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Process monitoring

Objectifs

les commandes `w`, `ps`, `kill`, `top`
  • w affiche les utilisateurs et les processus associés

  • ps liste les processus en train de tourner
  • ps -uax affiche la liste de tous les processus associés à chaque utilisateur

  • top liste les processus en train de tourner 
top - 16:44:51 up 156 days, 23:10,  1 user,  load average: 10,37, 9,80, 9,71
Tasks: 200 total,   3 running, 197 sleeping,   0 stopped,   0 zombie
%Cpu(s):  0,0 us,  0,1 sy, 88,5 ni, 11,5 id,  0,0 wa,  0,0 hi,  0,0 si,  0,0 st
KiB Mem : 65774384 total, 42442784 free,  1907228 used, 21424372 buff/cache
KiB Swap:  8388604 total,  5512296 free,  2876308 used. 62871460 avail Mem 

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND                                                                                                                   
18905 daron     30  10  916508 307308    976 R 960,8  0,5  51:38.57 admixture                                                                                                                 
 3446 daron     30  10 1130556 937640   2584 R 100,0  1,4 308:00.92 treemix                                                                                                                   
19307 trancha+  20   0  146164   2124   1424 R   0,3  0,0   0:00.02 top                                                                                                                       
22389 root      20   0       0      0      0 S   0,3  0,0   0:00.17 kworker/10:2

Tip

`c` → Afficher la commande complète en exécution  
`V` → Afficher en mode arborescence  
`M`,`P` -> Trier les ps par %mem et %cpu  
`1` → Afficher l’activité CPU (une ligne/CPU)  
`u` → Faire une recherche sur un utilisateur en particulier  
`i` → Ne pas afficher les tâches inactives (idle)  
`q` →  pour quitter
  • kill -9 <PID> tuer un processus
[tranchant@master0 ~]$ ps aux | grep “tranchant”
tranchant   20999  0.0  0.0 116748  3532 pts/1    Ss+  13:24   0:00 -bash
tranchant   21669  0.0  0.0 176384 22752 pts/1    R    13:33   0:00 perl toggleGenerator.pl -d /data3/projects/riceAnnot/TOG5681/Illumina/

[tranchant@master0 ~]$ kill -9 21669

Practice#

Displaying the list of processes#

  • Type the command w through 2 consoles : one connected on bioinfo-master, the other connected on one node
  • Type (on the node) the command ps without option, then with the option u, ua, uax
  • Type the command top on the node
  • Then use the "option" c to display the complete process
  • Then use the "option" u to display only your processes

Kill a process - downloading files from SRA through two ways#

  • Go into the directory LINUX4JEDI-TP/1-fastq
  • Display the size of all fastq files - ls -lh, du -h

We want to download one fastq file from NCBI SRA (available here https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=518559) using SRAtoolkit as below :

{% highlight bash %} module load bioinfo/sratoolkit/2.9.2 fastq-dump --gzip --split-files SRXXXX

This will download the SRA file (in sra format) and then convert them to fastq.gz file . More details on https://isugenomics.github.io/bioinformatics-workbook/dataAcquisition/fileTransfer/sra.html

  • Download the fastq file in the directory LINUX4JEDI-TP/1-fastq fastq-dump, &
  • Check that 2 fastq files are downloading ls -lhrt, watch -n 5 -d
  • Display the list of processes ps -ux, jobs
  • kill your process "fastq-dump" directly from bioinfo-master kill -9