Latest revision as of 15:27, 6 June 2019

MSI Tutorial Resources[edit]

Link to the semester long LATIS Tutorial

http://latis.umn.edu/services-and-programs/research-support/2016-research-workshop-series

Link to broader list of MSI Tutorials

https://www.msi.umn.edu/tutorials/current

Stratus[edit]

How to add a second user to a given instance:

# Add the user:
sudo useradd -m -d /home/<username> -s /bin/bash <username>

# Now setup the SSH key for the new user:
sudo mkdir -p /home/<username>/.ssh
sudo chmod 700 /home/<username>/.ssh
sudo vi /home/<username>/.ssh/authorized_keys
#         [... paste in your PUBLIC (*.pub) key, save and quit ...]
sudo chown -R <username>:<username> /home/<username>/.ssh
sudo chmod 600 /home/<username>/.ssh/authorized_keys

# If desired, give the user sudo privileges
sudo passwd <username> #give the user a password, maybe the same as their username
sudo adduser <username> sudo

Mesabi[edit]

Common PBS commands[edit]

MSI uses a PBS scheduler. It's easy to find a lot of information online about how to use PBS, but here are some commonly used functions.

qsub mypbsscript.pbs  # submit a PBS script to schedule a job
qsub -t 1-22 arrayscript.sh # submit an array of jobs
qstat                 # check on job status
showstart <jobid>     # check when your scheduled job is due to begin (note this is always 
                      #   an overestimate, as it depends on walltimes for all running 
                      #   and queued jobs
acctinfo              # see total account service unit allocation, service units used by
                      #   each person, and fairshare status.

Example code to submit jobs on Mesabi[edit]

First, submitting a job is easiest with a PBS batch script. The following script, called kinship.pbs, runs a program called vcf2kinship to create a kinship matrix on MCTFR genotypes. It requests a single node and 12 processors on that node. It requests 25 GB of memory.

#!/bin/bash -l                                                                                                                                                              
#PBS -l walltime=10:00:00,nodes=1:ppn=12,mem=25gb                                                                                                                           
/home/vrie0006/hyoung/software/rvtests/executable/vcf2kinship --inVcf /home/vrie0006/hyoung/genotypes.vcf.gz \
      --bn \
      --thread 10 \
      --out /home/vrie0006/hyoung/kinship

That script can then be submitted for scheduling to the mesabi short queue on msi (MSI list of queues) as follows:

qsub -q short kinship.sh

You can then check the status of this job by running various commands.

To see when your job might start running use showstart <jobid> like this:

[ln0006:hyoung] showstart 4560951
job 4560951 requires 10 procs for 10:00:00

Estimated Rsv based start in                 2:10:44 on Wed Nov 29 23:58:00
Estimated Rsv based completion in           12:10:44 on Thu Nov 30 09:58:00

Best Partition: mesabipar

To check status use qstat:

[ln0006:hyoung] qstat
Job ID                    Name             User            Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
4560955.mesabim3.msi.umn.edu kinship.sh       vrie0006        01:02:54 R small

Here's an example of an array of 22 jobs to perform rvtests, with 1 job per chromosome. Note that in the script ${PBS_ARRAYID} denotes the job number, and can be used to differentiate jobs.

#!/bin/bash

#PBS -l walltime=24:00:00,nodes=1:ppn=1,mem=2gb
#PBS -m abe
#PBS -M datt0019@umn.edu

/home/vrie0006/datt0019/tools/rvtests/executable/rvtest 
--inVcf /home/vrie0006/datt0019/mctfr/vcf_files/chr${PBS_ARRAYID}.withRS.filtered.PASS.beagled.MZadded.vcf.gz 
--boltPlink /home/vrie0006/datt0019/mctfr/bed/cpd_merged 
--pheno /home/vrie0006/datt0019/mctfr/phenotypes/residualized_phenotypes.ped 
--pheno-name cpd 
--meta bolt 
--inverseNormal --qtl 
--out /home/vrie0006/datt0019/mctfr/gwas/cpd/chr${PBS_ARRAYID} 
--boltPlinkNoCheck 
--siteMACMin 10

That script can then be submitted for scheduling to mesabi as follows:

qsub -t 1-22 rvtests.sh

Interactive job[edit]

qsub -I -l walltime=5:00:00,mem=10gb,nodes=1:ppn=1