Updated examples.

examples/fmri/biobank/2_train_hmm.py

@@ -35,7 +35,12 @@
     inputs = file.read().split("\n")
 
 # Create Data object for training
-data = Data(inputs, load_memmaps=False, n_jobs=8)
+data = Data(
+    inputs,
+    use_tfrecord=True,
+    store_dir=f"tmp_{id}",
+    n_jobs=8,
+)
 
 # Prepare data
 data.standardize()

examples/fmri/biobank/4_dual_estimation.py

@@ -47,7 +47,12 @@
     inputs = file.read().split("\n")
 
 # Create Data object for training
-data = Data(inputs, load_memmaps=False, n_jobs=8)
+data = Data(
+    inputs,
+    use_tfrecord=True,
+    store_dir=f"tmp_{id}",
+    n_jobs=16,
+)
 
 # Prepare data
 data.standardize()

examples/fmri/biobank/submit_jobs.py

@@ -4,8 +4,9 @@
 
 import os
 
-def write_job_script(run, queue="gpu_short"):
-    """Create a job script to submit."""
+
+def write_gpu_job_script(run, queue="gpu_short"):
+    """Create a job script to submit a job to the GPU queue."""
 
     with open("job.sh", "w") as file:
         name = f"ukb-hmm-{run}"
@@ -18,9 +19,25 @@ def write_job_script(run, queue="gpu_short"):
         file.write("source activate osld\n")
         file.write(f"python 2_train_hmm.py {run}\n")
 
+
+def write_cpu_job_script(run, queue="short", n_cpus=24):
+    """Create a job script to submit."""
+
+    with open("job.sh", "w") as file:
+        name = f"ukb-hmm-{run}"
+        file.write("#!/bin/bash\n")
+        file.write(f"#SBATCH -J {name}\n")
+        file.write(f"#SBATCH -o logs/{name}.out\n")
+        file.write(f"#SBATCH -e logs/{name}.err\n")
+        file.write(f"#SBATCH -p {queue}\n")
+        file.write(f"#SBATCH -c {n_cpus}\n")
+        file.write("source activate osld\n")
+        file.write(f"python 2_train_hmm.py {run}\n")
+
+
 os.makedirs("logs", exist_ok=True)
 
 for run in range(1, 11):
-    write_job_script(run)
+    write_cpu_job_script(run)
     os.system("sbatch job.sh")
     os.system("rm job.sh")

examples/fmri/hcp/2_train_hmm.py

@@ -35,7 +35,11 @@
     inputs = file.read().split("\n")
 
 # Create Data object for training
-data = Data(inputs, load_memmaps=False, n_jobs=8)
+data = Data(
+    inputs,
+    store_dir=f"tmp_{id}",
+    n_jobs=8,
+)
 
 # Prepare data
 data.standardize()

examples/fmri/hcp/4_dual_estimation.py

@@ -47,7 +47,11 @@
     inputs = file.read().split("\n")
 
 # Create Data object for training
-data = Data(inputs, load_memmaps=False, n_jobs=8)
+data = Data(
+    inputs,
+    store_dir=f"tmp_{id}",
+    n_jobs=8,
+)
 
 # Prepare data
 data.standardize()