[FIX] Prevent leaked semaphores on tracking

Author: dPys

.vagrant/rgloader/loader.rb

@@ -0,0 +1,9 @@
+# This file loads the proper rgloader/loader.rb file that comes packaged
+# with Vagrant so that encoded files can properly run with Vagrant.
+
+if ENV["VAGRANT_INSTALLER_EMBEDDED_DIR"]
+  require File.expand_path(
+    "rgloader/loader", ENV["VAGRANT_INSTALLER_EMBEDDED_DIR"])
+else
+  raise "Encoded files can't be read outside of the Vagrant installer."
+end

Dockerfile

@@ -87,6 +87,8 @@ RUN apt-get update -qq \
     && chmod 777 -R $FSLDIR/bin \
     && chmod 777 -R /usr/lib/fsl/5.0 \
     && echo "tmpfs   /tmp         tmpfs   rw,nodev,nosuid,size=10G          0  0" >> /etc/fstab
+#    && wget --retry-connrefused --waitretry=5 --read-timeout=60 --timeout=60 -t 0 -q -O examples.tar.gz "https://osf.io/ye4vf/download" && tar -xvzf examples.tar.gz -C /tmp \
+#    && rm -rf examples.tar.gz
 
 ENV FSLDIR=/usr/share/fsl/5.0 \
     FSLOUTPUTTYPE=NIFTI_GZ \

pynets/cli/pynets_run.py

@@ -795,7 +795,7 @@ def build_workflow(args, retval):
         import psutil
         nthreads = psutil.cpu_count()
         procmem = [int(nthreads),
-                   int(list(psutil.virtual_memory())[4]/1000000000) - 2]
+                   int(list(psutil.virtual_memory())[4]/1000000000) - 1]
     else:
         procmem = list(eval(str(resources)))
         procmem[1] = procmem[1] - 1

pynets/dmri/track.py

@@ -404,6 +404,7 @@ def track_ensemble(
     import os
     import gc
     import time
+    import warnings
     from joblib import Parallel, delayed
     import itertools
     from pynets.dmri.track import run_tracking
@@ -414,6 +415,7 @@ def track_ensemble(
     from nilearn.masking import intersect_masks
     from nilearn.image import math_img
     from pynets.core.utils import load_runconfig
+    warnings.filterwarnings("ignore")
 
     tmp_files_dir = f"{cache_dir}/tmp_files"
     joblib_dir = f"{cache_dir}/joblib_tracking"
@@ -480,7 +482,7 @@ def track_ensemble(
         while float(stream_counter) < float(target_samples) and float(ix) < 0.50*float(len(all_combs)):
             with Parallel(n_jobs=nthreads, backend='loky',
                           mmap_mode='r+', temp_folder=joblib_dir,
-                          verbose=2, max_nbytes='25000M',
+                          verbose=0, max_nbytes='50000M',
                           timeout=timeout) as parallel:
                 out_streams = parallel(
                     delayed(run_tracking)(
@@ -529,7 +531,7 @@ def track_ensemble(
                 )
                 gc.collect()
                 print(Style.RESET_ALL)
-            os.system(f"rm -f {joblib_dir}/* &")
+            os.system(f"rm -f {joblib_dir}/*")
     except BaseException:
         os.system(f"rm -f {tmp_files_dir} &")
         return None