retry_tasks

wlandau · Jul 10, 2024 · 5f43156 · 5f43156
1 parent 1adfceb
commit 5f43156
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Showing 13 changed files with 55 additions and 8 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: 0.3.1
+Version: 0.3.2
 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 (>= 0.8.0),
+  crew (>= 0.9.5),
   ps,
   lifecycle,
   R6,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# crew.cluster 0.3.2
+
+* Add `retry_tasks` argument.
+
 # crew.cluster 0.3.1
 
 * Add a SLURM monitor (#32, @brendanf).

diff --git a/R/crew_controller_lsf.R b/R/crew_controller_lsf.R
@@ -37,6 +37,7 @@ crew_controller_lsf <- function(
   seconds_idle = Inf,
   seconds_wall = Inf,
   seconds_exit = NULL,
+  retry_tasks = TRUE,
   tasks_max = Inf,
   tasks_timers = 0L,
   reset_globals = TRUE,
@@ -74,7 +75,8 @@ crew_controller_lsf <- function(
     tls_enable = tls_enable,
     tls_config = tls_config,
     seconds_interval = seconds_interval,
-    seconds_timeout = seconds_timeout
+    seconds_timeout = seconds_timeout,
+    retry_tasks = retry_tasks
   )
   launcher <- crew_launcher_lsf(
     name = name,

diff --git a/R/crew_controller_pbs.R b/R/crew_controller_pbs.R
@@ -33,6 +33,7 @@ crew_controller_pbs <- function(
   seconds_idle = Inf,
   seconds_wall = Inf,
   seconds_exit = NULL,
+  retry_tasks = TRUE,
   tasks_max = Inf,
   tasks_timers = 0L,
   reset_globals = TRUE,
@@ -71,7 +72,8 @@ crew_controller_pbs <- function(
     tls_enable = tls_enable,
     tls_config = tls_config,
     seconds_interval = seconds_interval,
-    seconds_timeout = seconds_timeout
+    seconds_timeout = seconds_timeout,
+    retry_tasks = retry_tasks
   )
   launcher <- crew_launcher_pbs(
     name = name,

diff --git a/R/crew_controller_sge.R b/R/crew_controller_sge.R
@@ -33,6 +33,7 @@ crew_controller_sge <- function(
   seconds_idle = Inf,
   seconds_wall = Inf,
   seconds_exit = NULL,
+  retry_tasks = TRUE,
   tasks_max = Inf,
   tasks_timers = 0L,
   reset_globals = TRUE,
@@ -73,7 +74,8 @@ crew_controller_sge <- function(
     tls_enable = tls_enable,
     tls_config = tls_config,
     seconds_interval = seconds_interval,
-    seconds_timeout = seconds_timeout
+    seconds_timeout = seconds_timeout,
+    retry_tasks = retry_tasks
   )
   launcher <- crew_launcher_sge(
     name = name,

diff --git a/R/crew_controller_slurm.R b/R/crew_controller_slurm.R
@@ -37,6 +37,7 @@ crew_controller_slurm <- function(
   seconds_idle = Inf,
   seconds_wall = Inf,
   seconds_exit = NULL,
+  retry_tasks = TRUE,
   tasks_max = Inf,
   tasks_timers = 0L,
   reset_globals = TRUE,
@@ -74,7 +75,8 @@ crew_controller_slurm <- function(
     tls_enable = tls_enable,
     tls_config = tls_config,
     seconds_interval = seconds_interval,
-    seconds_timeout = seconds_timeout
+    seconds_timeout = seconds_timeout,
+    retry_tasks = retry_tasks
   )
   launcher <- crew_launcher_slurm(
     name = name,

diff --git a/README.Rmd b/README.Rmd
@@ -51,7 +51,7 @@ controller <- crew_controller_sge(
 controller$start()
 ```
 
-At this point, usage is exactly the same as basic [`crew`](https://wlandau.github.io/crew). The `push()` method submits tasks and auto-scales SGE workers to meet demand.
+At this point, usage is exactly the same as basic [`crew`](https://wlandau.github.io/crew/). The `push()` method submits tasks and auto-scales SGE workers to meet demand.
 
 ```{r}
 controller$push(name = "do work", command = do_work())

diff --git a/README.md b/README.md
@@ -53,7 +53,7 @@ controller$start()
 ```
 
 At this point, usage is exactly the same as basic
-[`crew`](https://wlandau.github.io/crew). The `push()` method submits
+[`crew`](https://wlandau.github.io/crew/). The `push()` method submits
 tasks and auto-scales SGE workers to meet demand.
 
 ``` r

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
diff --git a/tests/testthat/test-crew_monitor_slurm.R b/tests/testthat/test-crew_monitor_slurm.R
@@ -0,0 +1,3 @@
+test_that("crew_monitor_slurm() validate", {
+  expect_silent(crew_monitor_slurm()$validate())
+})