[R] Cores hang when calling mcapply

[Deramus, Thomas Patrick]

About to try this implementation.

As a follow-up, this is the exact error:

Lost warning messages
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Execution halted
Error: cons memory exhausted (limit reached?)
Error: cons memory exhausted (limit reached?)
Error: cons memory exhausted (limit reached?)
Error: cons memory exhausted (limit reached?)

________________________________
From: Gregg Powell <g.a.powell using protonmail.com>
Sent: Tuesday, December 10, 2024 7:52 PM
To: Deramus, Thomas Patrick <tderamus using mgb.org>
Cc: r-help using r-project.org <r-help using r-project.org>
Subject: Re: [R] Cores hang when calling mcapply

Hello Thomas,

Consider that the primary bottleneck may be tied to memory usage and the complexity of pivoting extremely large datasets into wide formats with tens of thousands of unique values per column. Extremely large expansions of columns inherently stress both memory and CPU, and splitting into 110k separate data frames before pivoting and combining them again is likely causing resource overhead and system instability.

Perhaps, evaluate if the presence/absence transformation can be done in a more memory-efficient manner without pivoting all at once. Since you are dealing with extremely large data, a more incremental or streaming approach may be necessary. Instead of splitting into thousands of individual data frames and trying to pivot each in parallel, consider instead  a method that processes segments of data to incrementally build a large sparse matrix or a compressed representation, then combine results at the end.

It's probbaly better to move away from `pivot_wider()` on a massive scale and attempt a data.table-based approach, which is often more memory-efficient and faster for large-scale operations in R.


An alternate way would be data.table�s `dcast()` can handle large data more efficiently, and data.table�s in-memory operations often reduce overhead compared to tidyverse pivoting functions.

Also - consider using data.table�s `fread()` or `arrow::open_dataset()` directly with `as.data.table()` to keep everything in a data.table format. For example, you can do a large `dcast()` operation to create presence/absence columns by group. If your categories are extremely large, consider an approach that processes categories in segments as I mentioned earlier -  and writes intermediate results to disk, then combines/mergesresults at the end.

Limit parallelization when dealing with massive reshapes. Instead of trying to parallelize the entire pivot across thousands of subsets, run a single parallelized chunking approach that processes manageable subsets and writes out intermediate results (for example... using `fwrite()` for each subset). After processing, load and combine these intermediate results. This manual segmenting approach can circumvent the "zombie" processes you mentioned - that I think arise from overly complex parallel nesting and excessivememory utilization.

If the presence/absence indicators are ultimately sparse (many zeros and few ones), consider storing the result in a sparse matrix format (for exapmple- `Matrix` package in R). Instead of creating thousands of columns as dense integers, using a sparse matrix representation should dramatically reduce memory. After processing the data into a sparse format, you can then save it in a suitable file format and only convert to a dense format if absolutely necessary.

Below is a reworked code segment using data.table for a more scalable approach. Note that this is a conceptual template. In practice, adapt the chunk sizes and filtering operations to your workflow. The idea is to avoid creating 110k separate data frames and to handle the pivot in a data.table manner that�s more robust and less memory intensve. Here, presence/absence encoding is done by grouping and casting directly rather than repeatedly splitting and row-binding.

> library(data.table)
> library(arrow)
>
> # Step A: Load data efficiently as data.table
> dt <- as.data.table(
>   open_dataset(
>    sources = input_files,
>    format = 'csv',
>    unify_schema = TRUE,
>    col_types = schema(
>      "ID_Key" = string(),
>      "column1" = string(),
>      "column2" = string()
>    )
>  ) |>

>    collect()
> )
>
> # Step B: Clean names once
> # Assume `crewjanitormakeclean` essentially standardizes column names
> dt[, column1 := janitor::make_clean_names(column1, allow_dupes =

> TRUE)]
> dt[, column2 := janitor::make_clean_names(column2, allow_dupes =

>  TRUE)]
>
> # Step C: Create presence/absence indicators using data.table
> # Use dcast to pivot wide. Set n=1 for presence, 0 for absence.
> # For large unique values, consider chunking if needed.
> out1 <- dcast(dt[!is.na(column1)], ID_Key ~ column1, fun.aggregate =

> length, value.var = "column1")
> out2 <- dcast(dt[!is.na(column2)], ID_Key ~ column2, fun.aggregate =

> length, value.var = "column2")
>
> # Step D: Merge the two wide tables by ID_Key
> # Fill missing columns with 0 using data.table on-the-fly operations
> all_cols <- unique(c(names(out1), names(out2)))
> out1_missing <- setdiff(all_cols, names(out1))
> out2_missing <- setdiff(all_cols, names(out2))
>
> # Add missing columns with 0
> for (col in out1_missing) out1[, (col) := 0]
> for (col in out2_missing) out2[, (col) := 0]
>
> # Ensure column order alignment if needed
> setcolorder(out1, all_cols)
> setcolorder(out2, all_cols)
>
> # Combine by ID_Key (since they share same columns now)
> final_dt <- rbindlist(list(out1, out2), use.names = TRUE, fill = TRUE)
>
> # Step E: If needed, summarize across ID_Key to sum presence

> indicators
> final_result <- final_dt[, lapply(.SD, sum, na.rm = TRUE), by =

> ID_Key, .SDcols = setdiff(names(final_dt), "ID_Key")]
>
> # note that final_result should now contain summed presence/absence

> (0/1) indicators.




Hope this helps!
gregg
somewhereinArizona
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