cimendes
commented
4 months ago Test on HAV genome dataset (n=5)
User time (seconds): 1.65
System time (seconds): 0.14
Percent of CPU this job got: 3%
Elapsed (wall clock) time (h:mm:ss or m:ss): 0:50.70
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): 59228
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 1
Minor (reclaiming a frame) page faults: 25098
Voluntary context switches: 420
Involuntary context switches: 23
Swaps: 0
File system inputs: 8
File system outputs: 104
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0Test on K. pneumoniae dataset (n=5)
User time (seconds): 2.63
System time (seconds): 0.26
Percent of CPU this job got: 0%
Elapsed (wall clock) time (h:mm:ss or m:ss): 5:19.23
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): 58984
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 25137
Voluntary context switches: 2287
Involuntary context switches: 125
Swaps: 0
File system inputs: 0
File system outputs: 112
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0Mix bacterial dataset (n=10)
Command being timed: "miniwdl run --task ksnp3 /home/ines_mendes/Git/public_health_bioinformatics/tasks/phylogenetic_inference/task_ksnp3.wdl assembly_fasta= /home/ines_mendes/Test/klebsiella/ERR3671149_contigs.fasta samplename=ERR3671149 assembly_fasta= /home/ines_mendes/Test/klebsiella/INF001_contigs.fasta samplename=INF001 assembly_fasta= /home/ines_mendes/Test/klebsiella/INF088_contigs.fasta samplename=INF088 assembly_fasta= /home/ines_mendes/Test/klebsiella/INF100_contigs.fasta samplename=INF100 assembly_fasta= /home/ines_mendes/Test/klebsiella/klebsiella_pneumoniae_st111_NZ_CP013711.fasta samplename=NZ_CP013711 assembly_fasta= /home/ines_mendes/Test/a_baumannii/NZ_CP043953.fasta samplename=NZ_CP043953 assembly_fasta= /home/ines_mendes/Test/a_baumannii/NZ_CP072398.fasta samplename=NZ_CP072398 assembly_fasta= /home/ines_mendes/Test/a_baumannii/SRR23620612_contigs.fasta samplename=SRR23620612 assembly_fasta= /home/ines_mendes/Test/enterococcus_faecium/ERR2407653_contigs.fasta samplename=ERR2407653 assembly_fasta= /home/ines_mendes/Test/vibrio/ERR10146580_contigs.fasta samplename=ERR10146580 cluster_name=mix_samples"
User time (seconds): 4.26
System time (seconds): 0.35
Percent of CPU this job got: 0%
Elapsed (wall clock) time (h:mm:ss or m:ss): 9:52.20
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): 60536
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 25
Minor (reclaiming a frame) page faults: 25252
Voluntary context switches: 4260
Involuntary context switches: 183
Swaps: 0
File system inputs: 3248
File system outputs: 176
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0
:bug:
:pencil: Describe the Issue
The ksnp3 task doesnt take CPUs as input. Check what happens. Does it use all available CPUs?
This is the most expensive task to run currently ($30.80 per 1000 runs).
Run the task and figure out how much RAM is normally used (/usr/bin/time -v cmd). Does it really need 8GB? Does it require a 100GB local disk? How much processing time is used and calculate the utilisation of the CPUs? If its not making use of all 4, adjust the task to use less.