I'm trying to run stilt on a new MacBook Pro.

When I run Rscript -e "uataq::stilt_init('project_name')", I get:

Cloning into 'project_name'...
remote: Enumerating objects: 101, done.
remote: Counting objects: 100% (101/101), done.
remote: Compressing objects: 100% (93/93), done.
remote: Total 101 (delta 5), reused 66 (delta 4), pack-reused 0 (from 0)
Receiving objects: 100% (101/101), 19.46 MiB | 4.71 MiB/s, done.
Resolving deltas: 100% (5/5), done.
Compiling footprint kernel aggregation subroutine...
using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
using SDK: ‘MacOSX26.0.sdk’
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c r/src/permute.f90 -o r/src/permute.o
clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o r/src/permute.so r/src/permute.o -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
ld: warning: search path '/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0' not found
ld: library 'emutls_w' not found
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [r/src/permute.so] Error 1

I manually compiled permute.so and tried using terminal through Rosetta. When I then ran the script it would abort saying:

Initializing STILT
Commit ID: 0f9ff18
Number of receptors: 25
Number of parallel workers: 1
Parallelization disabled. Executing simulations sequentially...
Running simulation ID: 202305080000_-105.589_40.055_2
sh: line 1: 92401 Abort trap: 6 ./hycs_std >> stilt.log 2>&1

When I open hycs_std, I get this message:

Reason: tried: '/usr/local/gfortran/lib/libgfortran.5.dylib' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/gfortran/lib/libgfortran.5.dylib' (no such file), '/usr/local/gfortran/lib/libgfortran.5.dylib' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)
zsh: abort

It appears the incompatibility between arm64 and x86_64 is the issue. I tried running the code through the Dockerfile but ended up with other incompatibilities.

Has anyone had success running stilt on this version of MacBook Pro?

This is my run file in case that is helpful:

#!/usr/bin/env Rscript

STILT R Executable

For documentation, see https://uataq.github.io/stilt/

Ben Fasoli

dyn.load("/Users/millerh9/Desktop/Hg_air_source/r/src/permute.so")

User inputs ------------------------------------------------------------------

project <- 'Hg_air_source'
stilt_wd <- file.path('/Users/millerh9/Desktop', project)
output_wd <- file.path(stilt_wd, 'out')
lib.loc <- .libPaths()[1]

Parallel simulation settings

n_cores <- 1
n_nodes <- 1
processes_per_node <- n_cores
slurm <- n_nodes > 1
slurm_options <- list(
time = '300:00:00',
account = 'lin-kp',
partition = 'lin-kp'
)

Simulation timing, yyyy-mm-dd HH:MM:SS (UTC)

t_start <- '2023-05-08 00:00:00'
t_end <- '2023-05-09 00:00:00'
run_times <- seq(from = as.POSIXct(t_start, tz = 'UTC'),
to = as.POSIXct(t_end, tz = 'UTC'),
by = 'hour')

Receptor location(s)

lati <- 40.055
long <- -105.589
zagl <- 2

Expand the run times, latitudes, and longitudes to form the unique receptors

that are used for each simulation

receptors <- expand.grid(run_time = run_times, lati = lati, long = long,
zagl = zagl, KEEP.OUT.ATTRS = F, stringsAsFactors = F)

Footprint grid settings, must set at least xmn, xmx, ymn, ymx below

hnf_plume <- T
projection <- '+proj=longlat'
smooth_factor <- 1
time_integrate <- F
xmn <- -109.0
xmx <- -101.0
ymn <- 36
ymx <- 44
xres <- 0.01
yres <- xres

Meteorological data input

met_path <- '/Users/millerh9/Library/CloudStorage/Box-Box/STILT_weather_hrrr'
met_file_format <- '%Y%m%d'
met_file_tres <- '6 hours'
met_subgrid_buffer <- 0.2
met_subgrid_enable <- F
met_subgrid_levels <- NA
n_met_min <- 5

Model control

n_hours <- -24
numpar <- 1000
rm_dat <- T
run_foot <- T
run_trajec <- T
simulation_id <- NA
timeout <- 3600
varsiwant <- c('time', 'indx', 'long', 'lati', 'zagl', 'foot', 'mlht', 'dens',
'samt', 'sigw', 'tlgr')

Transport and dispersion settings

capemin <- -1
cmass <- 0
conage <- 48
cpack <- 1
delt <- 1
dxf <- 1
dyf <- 1
dzf <- 0.01
efile <- ''
emisshrs <- 0.01
frhmax <- 3
frhs <- 1
frme <- 0.1
frmr <- 0
frts <- 0.1
frvs <- 0.01
hscale <- 10800
ichem <- 8
idsp <- 2
initd <- 0
k10m <- 1
kagl <- 1
kbls <- 1
kblt <- 5
kdef <- 0
khinp <- 0
khmax <- 9999
kmix0 <- 150
kmixd <- 3
kmsl <- 0
kpuff <- 0
krand <- 4
krnd <- 6
kspl <- 1
kwet <- 1
kzmix <- 0
maxdim <- 1
maxpar <- numpar
mgmin <- 10
mhrs <- 9999
nbptyp <- 1
ncycl <- 0
ndump <- 0
ninit <- 1
nstr <- 0
nturb <- 0
nver <- 0
outdt <- 0
p10f <- 1
pinbc <- ''
pinpf <- ''
poutf <- ''
qcycle <- 0
rhb <- 80
rht <- 60
splitf <- 1
tkerd <- 0.18
tkern <- 0.18
tlfrac <- 0.1
tout <- 0
tratio <- 0.75
tvmix <- 1
veght <- 0.5
vscale <- 200
vscaleu <- 200
vscales <- -1
wbbh <- 0
wbwf <- 0
wbwr <- 0
wvert <- FALSE
w_option <- 0
zicontroltf <- 0
ziscale <- rep(list(rep(1, 24)), nrow(receptors))
z_top <- 25000

Transport error settings

horcoruverr <- NA
siguverr <- NA
tluverr <- NA
zcoruverr <- NA

horcorzierr <- NA
sigzierr <- NA
tlzierr <- NA

Interface to mutate the output object with user defined functions

before_trajec <- function() {output}
before_footprint <- function() {output}

Source dependencies ----------------------------------------------------------

setwd(stilt_wd)
source('r/dependencies.r')

Structure out directory ------------------------------------------------------

Outputs are organized in three formats. by-id contains simulation files by

unique simulation identifier. particles and footprints contain symbolic links

to the particle trajectory and footprint files in by-id

system(paste0('rm -r ', output_wd, '/footprints'), ignore.stderr = T)
if (run_trajec) {
system(paste0('rm -r ', output_wd, '/by-id'), ignore.stderr = T)
system(paste0('rm -r ', output_wd, '/met'), ignore.stderr = T)
system(paste0('rm -r ', output_wd, '/particles'), ignore.stderr = T)
}
for (d in c('by-id', 'particles', 'footprints')) {
d <- file.path(output_wd, d)
if (!file.exists(d))
dir.create(d, recursive = T)
}

Run trajectory simulations ---------------------------------------------------

stilt_apply(FUN = simulation_step,
simulation_id = simulation_id,
slurm = slurm,
slurm_options = slurm_options,
n_cores = n_cores,
n_nodes = n_nodes,
processes_per_node = processes_per_node,
before_footprint = list(before_footprint),
before_trajec = list(before_trajec),
lib.loc = lib.loc,
capemin = capemin,
cmass = cmass,
conage = conage,
cpack = cpack,
delt = delt,
dxf = dxf,
dyf = dyf,
dzf = dzf,
efile = efile,
emisshrs = emisshrs,
frhmax = frhmax,
frhs = frhs,
frme = frme,
frmr = frmr,
frts = frts,
frvs = frvs,
hnf_plume = hnf_plume,
horcoruverr = horcoruverr,
horcorzierr = horcorzierr,
hscale = hscale,
ichem = ichem,
idsp = idsp,
initd = initd,
k10m = k10m,
kagl = kagl,
kbls = kbls,
kblt = kblt,
kdef = kdef,
khinp = khinp,
khmax = khmax,
kmix0 = kmix0,
kmixd = kmixd,
kmsl = kmsl,
kpuff = kpuff,
krand = krand,
krnd = krnd,
kspl = kspl,
kwet = kwet,
kzmix = kzmix,
maxdim = maxdim,
maxpar = maxpar,
met_file_format = met_file_format,
met_file_tres = met_file_tres,
met_path = met_path,
met_subgrid_buffer = met_subgrid_buffer,
met_subgrid_enable = met_subgrid_enable,
met_subgrid_levels = met_subgrid_levels,
mgmin = mgmin,
n_hours = n_hours,
n_met_min = n_met_min,
ncycl = ncycl,
ndump = ndump,
ninit = ninit,
nstr = nstr,
nturb = nturb,
numpar = numpar,
nver = nver,
outdt = outdt,
output_wd = output_wd,
p10f = p10f,
pinbc = pinbc,
pinpf = pinpf,
poutf = poutf,
projection = projection,
qcycle = qcycle,
r_run_time = receptors$run_time,
r_lati = receptors$lati,
r_long = receptors$long,
r_zagl = receptors$zagl,
rhb = rhb,
rht = rht,
rm_dat = rm_dat,
run_foot = run_foot,
run_trajec = run_trajec,
siguverr = siguverr,
sigzierr = sigzierr,
smooth_factor = smooth_factor,
splitf = splitf,
stilt_wd = stilt_wd,
time_integrate = time_integrate,
timeout = timeout,
tkerd = tkerd,
tkern = tkern,
tlfrac = tlfrac,
tluverr = tluverr,
tlzierr = tlzierr,
tout = tout,
tratio = tratio,
tvmix = tvmix,
varsiwant = list(varsiwant),
veght = veght,
vscale = vscale,
vscaleu = vscaleu,
vscales = vscales,
w_option = w_option,
wbbh = wbbh,
wbwf = wbwf,
wbwr = wbwr,
wvert = wvert,
xmn = xmn,
xmx = xmx,
xres = xres,
ymn = ymn,
ymx = ymx,
yres = yres,
zicontroltf = zicontroltf,
ziscale = ziscale,
z_top = z_top,
zcoruverr = zcoruverr)