Last updated: 2022-04-04

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Knit directory: RECCAP2_ROMS_SO_ETHZ_submission/

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library(tidyverse)
library(gt)

1 Load data

This analysis is based on Table 3 of the RECCAP2-ocean protocol for model output, and statistics of the ETHZ CESM model output.

# read Table 3 from model protocol
table_3 <- read_csv(
  here::here(
    "data/overview",
    "RECCAP2-ocean_data_products_overview - Model_protocol_table3.csv"
  )
)

# replace placeholder variable name with actual CESM variable name
table_3_temp <- table_3 %>% 
  filter(variable_id == "epc100type / epc1000type") %>% 
  select(-variable_id)

table_3_temp <- expand_grid(
  table_3_temp,
  variable_id = c("epc100hard","epc1000hard","epc100soft","epc1000soft")
)

table_3 <- table_3 %>% 
  filter(variable_id != "epc100type / epc1000type")

table_3 <- bind_rows(table_3, table_3_temp)
rm(table_3_temp)

The list of files and sizes of the ETHZ CESM model output refers to the content in this folder:

# set path to output
path_ROMS <-
  "/net/kryo/work/loher/ROMS/RECCAP2_Jan2022/SO_d025_global_proto_runA/submit_20220404"
path_ROMS
[1] "/net/kryo/work/loher/ROMS/RECCAP2_Jan2022/SO_d025_global_proto_runA/submit_20220404"
# create list of CESM output files and sizes

ROMS_files_names <- list.files(path = path_ROMS,
                               pattern = ".nc")
ROMS_files_sizes <-
  file.size(paste(path_ROMS, ROMS_files_names, sep = "/"))

ROMS_files <- bind_cols(file_name = ROMS_files_names,
                        file_size_MB = round(ROMS_files_sizes * 1e-6, 1))

rm(ROMS_files_names, ROMS_files_sizes)

# extract variable_id and experiment_id from file name
ROMS_files <- ROMS_files %>%
  mutate(
    variable_id = str_split(file_name,
                            pattern = "_ROMS",
                            simplify = TRUE)[, 1],
    experiment_id = str_sub(string = file_name, -29, -29)
  ) %>%
  mutate(experiment_id = if_else(
    experiment_id %in% c("A", "B", "C", "D"),
    experiment_id,
    "ancillary"
  )) %>%
  select(-c(file_name))
# join file list and tab 3
overview <- full_join(table_3, ROMS_files) %>%
  arrange(variable_id) %>% 
  filter(!is.na(file_size_MB))

rm(ROMS_files, table_3)

# write overview file
overview %>%
  write_csv("data/overview/overview_files.csv")

2 Overview CESM output

Overview table of output files created. Please note, that for each listed variable, four experiment_id (A-D) versions exist.

overview %>% 
  group_by(variable_id, dimension, priority) %>% 
  summarise_at("file_size_MB", sum, na.rm = TRUE) %>% 
  arrange(dimension, priority) %>% 
  gt(
    rowname_col = "variable_id",
    groupname_col = c("dimension", "priority"),
    row_group.sep = " | Priority: "
  ) %>%
  summary_rows(groups = TRUE,
               fns = list(total = "sum"))
file_size_MB
2 | Priority: 1
chlos 79.3
dissicos 55.6
fgco2 78.6
fgco2_glob 0.0
fice 3.6
mld 73.1
sos 53.6
spco2 62.7
talkos 17.8
tos 73.0
total 497.30
2 | Priority: 2
dfeos 23.5
no3os 24.0
o2os 21.3
pco2atm 50.0
sios 24.7
total 143.50
2 | Priority: 3
alpha 64.9
total 64.90
3 | Priority: 1
dissic 387.4
so 341.1
talk 124.2
thetao 504.7
total 1,357.40
3 | Priority: 2
no3 151.2
o2 146.0
si 162.0
total 459.20
NA | Priority: NA
area 0.3
Area_tot_native 0.0
Atm_CO2 0.0
mask_sfc 0.3
mask_vol 35.5
Vol_tot_native 0.0
volume 35.5
total 71.60

2.1 Submission tar files

# create list of CESM output files and sizes

ROMS_files_names_tar <- list.files(path = path_ROMS,
                                   pattern = ".tar")
ROMS_files_sizes_tar <-
  file.size(paste(path_ROMS, ROMS_files_names_tar, sep = "/"))

ROMS_files_tar <- bind_cols(
  file_name = ROMS_files_names_tar,
  file_size_GB = round(ROMS_files_sizes_tar * 1e-9, 1))

rm(path_ROMS, ROMS_files_names_tar, ROMS_files_sizes_tar)

# extract variable_id and experiment_id from file name
ROMS_files_tar
# A tibble: 0 × 2
# … with 2 variables: file_name <chr>, file_size_GB <dbl>

sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.3

Matrix products: default
BLAS:   /usr/local/R-4.1.2/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.1.2/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] gt_0.3.1        forcats_0.5.1   stringr_1.4.0   dplyr_1.0.7    
 [5] purrr_0.3.4     readr_2.1.1     tidyr_1.1.4     tibble_3.1.6   
 [9] ggplot2_3.3.5   tidyverse_1.3.1 workflowr_1.7.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8       here_1.0.1       lubridate_1.8.0  getPass_0.2-2   
 [5] ps_1.6.0         assertthat_0.2.1 rprojroot_2.0.2  digest_0.6.29   
 [9] utf8_1.2.2       R6_2.5.1         cellranger_1.1.0 backports_1.4.1 
[13] reprex_2.0.1     evaluate_0.14    httr_1.4.2       pillar_1.6.4    
[17] rlang_0.4.12     readxl_1.3.1     rstudioapi_0.13  whisker_0.4     
[21] callr_3.7.0      jquerylib_0.1.4  checkmate_2.0.0  rmarkdown_2.11  
[25] bit_4.0.4        munsell_0.5.0    broom_0.7.11     compiler_4.1.2  
[29] httpuv_1.6.5     modelr_0.1.8     xfun_0.29        pkgconfig_2.0.3 
[33] htmltools_0.5.2  tidyselect_1.1.1 fansi_1.0.2      crayon_1.4.2    
[37] tzdb_0.2.0       dbplyr_2.1.1     withr_2.4.3      later_1.3.0     
[41] grid_4.1.2       jsonlite_1.7.3   gtable_0.3.0     lifecycle_1.0.1 
[45] DBI_1.1.2        git2r_0.29.0     magrittr_2.0.1   scales_1.1.1    
[49] vroom_1.5.7      cli_3.1.1        stringi_1.7.6    fs_1.5.2        
[53] promises_1.2.0.1 xml2_1.3.3       bslib_0.3.1      ellipsis_0.3.2  
[57] generics_0.1.1   vctrs_0.3.8      tools_4.1.2      bit64_4.0.5     
[61] glue_1.6.0       hms_1.1.1        parallel_4.1.2   processx_3.5.2  
[65] fastmap_1.1.0    yaml_2.2.1       colorspace_2.0-2 rvest_1.0.2     
[69] knitr_1.37       haven_2.4.3      sass_0.4.0