What tools/ commands must be used for time and memory usage estimation of an aligner
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14 months ago

Hi Everyone!!

I have been lately reading several papers on the comparison between different aligners, and measurement of the computation time and maximum memory usage. However, none of them specify/furnish the scripts used to do so.

Are their scripts/tools already existing that can help achieve the same that are otherwise not reported in the papers?

alignment assembly next-gen • 1.1k views
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Entering edit mode
14 months ago

you can search around for linux tools to measure this (given that you are on a linux system).

few that come to mind already: time , memrec , ps or top , or cluster monitoring tools if you run this on an HPC system

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14 months ago
shelkmike ▴ 550

If you want to see how much RAM a command used and how long it worked, instead of

command

run it as

/usr/bin/time -v command
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This gives RAM in percentage which sometimes goes above 100% (not here but I have noticed). Also, why does the two time command gives two different output and which one should be used to compare time involved in alignment using different genome sequence aligners?

(base) baadalvm@baadalvm:~$ /usr/bin/time -v conda install mamba -c conda-forge/label/mamba-alpha -c conda-forge
Collecting package metadata (current_repodata.json): done
Solving environment: done

All requested packages already installed.

    Command being timed: "conda install mamba -c conda-forge/label/mamba-alpha -c conda-forge"
    User time (seconds): 11.94
    System time (seconds): 3.47
    Percent of CPU this job got: 68%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:22.43
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 361928
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 135
    Minor (reclaiming a frame) page faults: 136303
    Voluntary context switches: 24018
    Involuntary context switches: 1338
    Swaps: 0
    File system inputs: 165096
    File system outputs: 101824
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0
(base) baadalvm@baadalvm:~$ time conda install mamba -c conda-forge/label/mamba-alpha -c conda-forge
Collecting package metadata (current_repodata.json): done
Solving environment: done

# All requested packages already installed.


real    0m7.687s
user    0m6.448s
sys     0m0.921s
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if % RAM goes above 100 it usually indicates a multithreaded process

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