Comments (7)
@clchand23 : this is now merged in and you can update EpiModelHPC with remotes::install_github("EpiModel/EpiModelHPC@main")
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@AdrienLeGuillou Do you think this may be the same underlying issue that is in #40 ?
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@sgoodreau yes, I am pretty sure it is. I'll look into it today
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Actually it may be different issue.
@clchand23 can you point me to the code that produced that error? I cannot replicate it on my projects
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Hi @AdrienLeGuillou - it is showing an error with the signalConditions()
function. Namely, the first time it says stop(condition)
below.
Error in names(z[[other.x[j]]]) <- newnames :
attempt to set an attribute on NULL
Called from: signalConditions(obj, exclude = getOption("future.relay.immediate",
"immediateCondition"), resignal = resignal, ...)
function (future, include = "condition", exclude = NULL, resignal = TRUE,
...)
{
if (!future$state %in% c("finished", "failed")) {
stop(FutureError(sprintf("Internal error: Cannot resignal future conditions. %s has not yet been resolved (state = %s)",
class(future)[1], paste(sQuote(future$state), collapse = ", ")),
future = future))
}
if (length(include) == 0L)
return(invisible(future))
result <- result(future)
stop_if_not(inherits(result, "FutureResult"))
conditions <- result$conditions
if (length(conditions) == 0)
return(invisible(future))
debug <- getOption("future.debug", FALSE)
if (debug) {
mdebug("signalConditions() ...")
mdebug(" - include = ", paste(sQuote(include), collapse = ", "))
mdebug(" - exclude = ", paste(sQuote(exclude), collapse = ", "))
mdebug(" - resignal = ", resignal)
mdebug(" - Number of conditions: ", length(conditions))
on.exit(mdebug("signalConditions() ... done"))
}
signaled <- logical(length(conditions))
for (kk in seq_along(conditions)) {
cond <- conditions[[kk]]
if (!resignal && !is.null(cond$signaled) && cond$signaled >
0L)
next
condition <- cond$condition
if (length(exclude) > 0L && inherits(condition, exclude))
next
if (length(include) > 0L && !inherits(condition, include))
next
mdebugf(" - Condition #%d: %s", kk, paste(sQuote(class(condition)),
collapse = ", "))
cond$signaled <- cond$signaled + 1L
conditions[[kk]] <- cond
if (inherits(condition, "error")) {
result$conditions <- conditions
future$result <- result
if (debug && !"future.info" %in% names(condition)) {
cond$calls <- c(future$calls, cond$calls)
condition$future.info <- cond
}
stop(condition)
}
else if (inherits(condition, "warning")) {
warning(condition)
}
else if (inherits(condition, "message")) {
message(condition)
}
else if (inherits(condition, "condition")) {
signalCondition(condition)
}
else {
stop_if_not(inherits(condition, "condition"))
}
signaled[kk] <- TRUE
}
if (isTRUE(attr(future$conditions, "drop"))) {
conditions <- conditions[!signaled]
}
result$conditions <- conditions
future$result <- result
invisible(future)
}
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sorry I was unclear, I need to see the code that produced the simulations. To see if the issue is with the function itself or in the code saving the sims.
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The simulations were created using the EpiModelHIV intervention scenarios workflow scripts and were downloaded directly from the HPC
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Related Issues (20)
- Change (make flexible) placement of loadR.sh in sbatch_master HOT 17
- Equivalent function to deactivate.edges HOT 3
- Function initialize_cp HOT 1
- Solidify new HPC methods from ALG into EpiModelHPC HOT 1
- EpiModelHPC: define a way to run all the calibrations at once on HPC and gather the final calibrated model. HOT 1
- add a slurmworkflow step_tmpl for scenarios with replication
- Implement checkpointing Slurm HOT 9
- wrong batch number in the log of `step_tmpl_netsim_scenarios` HOT 1
- merge_simfiles might be not working? HOT 1
- make `step_tmpl_renv_restore` init renv if not done
- revisit the tests
- Runs don't parallelize across cores when nsims = ncores (ie with only one node) HOT 19
- Fix vignette / doc related to `netsim_scenarios`
- Use [email protected] from `module` in SPH HOT 1
- merge_simfiles not working again HOT 9
- Update sbatch_master to output --ntasks instead of --cpus_per_task HOT 2
- `spack unload -a` still necessary
- `netsim_scenarios`: use future instead of inner parallelization
- do not `rep` the scenario list in `netsim_scenarios`
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