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The time -v output of the non-abund pangenome database curation suggesting the resources should be set to ~20GB and 2hrs per database.
Command being timed: "./make-pangenome-sketches.py /home/baumlerc/2022-database-covers/dbs/gtdb-rs214-k21.zip -t /home/baumlerc/2022-database-covers/dbs/gtdb-rs214.lineages.sqldb -o test-no-abund.zip -k 21
-r species --csv the-csv-file-you-desire_no-abund.csv"
User time (seconds): 4469.89
System time (seconds): 566.98
Percent of CPU this job got: 83%
Elapsed (wall clock) time (h:mm:ss or m:ss): 1:39:58
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): 17040560
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 96200
Minor (reclaiming a frame) page faults: 88823161
Voluntary context switches: 5672989
Involuntary context switches: 60363
Swaps: 0
File system inputs: 51679104
File system outputs: 5437344
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0
When running the script with all the bells and whistles this time -v output suggests that the slurm resources should be set to >40GB and >2hrs.
Command being timed: "./make-pangenome-sketches.py /home/baumlerc/2022-database-covers/dbs/gtdb-rs214-k21.zip -t /home/baumlerc/2022-database-covers/dbs/gtdb-rs214.lineages.sqldb -o test.zip -k 21 -r species -a --csv the-csv-file-you-desire.csv"
User time (seconds): 5800.88
System time (seconds): 717.47
Percent of CPU this job got: 87%
Elapsed (wall clock) time (h:mm:ss or m:ss): 2:04:42
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): 39818112
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 96751
Minor (reclaiming a frame) page faults: 162501748
Voluntary context switches: 5673639
Involuntary context switches: 67568
Swaps: 0
File system inputs: 51784920
File system outputs: 5634248
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0
The text was updated successfully, but these errors were encountered:
The
time -v
output of the non-abund pangenome database curation suggesting the resources should be set to ~20GB and 2hrs per database.When running the script with all the bells and whistles this
time -v
output suggests that the slurm resources should be set to >40GB and >2hrs.The text was updated successfully, but these errors were encountered: