update simulation code for examples 1-3

[ml_measurement_error_public.git] / simulations / Makefile

diff --git a/simulations/Makefile b/simulations/Makefile
index 01c34fc2e77e8b0ca3b545bfbaa6cafbe69d6f19..dec7889db143e7738293e5825094d7ccc9cac2df 100644 (file)
--- a/simulations/Makefile
+++ b/simulations/Makefile
@@ -1,52 +1,68 @@
 
 SHELL=bash
 
 
 SHELL=bash
 

-Ns=[500,1000,10000,25000]
-ms=[50, 100, 250, 500]
+Ns=[1000,3600,14400]
+ms=[75,150,300]

 seeds=[$(shell seq -s, 1 250)]
 seeds=[$(shell seq -s, 1 250)]

+explained_variances=[0.1]
+

 all:remembr.RDS
 
 all:remembr.RDS
 

-srun=srun -A comdata -p compute-bigmem --time=10:00:00 --mem 4G -c 1
+srun=srun -A comdata -p compute-bigmem --time=6:00:00 --mem 4G -c 1
+
+
+joblists:example_1_jobs example_2_jobs example_3_jobs
+
+# test_true_z_jobs: test_true_z.R simulation_base.R
+#      grid_sweep.py --command "Rscript test_true_z.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["test_true_z.feather"], "y_explained_variancevari":${explained_variances}, "Bzx":${Bzx}}' --outfile test_true_z_jobsb

 
 

-example_1_jobs: 01_two_covariates.R simulation_base.R grid_sweep.py
-       grid_sweep.py --command "Rscript 01_two_covariates.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_1.feather"]}' --outfile example_1_jobs
+# test_true_z.feather: test_true_z_jobs 
+#      rm -f test_true_z.feather
+#      sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 test_true_z_jobs
+#      sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 test_true_z_jobs

 
 

-example_1.feather: example_1_jobs
+
+example_1_jobs: 01_two_covariates.R simulation_base.R
+       grid_sweep.py --command "Rscript 01_two_covariates.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_1.feather"], "y_explained_variance":${explained_variances}, "Bzx":[0.1]}' --outfile example_1_jobs
+
+example_1.feather: example_1_jobs 

        rm -f example_1.feather
        rm -f example_1.feather

-       sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 example_1_jobs
-       sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_1_jobs
+       sbatch --wait --verbose --array=1-$(shell cat example_1_jobs | wc -l) run_simulation.sbatch 0 example_1_jobs
+#      sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_1_jobs

 
 

-example_2_jobs: example_2.R
-       grid_sweep.py --command "Rscript 02_indep_differential.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2.feather"]}' --outfile example_2_jobs
+example_2_jobs: 02_indep_differential.R simulation_base.R
+       grid_sweep.py --command "Rscript 02_indep_differential.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2.feather"],"y_explained_variance":${explained_variances}, "accuracy_imbalance_difference":[0.3], "Bzy":[0.3]}' --outfile example_2_jobs

 
 

-example_2.feather: example_2_jobs
+example_2.feather: example_2_jobs 

        rm -f example_2.feather
        rm -f example_2.feather

-       sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 example_2_jobs
-       sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_jobs
+       sbatch --wait --verbose --array=1-$(shell cat example_2_jobs | wc -l) run_simulation.sbatch 0 example_2_jobs
+#      sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_jobs

 
 

-example_2_B_jobs: example_2_B.R
-       grid_sweep.py --command "Rscript example_2_B.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2_B.feather"]}' --outfile example_2_B_jobs
+# example_2_B_jobs: example_2_B.R
+#      grid_sweep.py --command "Rscript example_2_B.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_2_B.feather"]}' --outfile example_2_B_jobs

 
 

-example_2_B.feather: example_2_B_jobs
-       rm -f example_2_B.feather
-       sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 example_2_B_jobs
+# example_2_B.feather: example_2_B_jobs
+#      rm -f example_2_B.feather
+#      sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 example_2_B_jobs

 
 

-example_3_jobs: example_3.R
-       grid_sweep.py --command "Rscript example_3.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_3.feather"]}' --outfile example_3_jobs
+example_3_jobs: 03_depvar_differential.R simulation_base.R
+       grid_sweep.py --command "Rscript 03_depvar_differential.R" --arg_dict '{"N":${Ns},"m":${ms}, "seed":${seeds}, "outfile":["example_3.feather"], "y_explained_variance":${explained_variances}}' --outfile example_3_jobs

 
 example_3.feather: example_3_jobs
 
 example_3.feather: example_3_jobs

-       rm -f example_3.feather
-       sbatch --wait --verbose --array=1-3000 run_simulation.sbatch 0 example_3_jobs
+       rm -f example_3.feather 
+       sbatch --wait --verbose --array=1-$(shell cat example_3_jobs | wc -l)  run_simulation.sbatch 0 example_3_jobs

 
 
 
 

-remembr.RDS:example_2_B.feather example_1.feather example_2.feather example_3.feather
+remembr.RDS:example_1.feather example_2.feather example_3.feather plot_example.R plot_dv_example.R
+       rm -f remembr.RDS

        ${srun} Rscript plot_example.R --infile example_1.feather --name "plot.df.example.1"
        ${srun} Rscript plot_example.R --infile example_2.feather --name "plot.df.example.2"
        ${srun} Rscript plot_example.R --infile example_1.feather --name "plot.df.example.1"
        ${srun} Rscript plot_example.R --infile example_2.feather --name "plot.df.example.2"

-       ${srun} Rscript plot_example.R --infile example_2_B.feather --name "plot.df.example.2B"
-       ${srun} Rscript plot_example.R --infile example_3.feather --name "plot.df.example.3"
-
-
+       ${srun} Rscript plot_dv_example.R --infile example_3.feather --name "plot.df.example.3"

 
 

+clean:
+       rm *.feather
+       rm -f remembr.RDS
+       rm -f example_*_jobs

 #      sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_B_jobs
 
 # example_2_B_mecor_jobs:
 #      sbatch --wait --verbose --array=3001-6001 run_simulation.sbatch 0 example_2_B_jobs
 
 # example_2_B_mecor_jobs: