Draft of submiModels for testing on slurm

michaelhallquist · May 5, 2024 · e4b4c4f · e4b4c4f
1 parent af33f6e
commit e4b4c4f
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Showing 11 changed files with 1,004 additions and 17 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -11,6 +11,7 @@ S3method(print,mplus.model)
 S3method(print,mplusObject)
 S3method(summary,mplus.model)
 S3method(summary,mplusObject)
+S3method(summary,mplus_submission_df)
 S3method(update,mplusObject)
 export(HTMLSummaryTable)
 export(LatexSummaryTable)
@@ -90,8 +91,10 @@ importFrom(checkmate,assert_string)
 importFrom(checkmate,assert_subset)
 importFrom(data.table,":=")
 importFrom(data.table,as.data.table)
+importFrom(data.table,fread)
 importFrom(data.table,fwrite)
 importFrom(data.table,is.data.table)
+importFrom(data.table,setnames)
 importFrom(digest,digest)
 importFrom(fastDummies,dummy_cols)
 importFrom(graphics,lines)

diff --git a/R/submitModels.R b/R/submitModels.R
diff --git a/man/checkSubmission.Rd b/man/checkSubmission.Rd
diff --git a/man/get_job_status.Rd b/man/get_job_status.Rd
diff --git a/man/local_job_status.Rd b/man/local_job_status.Rd
diff --git a/man/minutes_to_dhms.Rd b/man/minutes_to_dhms.Rd
diff --git a/man/slurm_job_status.Rd b/man/slurm_job_status.Rd
diff --git a/man/submitModels.Rd b/man/submitModels.Rd
diff --git a/man/summary.mplus_submission_df.Rd b/man/summary.mplus_submission_df.Rd
diff --git a/man/torque_job_status.Rd b/man/torque_job_status.Rd
diff --git a/tests/testthat/test-submitModels.R b/tests/testthat/test-submitModels.R
@@ -1,15 +1,22 @@
-# examine whether we get
+# tests for submitModels
 
 p <- testthat::test_path("submitModels")
 
+# checks on parsing of scheduling arguments and script setup
 track <- submitModels(p, sched_args=c("--mail=user", "--export=v"), debug=TRUE)
 
 test_that("submitModels job ID check", {
     expect_equal(track$jobid[1], "dummy_1")
 })
 
 test_that("submitModels job allocation checks", {
-    expect_equal(track$memgb[1], 16),
-    expect_equal(track$cores[1], 2),
+    expect_equal(track$memgb[1], 16)
+    expect_equal(track$cores[1], 2)
     expect_equal(track$wall_time[1], "3:00:00")
 })
+
+# checks on cluster (must be run on slurm cluster!)
+track <- submitModels(p,
+    scheduler = "slurm",
+    batch_outdir = "/proj/mnhallqlab/users/michael/submitModels_test"
+)