diff --git a/machines/archer/jobscript-precompile-no-run.template b/machines/archer/jobscript-precompile-no-run.template
index 0a800be4d..1acc243a3 100644
--- a/machines/archer/jobscript-precompile-no-run.template
+++ b/machines/archer/jobscript-precompile-no-run.template
@@ -22,6 +22,6 @@ export SRUN_CPUS_PER_TASK=$SLURM_CPUS_PER_TASK
 
 echo "precompiling $(date)"
 
-bin/julia --project -O3 --check-bounds=no precompile-no-run.jl
+bin/julia --project -O3 precompile-no-run.jl
 
 echo "finished! $(date)"
diff --git a/machines/archer/jobscript-precompile.template b/machines/archer/jobscript-precompile.template
index 8213b7e01..df989edc9 100644
--- a/machines/archer/jobscript-precompile.template
+++ b/machines/archer/jobscript-precompile.template
@@ -22,6 +22,6 @@ export SRUN_CPUS_PER_TASK=$SLURM_CPUS_PER_TASK
 
 echo "precompiling $(date)"
 
-bin/julia --project -O3 --check-bounds=no precompile.jl
+bin/julia --project -O3 precompile.jl
 
 echo "finished! $(date)"
diff --git a/machines/archer/jobscript-restart.template b/machines/archer/jobscript-restart.template
index 6ac1c50f9..5d105fd64 100644
--- a/machines/archer/jobscript-restart.template
+++ b/machines/archer/jobscript-restart.template
@@ -22,6 +22,6 @@ export SRUN_CPUS_PER_TASK=$SLURM_CPUS_PER_TASK
 
 echo "running INPUTFILE $(date)"
 
-srun --distribution=block:block --hint=nomultithread --ntasks=$SLURM_NTASKS bin/julia -Jmoment_kinetics.so --project -O3 --check-bounds=no run_moment_kinetics.jl --restart INPUTFILE RESTARTFROM
+srun --distribution=block:block --hint=nomultithread --ntasks=$SLURM_NTASKS bin/julia -Jmoment_kinetics.so --project -O3 run_moment_kinetics.jl --restart INPUTFILE RESTARTFROM
 
 echo "finished INPUTFILE $(date)"
diff --git a/machines/archer/jobscript-run.template b/machines/archer/jobscript-run.template
index ea2787bf0..d017ac17c 100644
--- a/machines/archer/jobscript-run.template
+++ b/machines/archer/jobscript-run.template
@@ -22,6 +22,6 @@ export SRUN_CPUS_PER_TASK=$SLURM_CPUS_PER_TASK
 
 echo "running INPUTFILE $(date)"
 
-srun --distribution=block:block --hint=nomultithread --ntasks=$SLURM_NTASKS bin/julia -Jmoment_kinetics.so --project -O3 --check-bounds=no run_moment_kinetics.jl INPUTFILE
+srun --distribution=block:block --hint=nomultithread --ntasks=$SLURM_NTASKS bin/julia -Jmoment_kinetics.so --project -O3 run_moment_kinetics.jl INPUTFILE
 
 echo "finished INPUTFILE $(date)"
diff --git a/machines/generic-batch-template/jobscript-precompile-no-run.template b/machines/generic-batch-template/jobscript-precompile-no-run.template
index af1b37369..8ed8778a5 100644
--- a/machines/generic-batch-template/jobscript-precompile-no-run.template
+++ b/machines/generic-batch-template/jobscript-precompile-no-run.template
@@ -15,6 +15,6 @@ source julia.env
 
 echo "precompiling $(date)"
 
-bin/julia --project -O3 --check-bounds=no precompile-no-run.jl
+bin/julia --project -O3 precompile-no-run.jl
 
 echo "finished! $(date)"
diff --git a/machines/generic-batch-template/jobscript-precompile.template b/machines/generic-batch-template/jobscript-precompile.template
index 212ac53fa..ba15862e8 100644
--- a/machines/generic-batch-template/jobscript-precompile.template
+++ b/machines/generic-batch-template/jobscript-precompile.template
@@ -15,6 +15,6 @@ source julia.env
 
 echo "precompiling $(date)"
 
-bin/julia --project -O3 --check-bounds=no precompile.jl
+bin/julia --project -O3 precompile.jl
 
 echo "finished! $(date)"
diff --git a/machines/generic-batch-template/jobscript-restart.template b/machines/generic-batch-template/jobscript-restart.template
index 52e70a63f..db440970a 100644
--- a/machines/generic-batch-template/jobscript-restart.template
+++ b/machines/generic-batch-template/jobscript-restart.template
@@ -19,6 +19,6 @@ source julia.env
 echo "running INPUTFILE $(date)"
 
 # May need to change this if mpirun` is not what should be used on your system
-mpirun -np $SLURM_NTASKS bin/julia -Jmoment_kinetics.so --project -O3 --check-bounds=no run_moment_kinetics.jl --restart INPUTFILE RESTARTFROM
+mpirun -np $SLURM_NTASKS bin/julia -Jmoment_kinetics.so --project -O3 run_moment_kinetics.jl --restart INPUTFILE RESTARTFROM
 
 echo "finished INPUTFILE $(date)"
diff --git a/machines/generic-batch-template/jobscript-run.template b/machines/generic-batch-template/jobscript-run.template
index dce67e2c9..e292a472c 100644
--- a/machines/generic-batch-template/jobscript-run.template
+++ b/machines/generic-batch-template/jobscript-run.template
@@ -19,6 +19,6 @@ source julia.env
 echo "running INPUTFILE $(date)"
 
 # May need to change this if mpirun` is not what should be used on your system
-mpirun -np $SLURM_NTASKS bin/julia -Jmoment_kinetics.so --project -O3 --check-bounds=no run_moment_kinetics.jl INPUTFILE
+mpirun -np $SLURM_NTASKS bin/julia -Jmoment_kinetics.so --project -O3 run_moment_kinetics.jl INPUTFILE
 
 echo "finished INPUTFILE $(date)"
diff --git a/machines/machine_setup.sh b/machines/machine_setup.sh
index 0d29ea3e5..bf93f9f6a 100755
--- a/machines/machine_setup.sh
+++ b/machines/machine_setup.sh
@@ -271,7 +271,7 @@ SEPARATE_POSTPROC_PROJECTS=$(bin/julia --project machines/shared/get_mk_preferen
 if [[ $BATCH_SYSTEM -eq 0 || $SEPARATE_POSTPROC_PROJECTS == "y" ]]; then
   # Batch systems can (conveniently) use different optimization flags for
   # running simulations and for post-processing.
-  OPTIMIZATION_FLAGS="-O3 --check-bounds=no"
+  OPTIMIZATION_FLAGS="-O3"
   POSTPROC_OPTIMIZATION_FLAGS="-O3"
 else
   # On interactive systems which use the same project for running simulations
diff --git a/machines/marconi/jobscript-precompile-no-run.template b/machines/marconi/jobscript-precompile-no-run.template
index 241f20956..bffe80164 100644
--- a/machines/marconi/jobscript-precompile-no-run.template
+++ b/machines/marconi/jobscript-precompile-no-run.template
@@ -15,6 +15,6 @@ source julia.env
 
 echo "precompiling $(date)"
 
-bin/julia --project -O3 --check-bounds=no precompile-no-run.jl
+bin/julia --project -O3 precompile-no-run.jl
 
 echo "finished! $(date)"
diff --git a/machines/marconi/jobscript-precompile.template b/machines/marconi/jobscript-precompile.template
index d7528d70e..85298d9bb 100644
--- a/machines/marconi/jobscript-precompile.template
+++ b/machines/marconi/jobscript-precompile.template
@@ -15,6 +15,6 @@ source julia.env
 
 echo "precompiling $(date)"
 
-bin/julia --project -O3 --check-bounds=no precompile.jl
+bin/julia --project -O3 precompile.jl
 
 echo "finished! $(date)"
diff --git a/machines/marconi/jobscript-restart.template b/machines/marconi/jobscript-restart.template
index ffbcc746f..20f82318a 100644
--- a/machines/marconi/jobscript-restart.template
+++ b/machines/marconi/jobscript-restart.template
@@ -18,6 +18,6 @@ source julia.env
 
 echo "running INPUTFILE $(date)"
 
-mpirun -np $SLURM_NTASKS bin/julia -Jmoment_kinetics.so --project -O3 --check-bounds=no run_moment_kinetics.jl --restart INPUTFILE RESTARTFROM
+mpirun -np $SLURM_NTASKS bin/julia -Jmoment_kinetics.so --project -O3 run_moment_kinetics.jl --restart INPUTFILE RESTARTFROM
 
 echo "finished INPUTFILE $(date)"
diff --git a/machines/marconi/jobscript-run.template b/machines/marconi/jobscript-run.template
index 131dbbb6e..01e2243cc 100644
--- a/machines/marconi/jobscript-run.template
+++ b/machines/marconi/jobscript-run.template
@@ -18,6 +18,6 @@ source julia.env
 
 echo "running INPUTFILE $(date)"
 
-mpirun -np $SLURM_NTASKS bin/julia -Jmoment_kinetics.so --project -O3 --check-bounds=no run_moment_kinetics.jl INPUTFILE
+mpirun -np $SLURM_NTASKS bin/julia -Jmoment_kinetics.so --project -O3 run_moment_kinetics.jl INPUTFILE
 
 echo "finished INPUTFILE $(date)"
diff --git a/machines/shared/submit-restart.sh b/machines/shared/submit-restart.sh
index 5589391ce..e308c0330 100755
--- a/machines/shared/submit-restart.sh
+++ b/machines/shared/submit-restart.sh
@@ -123,7 +123,7 @@ sed -e "s|NODES|$NODES|" -e "s|RUNTIME|$RUNTIME|" -e "s|ACCOUNT|$ACCOUNT|" -e "s
 
 if [[ "$WARN_OLD_SYSIMAGE" -eq 0 ]]; then
   # Check that source code has not been changed since moment_kinetics.so was created
-  bin/julia --project -O3 --check-bounds=no moment_kinetics/src/check_so_newer_than_code.jl moment_kinetics.so
+  bin/julia --project -O3 moment_kinetics/src/check_so_newer_than_code.jl moment_kinetics.so
 fi
 
 if [[ $SUBMIT -eq 0 ]]; then
diff --git a/machines/shared/submit-run.sh b/machines/shared/submit-run.sh
index b39efd4f6..5e1db9e1d 100755
--- a/machines/shared/submit-run.sh
+++ b/machines/shared/submit-run.sh
@@ -118,7 +118,7 @@ sed -e "s|NODES|$NODES|" -e "s|RUNTIME|$RUNTIME|" -e "s|ACCOUNT|$ACCOUNT|" -e "s
 
 if [[ "$WARN_OLD_SYSIMAGE" -eq 0 ]]; then
   # Check that source code has not been changed since moment_kinetics.so was created
-  bin/julia --project -O3 --check-bounds=no moment_kinetics/src/check_so_newer_than_code.jl moment_kinetics.so
+  bin/julia --project -O3 moment_kinetics/src/check_so_newer_than_code.jl moment_kinetics.so
 fi
 
 if [[ $SUBMIT -eq 0 ]]; then
diff --git a/precompile-kinetic-electrons.jl b/precompile-kinetic-electrons.jl
index 9922963aa..8f64b2f9e 100644
--- a/precompile-kinetic-electrons.jl
+++ b/precompile-kinetic-electrons.jl
@@ -12,5 +12,5 @@ using PackageCompiler
 create_sysimage(; sysimage_path="moment_kinetics.so",
                 precompile_execution_file="util/precompile_run_kinetic-electrons.jl",
                 include_transitive_dependencies=false, # This is needed to make MPI work, see https://github.com/JuliaParallel/MPI.jl/issues/518
-                sysimage_build_args=`-O3 --check-bounds=no`, # Assume if we are precompiling we want an optimized, production build
+                sysimage_build_args=`-O3`, # Assume if we are precompiling we want an optimized, production build
                )
diff --git a/precompile-makie-post-processing.jl b/precompile-makie-post-processing.jl
index 41674db91..f3f947798 100644
--- a/precompile-makie-post-processing.jl
+++ b/precompile-makie-post-processing.jl
@@ -9,5 +9,5 @@ using PackageCompiler
 create_sysimage(; sysimage_path="makie_postproc.so",
                 precompile_execution_file="util/precompile_makie_plots.jl",
                 include_transitive_dependencies=false, # This is needed to make MPI work, see https://github.com/JuliaParallel/MPI.jl/issues/518
-                sysimage_build_args=`-O3`, # Assume if we are precompiling we want an optimized, production build. No `--check-bounds=no` because Makie doesn' like it https://github.com/MakieOrg/Makie.jl/issues/3132
+                sysimage_build_args=`-O3`, # Assume if we are precompiling we want an optimized, production build. We do not use `--check-bounds=no` for any runs any more, but if we want to again in future, check whether Makie works well with it, see https://github.com/MakieOrg/Makie.jl/issues/3132
                )
diff --git a/precompile-no-run.jl b/precompile-no-run.jl
index e7a5fedee..71e134fa6 100644
--- a/precompile-no-run.jl
+++ b/precompile-no-run.jl
@@ -11,5 +11,5 @@ using PackageCompiler
 # need to re-precompile if you change anything.
 create_sysimage(; sysimage_path="moment_kinetics.so",
                 include_transitive_dependencies=false, # This is needed to make MPI work, see https://github.com/JuliaParallel/MPI.jl/issues/518
-                sysimage_build_args=`-O3 --check-bounds=no`, # Assume if we are precompiling we want an optimized, production build
+                sysimage_build_args=`-O3`, # Assume if we are precompiling we want an optimized, production build
                )
diff --git a/precompile-plots-post-processing.jl b/precompile-plots-post-processing.jl
index a2887282e..6c53fcd21 100644
--- a/precompile-plots-post-processing.jl
+++ b/precompile-plots-post-processing.jl
@@ -9,5 +9,5 @@ using PackageCompiler
 create_sysimage(; sysimage_path="plots_postproc.so",
                 precompile_execution_file="util/precompile_plots_plots.jl",
                 include_transitive_dependencies=false, # This is needed to make MPI work, see https://github.com/JuliaParallel/MPI.jl/issues/518
-                sysimage_build_args=`-O3`, # Assume if we are precompiling we want an optimized, production build. No `--check-bounds=no` because Makie doesn' like it https://github.com/MakieOrg/Makie.jl/issues/3132
+                sysimage_build_args=`-O3`, # Assume if we are precompiling we want an optimized, production build. For post-processing, we probably do not want `--check-bounds=no` even if we start using it again for simulations.
                )
diff --git a/precompile.jl b/precompile.jl
index 3876c246a..c6cca389d 100644
--- a/precompile.jl
+++ b/precompile.jl
@@ -12,5 +12,5 @@ using PackageCompiler
 create_sysimage(; sysimage_path="moment_kinetics.so",
                 precompile_execution_file="util/precompile_run.jl",
                 include_transitive_dependencies=false, # This is needed to make MPI work, see https://github.com/JuliaParallel/MPI.jl/issues/518
-                sysimage_build_args=`-O3 --check-bounds=no`, # Assume if we are precompiling we want an optimized, production build
+                sysimage_build_args=`-O3`, # Assume if we are precompiling we want an optimized, production build
                )
diff --git a/precompile_dependencies.jl b/precompile_dependencies.jl
index 881d8610c..e64a82eb2 100644
--- a/precompile_dependencies.jl
+++ b/precompile_dependencies.jl
@@ -14,5 +14,5 @@ packages = collect(Symbol(d) for d ∈ keys(project_file["deps"]))
 create_sysimage(packages; sysimage_path="dependencies.so",
                 precompile_execution_file="util/precompile_run_short.jl",
                 include_transitive_dependencies=false, # This is needed to make MPI work, see https://github.com/JuliaParallel/MPI.jl/issues/518
-                sysimage_build_args=`-O3 --check-bounds=no`, # Assume if we are precompiling we want an optimized, production build
+                sysimage_build_args=`-O3`, # Assume if we are precompiling we want an optimized, production build
                )