Paths are set by setup script.

Author: bbusemeyer

.gitignore

@@ -1,4 +1,4 @@
 examples
 intro
 tests
-paths.yaml
+autopaths.py

README.md

@@ -5,21 +5,27 @@ Goal: Provide tools that make it easy to manage and store QWalk runs.
 
 # Getting started.
 
+Run `setup.py` to fill in the locations of packages you may want to use with autogen, such as Crystal or PySCF.
+  - without this step autogen will not be able to run any executibles.
+
 Check out the intro folder, which constains a set of jupyter notebooks to help you understand how this package works.
+Alternative python scripts (which are just python downloads of the notebooks) are also there.
 
 Working through all the notebooks should only take ~10 minutes.
 
-# Object definitions
-
-## Level 1: constructing input files and gathering data
-
- * The Writer object has all options to set up a job as member variables, and can construct input files for a run given those input files.
- * The Reader object can read the output of a run and report on its completion or lack thereof. This object defines what a successful run is. 
- * The Runner object executes a set of runs for a given code on a given computer system.
-
-## Level 2: Manager
-
-The Manager object consists of at least one Writer, Reader, and Runner. The Manager owns the directory for the time of its execution, that is, until it says it's done.
-A manager may need multiple nextstep() calls before it's done. For example, one might want to run crystal and then properties using a queue to run both. 
-
-Calling `nextstep` repeatedly will attempt to finish the calculation, one step at a time.
+You can also checkout `tests/simple_test.py` for a more useful template to build scripts from.
+
+# Troubleshooting
+
+- autogen can't find an executible. 
+  - Make sure you've run `setup.py`.
+- The notebooks keep saying 'file not found'?
+  - If you have any error when running the notebook, try restarting the kernel.
+    Sometimes the current state of the kernel is the problem.
+- A manager isn't updating some attributes or is refusing to update some attributes. 
+  - Be careful! This sometimes means you've changed the input file but the old output is still around.
+    This can lead to bad data if not dealt with carefully!
+    Check that you didn't change any parameters that affect the accuracy of the calculation. 
+    If you want to force the change, you can delete the manager, and it'll go through with what you say. 
+    To be safe, you should probably remove all the output generated by that manager as well. 
+    `rm ${name}*` where name=[the manager's name].

__init__.py

@@ -15,7 +15,8 @@
     "pyscf2qwalk",
     "qwalkrunner",
     "runner",
+    "paths",
     "submitter",
     "trialfunc",
-    "variance"
+    "variance",
   ]

autorunner.py

@@ -275,7 +275,6 @@ class PySCFRunnerPBS(RunnerPBS):
   def __init__(self,queue='batch',
                     walltime='12:00:00',
                     np='allprocs',
-                    ppath=None,
                     nn=1,
                     jobname=os.getcwd().split('/')[-1]+'_pyscf',
                     prefix=None,
@@ -290,8 +289,6 @@ def __init__(self,queue='batch',
     self.prefix=prefix
     self.postfix=postfix
     self.exelines=[]
-    if ppath is None: self.ppath=[]
-    else:             self.ppath=ppath
     if prefix is None: self.prefix=[]
     else:              self.prefix=prefix
     if postfix is None: self.postfix=[]
@@ -327,7 +324,16 @@ def script(self,scriptfile):
     return True
 
   #-------------------------------------
-  def submit(self,jobname=None):
+  def submit(self,jobname=None,ppath=None):
+    ''' Submit any accumulated tasks.
+
+    Args:
+      jobname (str): name to appear in the queue.
+      ppath (list): python path needed for the run (default: current path).
+    '''
+      
+    if ppath is None: ppath=sys.path
+
     if len(self.exelines)==0: 
       #print(self.__class__.__name__,": All tasks completed or queued.")
       return
@@ -352,7 +358,7 @@ def submit(self,jobname=None):
          "#PBS -o %s"%jobout,
          "cd ${PBS_O_WORKDIR}",
          "export OMP_NUM_THREADS=%d"%(self.nn*self.np),
-         "export PYTHONPATH=%s"%(':'.join(self.ppath)),
+         "export PYTHONPATH=%s"%(':'.join(ppath)),
          "cwd=`pwd`"
        ] + self.prefix + self.exelines + self.postfix
     qsubfile=jobname+".qsub"

manager.py

@@ -22,6 +22,7 @@
 import crystal2qmc
 import pickle as pkl
 import autorunner
+from autopaths import paths
 
 from copy import deepcopy
 
@@ -261,7 +262,7 @@ def nextstep(self):
 
     if status=="not_started":
       self.runner.add_command("cp %s INPUT"%self.crysinpfn)
-      self.runner.add_task("Pcrystal &> %s"%self.crysoutfn)
+      self.runner.add_task("%s &> %s"%(paths['Pcrystal'],self.crysoutfn))
 
     elif status=="ready_for_analysis":
       #This is where we (eventually) do error correction and resubmits
@@ -286,7 +287,7 @@ def nextstep(self):
           sh.copy(self.writer.guess_fort,'fort.20')
           self.writer.write_crys_input(self.crysinpfn)
           sh.copy(self.crysinpfn,'INPUT')
-          self.runner.add_task("Pcrystal &> %s"%self.crysoutfn)
+          self.runner.add_task("%s &> %s"%(paths['Pcrystal'],self.crysoutfn))
           self.restarts+=1
     elif status=='done' and self.lev:
       # We used levshift to converge. Now let's restart to be sure.
@@ -302,7 +303,7 @@ def nextstep(self):
       sh.copy(self.writer.guess_fort,'fort.20')
       self.writer.write_crys_input(self.crysinpfn)
       sh.copy(self.crysinpfn,'INPUT')
-      self.runner.add_task("Pcrystal &> %s"%self.crysoutfn)
+      self.runner.add_task("%s &> %s"%(paths['Pcrystal'],self.crysoutfn))
       self.restarts+=1
 
     # Ready for bundler or else just submit the jobs as needed.
@@ -373,7 +374,7 @@ def export_qwalk(self):
       if status=='not_started':
         ready=False
         self.prunner.add_command("cp %s INPUT"%self.propinpfn)
-        self.prunner.add_task("Pproperties &> %s"%self.propoutfn)
+        self.prunner.add_task("%s &> %s"%(paths['Pproperties'],self.propoutfn))
 
         if self.bundle:
           self.scriptfile="%s.run"%self.name
@@ -527,7 +528,7 @@ def nextstep(self):
       self.scriptfile="%s.run"%self.name
       self.bundle_ready=self.runner.script(self.scriptfile,self.driverfn)
     else:
-      qsubfile=self.runner.submit()
+      qsubfile=self.runner.submit(jobname=self.name,ppath=[paths['pyscf']])
 
     self.completed=self.reader.completed
     # Update the file.
@@ -577,7 +578,7 @@ def status(self):
 #######################################################################
 class QWalkManager:
   def __init__(self,writer,reader,runner=None,trialfunc=None,
-      name='qw_run',path=None,bundle=False,qwalk='~/bin/qwalk'):
+      name='qw_run',path=None,bundle=False):
     ''' QWalkManager managers the writing of a QWalk input files, it's running, and keeping track of the results.
     Args:
       writer (qwalk writer): writer for input.
@@ -606,7 +607,6 @@ def __init__(self,writer,reader,runner=None,trialfunc=None,
     self.writer=writer
     self.reader=reader
     self.trialfunc=trialfunc
-    self.qwalk=qwalk
     if runner is not None: self.runner=runner
     else: self.runner=autorunner.RunnerPBS()
     self.bundle=bundle
@@ -683,7 +683,7 @@ def nextstep(self):
     status=resolve_status(self.runner,self.reader,self.outfile)
     print(self.logname,": %s status= %s"%(self.name,status))
     if status=="not_started" and self.writer.completed:
-      exestr="%s %s &> %s"%(self.qwalk,self.infile,self.stdout)
+      exestr="%s %s &> %s"%(paths['qwalk'],self.infile,self.stdout)
       self.runner.add_task(exestr)
       print(self.logname,": %s status= submitted"%(self.name))
     elif status=="ready_for_analysis":
@@ -694,7 +694,7 @@ def nextstep(self):
         self.completed=True
       else:
         print(self.logname,": %s status= %s, attempting rerun."%(self.name,status))
-        exestr="%s %s &> %s"%(self.qwalk,self.infile,self.stdout)
+        exestr="%s %s &> %s"%(paths['qwalk'],self.infile,self.stdout)
         self.runner.add_task(exestr)
     elif status=='done':
       self.completed=True

paths.yaml

@@ -1,11 +1,26 @@
-import yaml
+import os
 
-print("Setting up paths...")
-curpaths=yaml.load(open('paths.yaml','r'))
+print()
+print("Setting up paths.")
+print()
+print("You'll need to know the location of Crystal, Crystal's properties component, QWalk,")
+print("and the PySCF library if you want to use any of them in autogen.")
+print("Use absolute paths.")
+print()
 
-for key in curpaths:
-  path=input("Enter path for %s: "%key)
+curpaths={}
+keys=['Pcrystal','Pproperties','qwalk','pyscf']
+
+for key in sorted(keys):
+  path=input("--Enter path for %s (empty to disable): "%key)
+  if path=='': 
+    path=None
+  else:
+    assert os.path.exists(path),\
+        "Couldn't find '%s', you should check that it exists, or that it's spelled correctly."%path
   curpaths[key]=path
 
-yaml.dump(curpaths,open('paths.yaml','w'),default_flow_style=False)
-print("Done. paths.yaml should now be up-to-date.")
+with open('autopaths.py','w') as outf:
+  outf.write('paths={}'.format(curpaths))
+
+print("Done. autopaths.py should now be up-to-date.")