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nextflow.config
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nextflow.config
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manifest {
name = 'nf-core/MWAEoR-Pipeline'
description = 'MWA EoR pipeline'
}
params {
obsids_path = 'obsids.csv'
obsids_suffix = ''
quality_updates_path = 'quality-updates.csv'
tile_updates_path = 'tile-updates.csv'
visName = null
// //////// //
// metadata //
// //////// //
// set to 1 to include ppds in downloaded metafits
metafits_incl_ppds = 0
noppds = true
sky_chans = 131..154
filter_sweet_pointings = null
filter_ew_pointings = null
// (12.5%)
filter_bad_tile_frac = 16.01 / 128
filter_dead_dipole_frac = null
filter_quality = 1
filter_config = null
filter_eorfield = null
filter_eorband = null
filter_ra = null
filter_dec = null
filter_ionoqa = null
filter_sun_elevation = null
filter_min_sun_pointing_distance = null
asvo_api_key = "${MWA_ASVO_API_KEY}"
// disable all qa
noqa = false
nodemo = true
// ///////////// //
// preprocessing //
// ///////////// //
noprep = false
prepByCh = false
// pull prep from acacia if available
pullPrep = true
// tag to add to the end of prep files
prep_suffix = ''
prep_time_res_s = 2
prep_freq_res_khz = 40
prep_rfi = true
prep_pc = null
prep_edge_width = null
van_vleck = false
// use --nopreqa to disable prepVisQA and flagQA
noprepqa = false
noplotprepqa = false
nossins = false
// when you want to do prepVisQA but not use its filter
noprepqafilter = false
noautoplot = true
// //////// //
// flagging //
// //////// //
noflag = false
// add extra ssins plots for each rx
ssins_by_rx = false
flag_occupancy_threshold = 0.99
rfi_occupancy_threshold = 0.25
ssins_occupancy_threshold = 0.99
ssins_narrow_threshold = null
// arbitrary (1308 pass, 2024 fail of 17488)
ssins_dab_threshold = 0.05
// median=9% + std=22% * 1 = 31% (7059 pass, 2076 fail, of 17488 total)
ssins_streak_threshold = 0.31
ssins_apply = false
noplotprepqa = false
// /////////// //
// calibration //
// /////////// //
// use --nocal to skip calibration
nocal = false
// use --nophasefits to disable phase fit analysis
nophasefits = false
// use --fitphase to apply fitted phases
fitphase = false
// pull calsol from acacia if available
pullCalSol = true
// use --noManualFlags to disable reading flags from tile updates csv
noManualFlags = false
// use --noPrepFlags to disable flags from prepVisQA
noPrepFlags = false
// use --noCalFlags to disable flags from calQA
noCalFlags = false
nosrclist = true
noplotcalqa = false
// string to add to the end of the cal directory
cal_suffix = ''
// hyperdrive di-cal args
// - key: short name that appears in calibration solution filename
// - value: args for hyperdrive di-cal
dical_name = "30l_src8k_300it"
dical_args = "--uvw-min 30l -n 8000 --max-iterations 300 --stop-thresh 1e-20"
// mwa-reduce calibrate args
// rexcal_name = "30l_src100"
// rexcal_args = ""
// path/of/mwa_full_embedded_element_pattern.h5
beam_path = '<!!!>'
// path/of/sourcelist.txt
sourcelist = '<!!!>'
hyp_srclist_args = '--source-dist-cutoff=180 --veto-threshold 0.005'
// hyp_dical_args = "--max-iterations 300 --stop-thresh 1e-8"
hyp_dical_args = ""
hyp_sols_plot_args = '--no-ref-tile --max-amp 2'
hyp_peel_args = '--num-passes 5 --num-loops 6 --convergence 0.5'
nocalqa = false
filter_max_rms_convg = null
filter_max_unused_bl_frac = null
filter_max_unconvg_chs = null
// ///// //
// apply //
// ///// //
noapply = false
apply_time_res = 8
apply_freq_res = 80
apply_args = ''
nosub = true
noionosub = true
sub_nsrcs = 8000
ionosub_nsrcs = 1000
nocluster = true
// use --ignore-dut1 in hyperdrive apply
nodut1 = false
// file types
noms = true
nouv = false
// ////////// //
// visibility //
// ////////// //
noeor = true
nopsmetrics = false
nodelayspec = false
nopowerspec = false
noplotvisqa = false
nouvplot = true
// args to autoplot script, e.g. "--log_scale --transparent"
autoplot_args = ''
// filter (any) visibilities with too much window power
filter_max_ps_window_unsub = null
// filter unsubtracted visibilities with too little window power
filter_min_ps_window_unsub = null
// filter unsubtracted visibilities with too much window:wedge ratio
filter_max_ps_ratio_unsub = null
// filter unsubtracted visibilities with too little window:wedge ratio
filter_min_ps_ratio_unsub = null
// filter subtracted visibilities which subtract too little wedge power
filter_max_ps_wedge_ratio_sub = null
// filter subtracted visibilities which subtract too much wedge power
filter_min_ps_wedge_ratio_sub = null
// filter subtracted visibilities which subtract too little window power
filter_max_ps_win_ratio_sub = null
// filter subtracted visibilities which subtract too much window power
filter_min_ps_win_ratio_sub = null
// filter visibilities with too much ionospheric activity
filter_max_hyp_ionoqa = null
// /////// //
// imaging //
// /////// //
// -> dirty
noimg = false
noimgunsub = false
img_suffix = ''
img_weight = 'briggs -1.0'
img_size = 4096
img_scale = '40asec'
img_channels_out = '4 -join-channels'
img_intervals_out = '1'
img_split_intervals = false
img_split_coarse_chans = false
img_pol = 'xx,yy,v'
// -join-polarizations needs 2-4 polarizations
wsclean_args = ''
chgcentre_args = ''
// -> dconv only
nodeconv = false
wsclean_dconv_args = '-multiscale'
// https://wsclean.readthedocs.io/en/latest/basic_cleaning.html#threshold-and-maximum-number-of-iterations
img_niter = 1000
img_minor_clean_gain = 0.1
// https://wsclean.readthedocs.io/en/latest/basic_cleaning.html#using-cotton-schwab-the-mgain-parameter
img_major_clean_gain = 0.5
// https://wsclean.readthedocs.io/en/latest/basic_cleaning.html#automatic-threshold
img_auto_threshold = 1
// https://wsclean.readthedocs.io/en/latest/masking.html
img_auto_mask = 5
// path containing `mwa_full_embedded_element_pattern.h5`, can be symlink
img_mwa_path = '...'
// -> previews
krvis = false
nothumbnail = false
thumbnail_quantile = 0.95
thumbnail_vmin = null
thumbnail_vmax = null
thumbnail_args = ''
thumbnail_uvs = false
thumbnail_psfs = false
thumbnail_all_chans = false
thumbnail_limits = true
nopolcomp = true
nomontage = true
montage_by_pol = false
montage_by_sub = false
// -> videos:
// by default, only make videos for MFS thumbnails, polcomps and polmontages.
// -> make a video for each obsid, pol, img product scanning through channels
frame_chan_scan = false
// -> make a video for each channel, pol, img product scanning through obsids
frame_obs_scan = false
// -> imgqa
noimgqa = false
noplotimgqa = false
// filter images with too much stokes V RMS
filter_max_vrms_box_nosub = null
// filter images with too little unsubtracted stokes V RMS
filter_min_vrms_box_nosub = null
// filter images with too much integrated unsubtracted pks V power compared to (XX+YY)
filter_max_pks_int_v_ratio_nosub = null
// filter images with too little integrated unsubtracted pks V power compared to (XX+YY)
filter_min_pks_int_v_ratio_nosub = null
// filter images with too much difference between xx and yy integrated pks flux
filter_max_pks_int_diff_sub = null
// filter images with too little difference between xx and yy integrated pks flux
filter_min_pks_int_diff_sub = null
// filter images which don't subtract enough integrated pks flux xx
filter_max_pks_int_sub_ratio_xx = null
// filter images which subtract too much integrated pks flux xx
filter_min_pks_int_sub_ratio_xx = null
// filter images which don't subtract enough integrated pks flux yy
filter_max_pks_int_sub_ratio_yy = null
// filter images which subtract too much integrated pks flux yy
filter_min_pks_int_sub_ratio_yy = null
noimgcombine = true
nostackthumbs = true
// ///// //
// chips //
// ///// //
nochips = false
nochipscombine = true
groupByPointing = false
groupByLst = false
// lssa individual obs without combine
lssaObs = false
// number of obs in each chunk ()
chunkSize = 80
// allow incomplete chunks
chunkRemainder = true
// limit number of chunks in each group
chunkCount = 50
// bias modes (0/10/11/12) - 0 = full, 10 = high
lssa_bias_mode = 0
// maximum u coordinate
lssa_maxu = 300
// number of bins
lssa_nbins = 80
// lssa binary name, e.g. 'lssa_fg_simple', 'lssa_fg_nfft'
lssa_bin = 'lssa_fg_simple'
// chips plotting
noplotchips = false
kperp_max = 0.03
kperp_min = 0.02
kparra_min = 0.11
// cmt
k_edges = [0.00000, 0.0353895, 0.0707791, 0.106169, 0.141558, 0.176948, 0.212337, 0.247727, 0.283116, 0.318506, 0.353895, 0.389285, 0.424674, 0.460064, 0.495453, 0.530843, 0.566232, 0.601622, 0.637012, 0.672401, 0.707791, 0.743180, 0.778570, 0.813959, 0.849349, 0.884738, 0.920128, 0.955517, 0.990907, 1.02630, 1.06169, 1.09708, 1.13246, 1.16785, 1.20324, 1.23863, 1.27402, 1.30941, 1.34480, 1.38019, 1.41558, 1.45097, 1.48636, 1.52175, 1.55714, 1.59253, 1.62792, 1.66331, 1.69870, 1.73409]
// cmt / 2
// k_edges = [ 0.00000, 0.0707791, 0.141558, 0.212337, 0.283116, 0.353895, 0.424674, 0.495453, 0.566232, 0.637012, 0.707791, 0.778570, 0.849349, 0.920128, 0.990907, 1.06169, 1.13246, 1.20324, 1.27402, 1.34480, 1.41558, 1.48636, 1.55714, 1.62792, 1.69870 ]
demo_prelude = null
// results
result_suffix = ''
// novideo = false // use `--novideo=true` to skip video generation
novideo = true
// /////// //
// archive //
// /////// //
// use `--tarchive=true` to create tarballs of qa files
tarchive = false
// use `--archive=true` to enable archiving
archive = false
// use `--archive_prep=true` to enable archiving of preprocessed vis
archive_prep = false
// use `--archive_uvfits=true` to enable archiving of calibrated vis
archive_uvfits = false
// prefix for acacia bucket names
bucket_prefix = "mwaeor:high0"
// //// //
// lmod //
// //// //
singularity_lmod = 'singularity'
rclone_lmod = 'rclone'
squid_lmod = 'giant-squid/default'
birli_lmod = "birli/default"
hyperdrive_lmod = "hyperdrive/default"
wsclean_lmod = "wsclean/default"
// ///// //
// shims //
// ///// //
hyperdrive = 'hyperdrive'
birli = 'birli'
giant_squid = 'giant-squid'
rclone = 'rclone'
jq = 'jq'
ps_metrics = "ps_metrics"
proxy_prelude = ''
casa = 'casa'
wsclean = 'wsclean'
chgcentre = 'chgcentre'
mwa_reduce = ''
// misc defaults
num_gpus = 1
// /////////// //
// singularity //
// /////////// //
birli_sif = 'docker://mwatelescope/birli:latest'
giant_squid_sif = 'docker://mwatelescope/giant-squid:latest'
// hyperdrive_sif = 'docker://d3vnull0/mwa_hyperdrive:peel'
// hyperdrive_sif = 'docker://d3vnull0/mwa_hyperdrive:dev-cuda11.4.3-cascadelake'
// hyperdrive_sif = 'docker://d3vnull0/mwa_hyperdrive:peel-cuda11.4.3-cc70-x86-64-v2'
hyperdrive_sif = 'docker://d3vnull0/mwa_hyperdrive:peel-experiment'
mwa_qa_sif = 'docker://d3vnull0/mwa_qa:latest'
fitcal_sif = 'docker://d3vnull0/fitcal:latest'
tap_sif = 'docker://d3vnull0/tap:latest'
cotter_sif = 'docker://mwatelescope/cotter:latest'
casa_sif = 'docker://d3vnull0/casa:latest'
wsclean_sif = 'docker://paulhancock/wsclean:2.10.0-build-1'
ffmpeg_sif = 'docker://jrottenberg/ffmpeg:latest'
mwa_reduce_sif = ''
imagemagick_sif = 'docker://dpokidov/imagemagick:latest'
ssins_sif = 'docker://d3vnull0/ssins:latest'
mwax_mover_sif = 'docker://d3vnull0/mwax_mover:latest'
chips_sif = 'docker://d3vnull0/chips:latest'
chips_wrappers_sif = 'docker://d3vnull0/chips_wrappers:latest'
mwa_demo_sif = 'docker://mwatelescope/mwa-demo:main'
// give jobs longer runtimes to account for filesystem mismanagement
scratchFactor = 1
// command for counting the nubmer of GPUs
cmd_gpu_count = "nvidia-smi -L | wc -l"
}
process {
errorStrategy = 'ignore'
afterScript = 'set -x; ls -alh'
// cache = false
// global per-process rate limit
maxForks = 60
withLabel: rate_limit {
maxForks = 5
}
withLabel: rate_limit_20 {
maxForks = 20
}
withLabel: rate_limit_50 {
maxForks = 50
}
withLabel: mwa_demo {
container = "${params.mwa_demo_sif}"
}
}
executor {
exitReadTimeout = '5min'
queueSize = 10
jobName = { "nf-${task.process.split(':')[-1]}.${task.tag}" }
}
profiles {
hpc_data {
// aka zeus
singularity {
cacheDir = "/scratch/${PAWSEY_PROJECT}/${USER}/singularity"
enabled = true
runOptions = '--bind /scratch'
}
executor.queueSize = 50
process {
executor = 'slurm'
queue = 'copyq'
// memory = '60G'
// scratch = 'ram-disk'
// stageInMode = 'copy'
// stageOutMode = 'copy'
scratch = false
clusterOptions = "--account=${PAWSEY_PROJECT}"
withLabel: rclone {
module = 'rclone'
}
}
workDir = "${MYSCRATCH}/nfwork"
params {
outdir = "${MYSCRATCH}/nfdata"
resultsdir = "${MYSCRATCH}/nfresults"
giant_squid_sif = '/pawsey/mwa/singularity/giant-squid/giant-squid_latest.sif'
singularity_prefix = '[ $(command -v singularity) ] || module load singularity; singularity exec --bind /scratch'
giant_squid = "${params.singularity_prefix} ${params.giant_squid_sif} /opt/cargo/bin/giant-squid"
scratchFactor = 4
}
}
setonix {
// HPE Cray EX 235A
// work (1592):
// - 2 * EPYC 7763, “Milan” 64-Core 2.45GHz,
// - 256 GB RAM
// highmem (8) has 1TB RAM
// gpu (154):
// - 1 * EPYC 7A53 “Trento” 64-Core
// - 8 * AMD Instinct MI250X GPUs
// - 256 GB RAM
// gpu-highmem (38) has 512GB RAM
// no nvme!
// cd $MYSOFTWARE/MWAEoR-Pipeline; module load java/default singularity/default spack/default; nextflow run main.nf -profile setonix -w $MYSCRATCH/nfwork -c eor0high-dn-2024-04-03.conf --nothumbnail --nopolcomp --thumbnail_limits=false --novideo --obsids_suffix=-test --outdir=/scratch/${PAWSEY_PROJECT}/${USER}/nftest/
singularity {
cacheDir = "/scratch/${PAWSEY_PROJECT}/${USER}/singularity"
runOptions = '--home ${PWD} --cleanenv --bind /scratch --bind /software'
enabled = true
autoMounts = true
}
spack {
enabled = true
}
executor {
queueSize = 100
submitRateLimit = '20/1min'
jobName = { "nf-${task.process.split(':')[-1]}.${task.tag}" }
}
workDir = "${MYSCRATCH}/nfwork"
params {
outdir = "${MYSCRATCH}/nfdata"
resultsdir = "${MYSCRATCH}/nfresults"
// program shims
hyperdrive_sif = 'docker://d3vnull0/hyperdrive:v0.3.0-setonix-rocm6.1'
singularity_lmod = 'singularity/default'
spack_lmod = 'spack/default'
rclone_lmod = 'rclone/default'
squid_lmod = "giant-squid/1.0.3"
// birli_lmod = "birli/van_vleck-iqa7dmx"
birli_lmod = "birli/0.15.1"
hyperdrive_lmod = "hyperdrive-amd-gfx90a/0.4.1"
wsclean_lmod = "wsclean/3.4-idg-everybeam"
singularity_prefix = '[ $(command -v singularity) ] || ' + "module load ${params.singularity_lmod}; singularity exec --bind /scratch --bind /software"
giant_squid = "giant-squid"
rclone = "rclone"
jq = "/software/projects/mwaeor/dev/bin/jq"
casa = '' + "${params.singularity_prefix}" + ' --bind ${PWD} --writable-tmpfs --pwd ${PWD} --home ${PWD} --cleanenv ' + "${params.casa_sif} casa"
// calibration
sourcelist = '/software/projects/mwaeor/dev/srclist_pumav3_EoR0LoBES_EoR1pietro_CenA-GP_2023-11-07.yaml'
// https://github.com/JLBLine/srclists/blob/master/srclist_pumav3_EoR0LoBES_EoR1pietro_CenA-GP_2023-11-07.fits
beam_path = '/software/projects/mwaeor/dev/MWA_embedded_element_pattern_rev2_interp_167_197MHz.h5'
img_mwa_path = '/software/projects/mwaeor/dev/'
scratchFactor = 4
// cmd_gpu_count = "rocm-smi -a --json | jq -r '.|keys|.[]|select(startswith(\"card\"))' | wc -l"
cmd_gpu_count = "echo 1"
}
process {
executor = 'slurm'
queue = 'work'
// about 1/128 of a node
cpus = 2
// about 1/18 of a node
memory = 16.GB
time = 15.minute
clusterOptions = { "--nodes=1 --cpus-per-task=${task.cpus} --account=${PAWSEY_PROJECT}" }
scratch = 'ram-disk'
stageInMode = 'symlink'
stageOutMode = 'move'
beforeScript = 'set -x; chown ${USER}:${PAWSEY_PROJECT} ${NXF_SCRATCH:="."}; chmod g+rs ${NXF_SCRATCH:="."}; hostname; env | grep SLURM; sleep $((2 + $RANDOM % 15)); module load spack/default; date -Is; scontrol -d show node $SLURM_JOB_NODELIST'
withLabel: cpu_quarter {
cpus = 16
}
withLabel: cpu_half {
cpus = 32
}
withLabel: cpu_full {
cpus = 64
}
withLabel: mem_tiny {
memory = 1024.MB
}
withLabel: mem_quarter {
memory = 58880.MB
}
withLabel: mem_half {
memory = 117760.MB
}
withLabel: mem_full {
memory = 235520.MB
}
withLabel: mem_super {
queue = 'highmem'
memory = 505260.MB
}
withLabel: mem_ultra {
queue = 'highmem'
memory = 1010520.MB
}
// no nvme!
withLabel: gpu {
queue = 'gpu'
cpus = null
memory = null
clusterOptions = { "--nodes=1 --account=${PAWSEY_PROJECT}-gpu --gres=gpu:1" }
}
withLabel: gpu_nvme {
queue = 'gpu-highmem'
cpus = null
memory = null
clusterOptions = { "--nodes=1 --account=${PAWSEY_PROJECT}-gpu --gres=gpu:8" }
}
// withLabel: 'birli|hyperdrive|wsclean' {
// module = "spack/default"
// spack = "/software/projects/mwaeor/dev/setonix/2024.05/environments/astrospecs-dev/spack.yaml"
// container = null
// }
withLabel: birli {
module = "${params.birli_lmod}"
container = null
}
withLabel: hyperdrive {
module = { "${params.hyperdrive_lmod}" + (params.pullCalSol ? ":${params.rclone_lmod}" : "") }
container = null
}
withLabel: wsclean {
module = "${params.wsclean_lmod}"
container = null
}
withLabel: mwa_reduce {
module = "${params.singularity_lmod}"
container = "${params.mwa_reduce_sif}"
}
// withLabel: python {
// module = "${params.singularity_lmod}"
// container = "${params.mwa_qa_sif}"
// }
withLabel: fitcal {
module = "${params.singularity_lmod}"
container = "${params.fitcal_sif}"
}
withLabel: casa {
module = "${params.singularity_lmod}"
container = "${params.casa_sif}"
}
// withLabel: tap {
// module = "${params.singularity_lmod}"
// container = "${params.tap_sif}"
// }
withLabel: giant_squid {
module = { "${params.squid_lmod}" + (params.pullPrep ? ":${params.rclone_lmod}" : "") }
}
withLabel: chips {
module = "${params.singularity_lmod}"
container = "${params.chips_sif}"
afterScript = 'for log in $(ls -t syslog*.txt *.log); do echo "-> head $log"; head -n 100 $log; echo "-> tail $log"; tail -n 100 $log; done; ls -alh; du -hd0'
}
withLabel: chips_wrappers {
module = "${params.singularity_lmod}"
container = "${params.chips_wrappers_sif}"
}
withLabel: ffmpeg {
module = "${params.singularity_lmod}"
container = "${params.ffmpeg_sif}"
}
withLabel: imagemagick {
module = "${params.singularity_lmod}"
container = "${params.imagemagick_sif}"
}
// withLabel: ssins {
// module = "${params.singularity_lmod}"
// container = "${params.ssins_sif}"
// }
withLabel: mwax_mover {
module = "${params.singularity_lmod}"
container = "${params.mwax_mover_sif}"
}
withLabel: 'mwa_demo|python|tap|ssins' {
module = "${params.singularity_lmod}"
container = "${params.mwa_demo_sif}"
}
}
}
garrawarla {
// workq and gpuq:
// - 78 * HPE ProLiant XL190r Gen10 Servers
// - 2 * Xeon Gold 6230 “Cascade Lake” (20 core, 2.1GHz CPU)
// - 1 * NVIDIA Tesla V100 Tensor Core 32GB GPU
// - 38 usable cores when gpu enabled
// - 384 GB of DDR4-2933 RAM (360G usable)
// - 960GB NVMe drive (890G usable)
singularity {
cacheDir = "/scratch/${PAWSEY_PROJECT}/${USER}/singularity"
runOptions = '--home ${PWD} --cleanenv --bind /scratch'
enabled = true
autoMounts = true
}
executor {
queueSize = 100
submitRateLimit = '20/1min'
jobName = { "nf-${task.process.split(':')[-1]}.${task.tag}" }
}
workDir = "${MYSCRATCH}/nfwork"
params {
outdir = "${MYSCRATCH}/nfdata"
resultsdir = "${MYSCRATCH}/nfresults"
// binaries
singularity_prefix = '[ $(command -v singularity) ] || module load singularity; singularity exec --bind /scratch --bind /pawsey'
// hyperdrive = 'module use /pawsey/mwa/software/python3/modulefiles; module load hyperdrive; hyperdrive'
birli = "${params.singularity_prefix}" + ' --bind ${PWD}:/tmp --writable-tmpfs --pwd /tmp --home ${PWD} ' + " --cleanenv ${params.birli_sif} /opt/cargo/bin/birli"
// giant_squid = "${params.singularity_prefix} ${params.giant_squid_sif} /opt/cargo/bin/giant-squid"
giant_squid = "/pawsey/mwa/bin/giant-squid"
rclone = "/pawsey/mwa/bin/rclone"
jq = "/pawsey/mwa/bin/jq"
// wsclean = '${params.singularity_prefix} ${params.wsclean_sif} wsclean'
casa = "${params.singularity_prefix}" + ' --bind ${PWD}:/tmp --writable-tmpfs --pwd /tmp --home ${PWD} ' + " --cleanenv ${params.casa_sif} casa"
ps_metrics = 'ps_metrics'
mwa_reduce = "singularity exec -B /pawsey/mwa:/usr/lib/python3/dist-packages/mwapy/data ${params.mwa_reduce_sif}"
// calibration
// sourcelist = '/pawsey/mwa/software/python3/srclists/master/srclist_pumav3_EoR0LoBESv2_fixedEoR1pietro+ForA_phase1+2_edit.txt'
// sourcelist = '/pawsey/mwa/mwaeor/dev/srclists/srclist_pumav3_EoR0LoBESv2_fixedEoR1pietro+ForA_phase1+2_edit.txt'
sourcelist = '/pawsey/mwa/mwaeor/dev/LoBES/srclist_pumav3_EoR0LoBES_EoR1pietro_CenA-GP_2023-11-07.yaml'
// https://github.com/JLBLine/srclists/blob/master/srclist_pumav3_EoR0LoBES_EoR1pietro_CenA-GP_2023-11-07.fits
// beam_path = '/pawsey/mwa/mwa_full_embedded_element_pattern.h5'
beam_path = '/pawsey/mwa/MWA_embedded_element_pattern_rev2_interp_167_197MHz.h5'
img_mwa_path = '/pawsey/mwa'
singularity_lmod = 'singularity'
scratchFactor = 4
}
process {
executor = 'slurm'
queue = 'workq'
cpus = 2
// about 1/20 of a node
memory = 16.GB
// about 1/20 of a node
time = 15.minute
clusterOptions = { "--nodes=1 --cpus-per-task=${task.cpus} --account=${PAWSEY_PROJECT}" }
scratch = 'ram-disk'
stageInMode = 'copy'
stageOutMode = 'move'
beforeScript = 'set -x; chown ${USER}:${PAWSEY_PROJECT} ${NXF_SCRATCH:="."}; chmod g+rs ${NXF_SCRATCH:="."}; module use /pawsey/mwa/software/python3/modulefiles; module use /astro/mwaeor/software/modulefiles; hostname; env | grep SLURM; sleep $((2 + $RANDOM % 15)); date -Is'
// jobs which actually make use of multiprocessing
withLabel: cpu_quarter {
cpus = 9
}
withLabel: cpu_half {
cpus = 18
}
// jobs which will need maximum cpu count
withLabel: cpu_full {
cpus = 36
}
withLabel: mem_tiny {
memory = 1.GB
}
// jobs which need a bit more memory
withLabel: mem_quarter {
memory = 90.GB
}
withLabel: mem_half {
memory = 180.GB
}
// jobs which will need maximum memory
withLabel: mem_full {
memory = 360.GB
}
// processes which handle big files that don't fit in ramdisk
withLabel: nvme {
scratch = "/nvmetmp/"
clusterOptions = { "--nodes=1 --cpus-per-task=${task.cpus} --account=${PAWSEY_PROJECT} --tmp=100G" }
}
withLabel: nvme_full {
scratch = "/nvmetmp/"
clusterOptions = { "--nodes=1 --cpus-per-task=${task.cpus} --account=${PAWSEY_PROJECT} --tmp=880G" }
}
withLabel: gpu {
queue = 'gpuq'
clusterOptions = { "--nodes=1 --cpus-per-task=${task.cpus} --account=${PAWSEY_PROJECT} --gres=gpu:1" }
}
withLabel: gpu_nvme {
scratch = "/nvmetmp/"
queue = 'gpuq'
clusterOptions = { "--nodes=1 --cpus-per-task=${task.cpus} --account=${PAWSEY_PROJECT} --gres=gpu:1 --tmp=100G" }
}
// salloc --nodes=1 --mem=1G --time=1:00:00 --clusters=setonix --partition=copy --account=mwaeor --tasks 1 --cpus-per-task=1
withLabel: datamover {
scratch = 'ram-disk'
stageInMode = "symlink"
module = 'rclone'
cpus = 1
maxForks = 8
memory = 8.GB
time = 2.hour
clusterOptions = { "--nodes=1 --cpus-per-task=${task.cpus} --account=${PAWSEY_PROJECT}" }
queue = 'copyq'
}
withLabel: datamover_dl {
scratch = 'ram-disk'
stageInMode = "symlink"
module = 'rclone'
cpus = 1
maxForks = 8
memory = 31500.MB
time = 2.hour
clusterOptions = { "--nodes=1 --cpus-per-task=${task.cpus} --account=${PAWSEY_PROJECT}" }
queue = 'copyq'
}
withLabel: hyperdrive {
module = 'hyperdrive/peel-experiment'
}
withLabel: wsclean {
module = 'wsclean/2.9'
}
withLabel: mwa_reduce {
module = "${params.singularity_lmod}"
container = "${params.mwa_reduce_sif}"
}
withLabel: python {
module = "${params.singularity_lmod}"
container = "${params.mwa_qa_sif}"
}
withLabel: fitcal {
module = "${params.singularity_lmod}"
container = "${params.fitcal_sif}"
}
withLabel: casa {
module = "${params.singularity_lmod}"
container = "${params.casa_sif}"
}
withLabel: tap {
module = "${params.singularity_lmod}"
container = "${params.tap_sif}"
}
withLabel: rclone {
module = 'rclone'
}
withLabel: chips {
module = "${params.singularity_lmod}"
container = "${params.chips_sif}"
afterScript = 'for log in $(ls -t syslog*.txt *.log); do echo "-> head $log"; head -n 100 $log; echo "-> tail $log"; tail -n 100 $log; done; ls -alh; du -hd0'
}
withLabel: chips_wrappers {
module = "${params.singularity_lmod}"
container = "${params.chips_wrappers_sif}"
}
withLabel: ffmpeg {
module = "${params.singularity_lmod}"
container = "${params.ffmpeg_sif}"
}
withLabel: imagemagick {
module = "${params.singularity_lmod}"
container = "${params.imagemagick_sif}"
}
withLabel: ssins {
module = "${params.singularity_lmod}"
container = "${params.ssins_sif}"
}
withLabel: mwax_mover {
module = "${params.singularity_lmod}"
container = "${params.mwax_mover_sif}"
}
withLabel: mwa_demo {
module = "${params.singularity_lmod}"
container = "${params.mwa_demo_sif}"
}
}
}
dug {
singularity {
cacheDir = '/data/curtin_mwaeor/singularity'
}
executor {
queueSize = 200
// submitRateLimit = '1/30s'
jobName = { "nf-${task.process.split(':')[-1]}.${task.tag}" }
exitReadTimeout = '5min'
}
process {
scratch = '$TMPDIR_SHM'
executor = 'slurm'
queue = 'curtin_mwaeor'
cpus = 18
memory = '60G'
clusterOptions = '--constraint=knl&nogpu'
stageInMode = 'copy'
stageOutMode = 'copy'
withLabel: cpu {
cpus = 36
}
withLabel: wsclean {
clusterOptions = '--constraint=clx&nogpu'
}
withLabel: hyperdrive {
module = 'cuda/11.3.1:gcc-rt/9.2.0'
clusterOptions = "--constraint='v100'"
}
withLabel: python {
module = 'miniconda/4.8.3'
conda = '/data/curtin_mwaeor/sw/conda/dev'
}
withLabel: rclone {
module = 'rclone'
}
withLabel: chips {
module = 'cfitsio/3.470'
}
withLabel: python {
conda = "${params.astro_conda}"
}
}
params {
outdir = '/data/curtin_mwaeor/data'
proxy_prelude = 'export http_proxy="http://proxy.per.dug.com:3128" https_proxy="http://proxy.per.dug.com:3128" all_proxy="proxy.per.dug.com:3128" ftp_proxy="http://proxy.per.dug.com:3128"'
// sifs
// birli_sif = '/data/curtin_mwaeor/sw/singularity/birli/birli_mwaf.sif'
// mwa_qa_sif = '/data/curtin_mwaeor/sw/singularity/mwa_qa/mwa_qa_latest.sif'
// cotter_sif = '/data/curtin_mwaeor/sw/singularity/cotter/cotter_latest.sif'
// casa_sif = '/data/curtin_mwaeor/sw/singularity/casa/casa_latest.sif'
// binaries
hyperdrive = '/data/curtin_mwaeor/sw/bin/hyperdrive'
birli = 'singularity exec --bind ${PWD}:/tmp --writable-tmpfs --pwd /tmp --home ${PWD} --cleanenv ' + " ${params.birli_sif} /opt/cargo/bin/birli"
giant_squid = '/data/curtin_mwaeor/sw/bin/giant-squid'
jq = '/data/curtin_mwaeor/sw/bin/jq'
wsclean = '/data/curtin_mwaeor/sw/bin/wsclean'
// wsclean = '/data/curtin_mwaeor/sw/wsclean/3.1-knl-icc/bin/wsclean'
// wsclean = 'module use /data/curtin_mwaeor/sw/modules; module load wsclean/3.1-knl-icc; /data/curtin_mwaeor/sw/wsclean/3.1-knl-icc/bin/wsclean -j 60'
// wsclean = 'module use /data/curtin_mwaeor/sw/modules; module load wsclean/3.1-knl-icc; mpirun -np 30 /data/curtin_mwaeor/sw/wsclean/3.1-knl-icc/bin/wsclean-mp'
casa = 'singularity exec --bind ${PWD}:/tmp --writable-tmpfs --pwd /tmp --home ${PWD} --cleanenv ' + " ${params.casa_sif} /usr/bin/casa"
ps_metrics = "/data/curtin_mwaeor/src/chips/src/ps_metrics"
// calibration
sourcelist = '/data/curtin_mwaeor/data/srclist_pumav3_EoR0LoBESv2_fixedEoR1pietro+ForA_phase1+2_edit.txt'
beam_path = '/data/curtin_mwaeor/data/mwa_full_embedded_element_pattern.h5'
// todo: can't determine this from nvidia-smi
// v100 => 70, a100 => 80
cuda_compute = 70
}
}
genericHPC {
singularity {
cacheDir = '.'
enabled = true
autoMounts = true
}
params {
outdir = './nfdata'
resultsdir = './nfresults'
}
process {
executor = 'slurm'
queue = 'workq'
cpus = 2
// about 1/18 of a node
memory = 10.GB
// about 1/18 of a node
time = 15.minute
clusterOptions = { "--nodes=1 --cpus-per-task=${task.cpus} --account=${PAWSEY_PROJECT}" }
scratch = 'ram-disk'
stageInMode = 'copy'
stageOutMode = 'move'
beforeScript = 'set -x; chown ${USER}:${PAWSEY_PROJECT} ${NXF_SCRATCH:="."}; chmod g+rs ${NXF_SCRATCH:="."}; module use /pawsey/mwa/software/python3/modulefiles; module use /astro/mwaeor/software/modulefiles; hostname; env | grep SLURM; sleep $((2 + $RANDOM % 15)); date -Is'
errorStrategy = 'terminate'
withLabel: python {
module = 'singularity'
container = "${params.mwa_qa_sif}"
}
}
}
sirius {
process {
scratch = '/tmp/mwaeor'
executor = 'local'
}
params {
outdir = '/data/dev'
hyperdrive = '/usr/local/bin/hyperdrive'
sourcelist = '/data/dev/calibration/srclist_pumav3_EoR0LoBESv2_fixedEoR1pietro+ForA_phase1+2.txt'
beam_path = '/data/dev/calibration/mwa_full_embedded_element_pattern.h5'
cuda_compute = 75
}
}
gacrux {
singularity {
cacheDir = "/data/${USER}/.singularity"
enabled = true
runOptions = '--bind /data --bind /cygnus'
}
process {
scratch = '/tmp/mwaeor'
executor = 'local'
beforeScript = 'set -x; pwd; date -Is'
maxForks = 1
withLabel: rate_limit {
maxForks = 1
}
withLabel: rate_limit_20 {
maxForks = 2
}
withLabel: rate_limit_50 {
maxForks = 5
}
withLabel: 'mem_quarter|cpu_quarter' {
maxForks = 4
}
withLabel: 'mem_half|cpu_half' {
maxForks = 2
}
withLabel: 'mem_full|cpu_full' {
maxForks = 1
}
withLabel: mwa_reduce {
container = "${params.mwa_reduce_sif}"
}
withLabel: 'mwa_demo|ssins' {
maxForks = 5
container = null
}
withLabel: fitcal {
container = "${params.fitcal_sif}"
}
withLabel: chips {
container = "${params.chips_sif}"
}
withLabel: chips_wrappers {
container = "${params.chips_wrappers_sif}"
}
withLabel: ffmpeg {
container = "${params.ffmpeg_sif}"
}
withLabel: imagemagick {
container = "${params.imagemagick_sif}"
}
withLabel: mwax_mover {
container = "${params.mwax_mover_sif}"
}
}
executor {
queueSize = 10
}
params {
// outdir = '/data/dev'
outdir = '/cygnus/dev'
resultsdir = '/data/dev/nfresults'
demo_prelude = '. /home/dev/src/mwa-nextflow-starter/.venv/bin/activate'
// wsclean = '/usr/bin/wsclean'
// nouv = true
// sourcelist = '/opt/cal/srclist_pumav3_EoR0LoBESv2_fixedEoR1pietro+ForA_phase1+2_edit.txt'
sourcelist = '/opt/cal/srclist_pumav3_EoR0LoBES_EoR1pietro_CenA-GP_2023-11-07.yaml'
beam_path = '/opt/cal/mwa_full_embedded_element_pattern.h5'
img_mwa_path = '/opt/cal/'
cuda_compute = 86
}