The p53-tutorial from astatide

python does not like max_run_wallclock to have leading zeros

Running out of the box on Frank:

php8@login0a:~/run/p53-tutorial-patrick$ ./init.sh 
LOADING MODULES FOR FRANK.
simulation p53-tutorial-patrick root is /ihome/pgivi/php8/run/p53-tutorial-patrick
mv: cannot stat `traj_segs': No such file or directory
mv: cannot stat `seg_logs': No such file or directory
mv: cannot stat `istates': No such file or directory
Updating system with the options from the configuration file
Creating HDF5 file '/ihome/pgivi/php8/run/p53-tutorial-patrick/west.h5'
0 target state(s) present
Calculating progress coordinate values for basis states.
1 basis state(s) present
Preparing initial states

        Total bins:            294
        Initial replicas:      8 in 1 bins, total weight = 1
        Total target replicas: 2352

Simulation prepared.
1 of 294 (0.340136%) active bins are populated
per-bin minimum non-zero probability:       1
per-bin maximum probability:                1
per-bin probability dynamic range (kT):     0
per-segment minimum non-zero probability:   0.125
per-segment maximum non-zero probability:   0.125
per-segment probability dynamic range (kT): 0
norm = 1, error in norm = 0 (0*epsilon)

php8@login0a:~/run/p53-tutorial-patrick$ ./run.sh 
LOADING MODULES FOR FRANK.
simulation p53-tutorial-patrick root is /ihome/pgivi/php8/run/p53-tutorial-patrick

php8@login0a:~/run/p53-tutorial-patrick$ cat west.log 
Updating system with the options from the configuration file
exception caught; shutting down
-- ERROR    [w_run] -- Traceback (most recent call last):
  File "/opt/sam/rhel6/westpa/1.0/gcc/4.8.2/westpa-yaml/lib/cmds/w_run.py", line 65, in <module>
    sim_manager.run()
  File "/opt/sam/rhel6/westpa/1.0/gcc/4.8.2/westpa-yaml/src/west/sim_manager.py", line 617, in run
    run_killtime = run_starttime + max_walltime
TypeError: unsupported operand type(s) for +: 'float' and 'str'

Removing the leading zeroes in west.cfg fixes this issue

Dimension mismatch with basis_states

To pick up from our discussion via email.

Here are my Env variables on Frank module load westpa/anaconda2-2.4.1:

php8@login0b:~/run/p53-tutorial$ echo $WEST_PYTHON
/opt/sam/anaconda/2.4.1/bin/python2.7
php8@login0b:~/run/p53-tutorial$ echo $WEST_ROOT  
/opt/sam/westpa-mpi

If I run the p53 tutorial with changes to use my environment I get the following error:

php8@login0b:~/run/p53-tutorial$ ./init.sh 
simulation p53-tutorial root is /ihome/pgivi/php8/run/p53-tutorial
Creating HDF5 file '/ihome/pgivi/php8/run/p53-tutorial/west.h5'
0 target state(s) present
Calculating progress coordinate values for basis states.
Traceback (most recent call last):
  File "/opt/sam/westpa-mpi/lib/cmds/w_init.py", line 125, in <module>
    suppress_we=args.shotgun)
  File "/opt/sam/westpa-mpi/src/west/sim_manager.py", line 250, in initialize_simulation
    self.data_manager.create_ibstate_group(basis_states)
  File "/opt/sam/westpa-mpi/src/west/data_manager.py", line 512, in create_ibstate_group
    state_pcoords[i] = state.pcoord
ValueError: could not broadcast input array from shape (2) into shape (1)

@ajoshpratt If I take your suggest to remove lines 52-54 in west.cfg I get the following error:

php8@login0b:~/run/p53-tutorial$ ./init.sh 
simulation p53-tutorial root is /ihome/pgivi/php8/run/p53-tutorial
Creating HDF5 file '/ihome/pgivi/php8/run/p53-tutorial/west.h5'
0 target state(s) present
Calculating progress coordinate values for basis states.
1 basis state(s) present
Preparing initial states
Traceback (most recent call last):
  File "/opt/sam/westpa-mpi/lib/cmds/w_init.py", line 125, in <module>
    suppress_we=args.shotgun)
  File "/opt/sam/westpa-mpi/src/west/sim_manager.py", line 291, in initialize_simulation
    self.we_driver.populate_initial(initial_states, weights, system)
  File "/opt/sam/westpa-mpi/src/west/we_driver.py", line 616, in populate_initial
    self.construct_next()
  File "/opt/sam/westpa-mpi/src/west/we_driver.py", line 711, in construct_next
    self._run_we()
  File "/opt/sam/westpa-mpi/src/west/we_driver.py", line 554, in _run_we
    self._check_pre()
  File "/opt/sam/westpa-mpi/src/west/we_driver.py", line 535, in _check_pre
    if self.bin_target_counts[ibin] == 0 and len(_bin) > 0:
IndexError: index 1 is out of bounds for axis 0 with size 1

I started inserting print statements trying to figure out what is going on. I am not too familiar with these parts of westpa. But I will continue to drill down tomorrow.

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python does not like max_run_wallclock to have leading zeros

Dimension mismatch with basis_states

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