Commit ad05e046 authored by Gökçe Aydos's avatar Gökçe Aydos 🎨
Browse files

Update README.md

parent 459abbf5
# 2021-06-18
STAR resource utilization using `/usr/bin/time -v ...` for indexing and mapping a human genome sample:
```
Command being timed: "make mapping"
User time (seconds): 95696.46
System time (seconds): 186.39
Percent of CPU this job got: 2717%
Elapsed (wall clock) time (h:mm:ss or m:ss): 58:47.95
...
Maximum resident set size (kbytes): 8569896
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 105
Minor (reclaiming a frame) page faults: 41258618
Voluntary context switches: 105982
Involuntary context switches: 170863
Swaps: 0
File system inputs: 61438504
File system outputs: 101940632
...
Page size (bytes): 4096
```
- resident set size (RSS): portion of process memory held in RAM but not swap
- [page fault](https://en.wikipedia.org/wiki/Page_fault)
- minor: data was loaded already by another process, but needs to be mapped by the MMU to the process'es memory range
- major: data loaded to RAM
- (invalid): cannot be read (segmentation fault), e.g., reading a null pointer
- context switches
- voluntary: process has nothing to do, so CPU can switch to another process
- involuntary: CPU switches to another process (enforces) even process can continue processing
- source: https://unix.stackexchange.com/questions/442969/what-exactly-are-voluntary-context-switches
- file system inputs/outputs: the total number of bytes read/written / 512
- source: https://stackoverflow.com/questions/42126913/what-does-file-system-outputs-mean-with-time-v
# 2021-06-16
- using Kubernetes one can start different Jupyter profiles reserving different resources
- some programs may require more than 1024 open files (e.g., STAR)
- configurable through https://wiki.archlinux.org/title/Limits.conf
- slurm srun funktioniert
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment