Brough in some changes to cadnano_segments.py from origamitwo server

cadnano_segments.py

@@ -2,8 +2,10 @@
 import pdb
 import numpy as np
 import os,sys
-from coords import readArbdCoords, readAvgArbdCoords
+from glob import glob
+import re
 
+from coords import readArbdCoords, readAvgArbdCoords
 from segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
 
 arbd="/home/cmaffeo2/development/cuda/arbd.dbg/src/arbd" # reduced the mem footprint cause vmd
@@ -276,7 +278,7 @@ def decode_cadnano_part(json_data):
 def package_archive( name, directory ):
     ...
 
-def run_simulation_protocol( output_name, json_data,
+def run_simulation_protocol( output_name, job_id, json_data,
                              sequence=None,
                              remove_long_bonds=False,
                              gpu = 0,
@@ -284,14 +286,14 @@ def run_simulation_protocol( output_name, json_data,
                          ):
 
     coarseSteps = 1e7
-    fineSteps = 1e6    
-    
+    fineSteps = 1e6
+
     ret = None
     d_orig = os.getcwd()
     try:
         if directory is None:
             import tempfile
-            directory = tempfile.mkdtemp(prefix='origami-'+output_name, dir='./')
+            directory = tempfile.mkdtemp(prefix='origami-%s-' % job_id, dir='/dev/shm/')
         elif not os.path.exists(directory):
             os.makedirs(directory)
         os.chdir(directory)
@@ -320,8 +322,7 @@ def run_simulation_protocol( output_name, json_data,
         # print(sequence)
         # for i in sequence:
         #     print( i, i in ('A','T','C','G') )
-        # model.strands[0].set_sequence(sequence)
-
+        model.strands[0].set_sequence(sequence)
 
         for s in model.segments:
             s.randomize_unset_sequence()
@@ -380,16 +381,8 @@ def run_simulation_protocol( output_name, json_data,
         model._generate_atomic_model(scale=0.25)
         model.atomic_simulate( outputPrefix = full_output_prefix )
 
-        # if not os.path.exists(output_directory):
-        #     os.makedirs(output_directory)
-        # elif not os.path.isdir(output_directory):
-        #     raise Exception("output_directory '%s' is not a directory!" % output_directory)
+        ret = directory
         
-
-        """ Package result """
-        ret = "{}@{}:{}".format( os.environ["USER"],
-                                 os.environ["HOSTNAME"],
-                                 "/path/to/archive.tar.gz" )
     except:
         raise
     finally:
@@ -405,11 +398,8 @@ def run_simulation_protocol( output_name, json_data,
 
 
 if __name__ == '__main__':
-    from glob import glob
-    import re
-
     for f in glob('json/*'):
         print("Working on {}".format(f))
         out = re.match('json/(.*).json',f).group(1)
         data = read_json_file(f)
-        run_simulation_protocol( out, data, gpu=0 )
+        run_simulation_protocol( out, "job-id", data, gpu=0 )

run.py

@@ -9,4 +9,4 @@ if __name__ == '__main__':
         print("Working on {}".format(f))
         out = re.match('json/(.*).json',f).group(1)
         data = read_json_file(f)
-        run_simulation_protocol( out, data, gpu=0 )
+        run_simulation_protocol( out, "job-id", data, gpu=0 )