Updated OMP_NUM_THREADS in use_crew_lsf; fusen updates

mglev1n · Oct 27, 2023 · 0cc4342 · 0cc4342
1 parent f5ba512
commit 0cc4342
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diff --git a/R/use_crew_lsf.R b/R/use_crew_lsf.R
@@ -41,6 +41,7 @@ controller_lsf_normal <- crew.cluster::crew_controller_lsf(
   script_lines = c(
     \"#BSUB-q voltron_normal\",
     \"export R_LIBS_USER=$HOME/R/rocker-rstudio/bioconductor-tidyverse_3.17\",
+    \"export OMP_NUM_THREADS=1\",
     \"export SINGULARITY_BIND='/project/:/project/, /appl/:/appl/, /lsf/:/lsf/, /scratch/:/scratch, /static:/static'\",
     \"singularity exec --pwd {getwd()} /project/voltron/rstudio/containers/bioconductor-tidyverse_3.17.sif \\\\\"
   ),
@@ -57,6 +58,7 @@ controller_lsf_long <- crew.cluster::crew_controller_lsf(
   script_lines = c(
     \"#BSUB-q voltron_long\",
     \"export R_LIBS_USER=$HOME/R/rocker-rstudio/bioconductor-tidyverse_3.17\",
+    \"export OMP_NUM_THREADS=1\",
     \"export SINGULARITY_BIND='/project/:/project/, /appl/:/appl/, /lsf/:/lsf/, /scratch/:/scratch, /static:/static'\",
     \"singularity exec --pwd {getwd()} /project/voltron/rstudio/containers/bioconductor-tidyverse_3.17.sif \\\\\"
   ),
@@ -73,6 +75,7 @@ controller_lsf_highmem <- crew.cluster::crew_controller_lsf(
   script_lines = c(
     \"#BSUB-q voltron_normal\",
     \"export R_LIBS_USER=$HOME/R/rocker-rstudio/bioconductor-tidyverse_3.17\",
+    \"export OMP_NUM_THREADS=1\",
     \"export SINGULARITY_BIND='/project/:/project/, /appl/:/appl/, /lsf/:/lsf/, /scratch/:/scratch, /static:/static'\",
     \"singularity exec --pwd {getwd()} /project/voltron/rstudio/containers/bioconductor-tidyverse_3.17.sif \\\\\"
   ),
@@ -90,6 +93,7 @@ controller_lsf_multicore <- crew.cluster::crew_controller_lsf(
   script_lines = c(
     \"#BSUB-q voltron_normal\",
     \"export R_LIBS_USER=$HOME/R/rocker-rstudio/bioconductor-tidyverse_3.17\",
+    \"export OMP_NUM_THREADS=16\",
     \"export SINGULARITY_BIND='/project/:/project/, /appl/:/appl/, /lsf/:/lsf/, /scratch/:/scratch, /static:/static'\",
     \"singularity exec --pwd {getwd()} /project/voltron/rstudio/containers/bioconductor-tidyverse_3.17.sif \\\\\"
   ),

diff --git a/dev/LPC_targets_project.Rmd b/dev/LPC_targets_project.Rmd
@@ -278,6 +278,7 @@ controller_lsf_normal <- crew.cluster::crew_controller_lsf(
   script_lines = c(
     \"#BSUB-q voltron_normal\",
     \"export R_LIBS_USER=$HOME/R/rocker-rstudio/bioconductor-tidyverse_3.17\",
+    \"export OMP_NUM_THREADS=1\",
     \"export SINGULARITY_BIND='/project/:/project/, /appl/:/appl/, /lsf/:/lsf/, /scratch/:/scratch, /static:/static'\",
     \"singularity exec --pwd {getwd()} /project/voltron/rstudio/containers/bioconductor-tidyverse_3.17.sif \\\\\"
   ),
@@ -294,6 +295,7 @@ controller_lsf_long <- crew.cluster::crew_controller_lsf(
   script_lines = c(
     \"#BSUB-q voltron_long\",
     \"export R_LIBS_USER=$HOME/R/rocker-rstudio/bioconductor-tidyverse_3.17\",
+    \"export OMP_NUM_THREADS=1\",
     \"export SINGULARITY_BIND='/project/:/project/, /appl/:/appl/, /lsf/:/lsf/, /scratch/:/scratch, /static:/static'\",
     \"singularity exec --pwd {getwd()} /project/voltron/rstudio/containers/bioconductor-tidyverse_3.17.sif \\\\\"
   ),
@@ -310,6 +312,7 @@ controller_lsf_highmem <- crew.cluster::crew_controller_lsf(
   script_lines = c(
     \"#BSUB-q voltron_normal\",
     \"export R_LIBS_USER=$HOME/R/rocker-rstudio/bioconductor-tidyverse_3.17\",
+    \"export OMP_NUM_THREADS=1\",
     \"export SINGULARITY_BIND='/project/:/project/, /appl/:/appl/, /lsf/:/lsf/, /scratch/:/scratch, /static:/static'\",
     \"singularity exec --pwd {getwd()} /project/voltron/rstudio/containers/bioconductor-tidyverse_3.17.sif \\\\\"
   ),
@@ -327,6 +330,7 @@ controller_lsf_multicore <- crew.cluster::crew_controller_lsf(
   script_lines = c(
     \"#BSUB-q voltron_normal\",
     \"export R_LIBS_USER=$HOME/R/rocker-rstudio/bioconductor-tidyverse_3.17\",
+    \"export OMP_NUM_THREADS=16\",
     \"export SINGULARITY_BIND='/project/:/project/, /appl/:/appl/, /lsf/:/lsf/, /scratch/:/scratch, /static:/static'\",
     \"singularity exec --pwd {getwd()} /project/voltron/rstudio/containers/bioconductor-tidyverse_3.17.sif \\\\\"
   ),

diff --git a/dev/config_fusen.yaml b/dev/config_fusen.yaml
@@ -50,6 +50,16 @@ flat_miscellaneous.Rmd:
     check: false
     document: true
     overwrite: 'yes'
+keep:
+  path: keep
+  state: active
+  R:
+  - R/levinmisc-package.R
+  - R/utils-pipe.R
+  tests:
+  - tests/testthat/test-description-of-your-package-submit-targets-sh.R
+  - tests/testthat/test-populate_targets_proj.R
+  vignettes: []
 LPC_targets_project.Rmd:
   path: dev/LPC_targets_project.Rmd
   state: active