support log_resources

wlandau · Aug 2, 2024 · a35c967 · a35c967
1 parent 000ae59
commit a35c967
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Showing 10 changed files with 144 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -15,7 +15,7 @@ Description: In computationally demanding analysis projects,
   'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
   and 'batchtools' by Lang, Bischl, and Surmann (2017).
   <doi:10.21105/joss.00135>.
-Version: 0.3.2.9003
+Version: 0.3.2.9004
 License: MIT + file LICENSE
 URL: https://wlandau.github.io/crew.cluster/,
   https://github.com/wlandau/crew.cluster
@@ -49,7 +49,7 @@ Authors@R: c(
 Depends:
   R (>= 4.0.0)
 Imports:
-  crew (>= 0.9.5.9003),
+  crew (>= 0.9.5.9007),
   ps,
   lifecycle,
   R6,

diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,8 @@
-# crew.cluster 0.3.2.9003 (development)
+# crew.cluster 0.3.2.9004 (development)
 
 * Add `slurm_memory_gigabytes_required` to set `--mem` in SLURM (#44, @multimeric).
 * Add `r_arguments` to accept R command line arguments for workers.
+* Support `log_resources` in controllers.
 
 # crew.cluster 0.3.2
 

diff --git a/R/crew_controller_lsf.R b/R/crew_controller_lsf.R
@@ -38,6 +38,7 @@ crew_controller_lsf <- function(
   seconds_wall = Inf,
   seconds_exit = NULL,
   retry_tasks = TRUE,
+  log_resources = NULL,
   tasks_max = Inf,
   tasks_timers = 0L,
   reset_globals = TRUE,
@@ -77,7 +78,8 @@ crew_controller_lsf <- function(
     tls_config = tls_config,
     seconds_interval = seconds_interval,
     seconds_timeout = seconds_timeout,
-    retry_tasks = retry_tasks
+    retry_tasks = retry_tasks,
+    log_resources = log_resources
   )
   launcher <- crew_launcher_lsf(
     name = name,

diff --git a/R/crew_controller_pbs.R b/R/crew_controller_pbs.R
@@ -34,6 +34,7 @@ crew_controller_pbs <- function(
   seconds_wall = Inf,
   seconds_exit = NULL,
   retry_tasks = TRUE,
+  log_resources = NULL,
   tasks_max = Inf,
   tasks_timers = 0L,
   reset_globals = TRUE,
@@ -74,7 +75,8 @@ crew_controller_pbs <- function(
     tls_config = tls_config,
     seconds_interval = seconds_interval,
     seconds_timeout = seconds_timeout,
-    retry_tasks = retry_tasks
+    retry_tasks = retry_tasks,
+    log_resources = log_resources
   )
   launcher <- crew_launcher_pbs(
     name = name,

diff --git a/R/crew_controller_sge.R b/R/crew_controller_sge.R
@@ -34,6 +34,7 @@ crew_controller_sge <- function(
   seconds_wall = Inf,
   seconds_exit = NULL,
   retry_tasks = TRUE,
+  log_resources = NULL,
   tasks_max = Inf,
   tasks_timers = 0L,
   reset_globals = TRUE,
@@ -76,7 +77,8 @@ crew_controller_sge <- function(
     tls_config = tls_config,
     seconds_interval = seconds_interval,
     seconds_timeout = seconds_timeout,
-    retry_tasks = retry_tasks
+    retry_tasks = retry_tasks,
+    log_resources = log_resources
   )
   launcher <- crew_launcher_sge(
     name = name,

diff --git a/R/crew_controller_slurm.R b/R/crew_controller_slurm.R
@@ -38,6 +38,7 @@ crew_controller_slurm <- function(
   seconds_wall = Inf,
   seconds_exit = NULL,
   retry_tasks = TRUE,
+  log_resources = NULL,
   tasks_max = Inf,
   tasks_timers = 0L,
   reset_globals = TRUE,
@@ -78,7 +79,8 @@ crew_controller_slurm <- function(
     tls_config = tls_config,
     seconds_interval = seconds_interval,
     seconds_timeout = seconds_timeout,
-    retry_tasks = retry_tasks
+    retry_tasks = retry_tasks,
+    log_resources = log_resources
   )
   launcher <- crew_launcher_slurm(
     name = name,

diff --git a/man/crew_controller_lsf.Rd b/man/crew_controller_lsf.Rd
diff --git a/man/crew_controller_pbs.Rd b/man/crew_controller_pbs.Rd
diff --git a/man/crew_controller_sge.Rd b/man/crew_controller_sge.Rd
diff --git a/man/crew_controller_slurm.Rd b/man/crew_controller_slurm.Rd