have any questions by emailing rchelp@hms.harvard.edu. Please include your working folder and the commands used in your email. Any comments and suggestions are welcome!
We have additional example ready-to-run workflows available, which may be of interest to you.