Using https://github.com/HenrikBengtsson/easycatfs/blob/develop/tests/bench-salmon-quant.sh, I get:

Wynton HPC

With low BeeGFS load:

easycatfs and catfs versions:
0.1.3
0.8.0-9000

salmon version:
salmon 1.6.0

Benchmark target:
 - Targets:
   1. ./athal_index
   2. ./data
cp: 0:03.56 (user=0.00 kernel=1.95) CPU=55% IO=(in=3845587 out=3845592)
1. salmon: 0:54.28 (user=311.17 kernel=5.10) CPU=582% IO=(in=4315848 out=3824)
2. salmon: 0:52.79 (user=308.42 kernel=4.70) CPU=593% IO=(in=4315848 out=3824)
3. salmon: 0:54.80 (user=320.56 kernel=4.86) CPU=593% IO=(in=4315848 out=3824)

Benchmark local mount:
 - Mount points:
   1. /scratch/535541.1.long.q/hb/ppid=14622/wynton/home/cbi/hb/repositories/ucsf-wynton/wynton-demo/easycatfs/salmon_tutorial/athal_index
   2. /scratch/535541.1.long.q/hb/ppid=14622/wynton/home/cbi/hb/repositories/ucsf-wynton/wynton-demo/easycatfs/salmon_tutorial/data
1. salmon: 0:45.29 (user=295.97 kernel=3.33) CPU=660% IO=(in=4315908 out=3824)
2. salmon: 0:44.27 (user=287.59 kernel=3.28) CPU=657% IO=(in=4315908 out=3824)
3. salmon: 0:43.77 (user=272.22 kernel=2.43) CPU=627% IO=(in=4315908 out=3824)

Another example with more load on BeeGFS:

easycatfs and catfs versions:
0.1.3
0.8.0-9000

salmon version:
salmon 1.6.0

Benchmark targets:
 - Targets
   1. ./athal_index
   2. ./data
cp: 0:10.22 (user=0.01 kernel=3.56) CPU=35% IO=(in=3845587 out=3845592)
1. salmon: 2:08.81 (user=388.51 kernel=14.41) CPU=312% IO=(in=4319888 out=3824)
2. salmon: 2:05.80 (user=405.19 kernel=13.87) CPU=333% IO=(in=4314216 out=3824)
3. salmon: 2:05.78 (user=396.45 kernel=13.20) CPU=325% IO=(in=4313456 out=3824)

Benchmark local mounts:
 - Mountpoints
   1. /scratch/537657.1.long.q/hb/ppid=176361/wynton/home/cbi/hb/repositories/ucsf-wynton/wynton-demo/easycatfs/salmon_tutorial/athal_index
   2. /scratch/537657.1.long.q/hb/ppid=176361/wynton/home/cbi/hb/repositories/ucsf-wynton/wynton-demo/easycatfs/salmon_tutorial/data
1. salmon: 0:45.28 (user=309.86 kernel=3.26) CPU=691% IO=(in=4319348 out=3824)
2. salmon: 0:44.77 (user=284.02 kernel=3.11) CPU=641% IO=(in=4313068 out=3824)
3. salmon: 0:44.77 (user=306.04 kernel=3.39) CPU=691% IO=(in=4306212 out=3824)

Rerunning with catfs using 2+3+10=15 threads instead of the default 2+5+100=107, cf. https://github.com/HenrikBengtsson/catfs/commit/8d2c1b0d2418a7a4b04002ef1f26465525a302f7. Seem to have no negative impact on these tests. Good.

easycatfs and catfs versions:
0.1.3-9002
0.8.0-9001

salmon version:
salmon 1.6.0

Benchmark targets:
 - Targets
   1. ./athal_index
   2. ./data
cp: 0:08.11 (user=0.02 kernel=3.04) CPU=37% IO=(in=3845587 out=3845592)
1. salmon: 1:32.30 (user=336.18 kernel=11.26) CPU=376% IO=(in=4310640 out=3824)
2. salmon: 1:35.85 (user=330.29 kernel=12.13) CPU=357% IO=(in=4317552 out=3824)
3. salmon: 1:08.80 (user=316.59 kernel=7.75) CPU=471% IO=(in=4319720 out=3824)

Benchmark local mounts:
 - Mountpoints
   1. /scratch/543116.1.long.q/hb/ppid=12772/wynton/home/cbi/hb/repositories/ucsf-wynton/wynton-demo/easycatfs/salmon_tutorial/athal_index
   2. /scratch/543116.1.long.q/hb/ppid=12772/wynton/home/cbi/hb/repositories/ucsf-wynton/wynton-demo/easycatfs/salmon_tutorial/data
1. salmon: 0:42.27 (user=275.00 kernel=2.83) CPU=657% IO=(in=4320980 out=3824)
2. salmon: 0:45.77 (user=288.46 kernel=3.42) CPU=637% IO=(in=4308124 out=3824)
3. salmon: 0:42.36 (user=287.51 kernel=3.31) CPU=686% IO=(in=4315908 out=3824)

HenrikBengtsson / easycatfs

BENCHMARK: RNAseq alignment using Salmon #9

Wynton HPC