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Print cosmology before evaluating loglkl #4

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e8e356b
Introduced --print-cosmo flag
EBHolm Feb 15, 2023
cde4adf
Fixed multiplicity of cosmo writes
EBHolm Feb 15, 2023
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11 changes: 11 additions & 0 deletions montepython/io_mp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -284,11 +284,22 @@ def create_output_files(command_line, data):
data.out_name = os.path.join(
command_line.folder, outname_base)+str(suffix)+'.txt'
print('Creating %s\n' % data.out_name)
if command_line.print_cosmo:
data.cosmo_out_name = os.path.join(
command_line.folder, outname_base)+str(suffix)+'.cosmo'
data.cosmo_out = open(data.cosmo_out_name, 'w')
print('Creating %s\n' % data.cosmo_out_name)
else:
data.out_name = os.path.join(
command_line.folder, outname_base)+command_line.chain_number+'.txt'
data.out = open(data.out_name, 'w')
print('Creating %s\n' % data.out_name)
if command_line.print_cosmo:
data.cosmo_out_name = os.path.join(
command_line.folder, outname_base)+command_line.chain_number+'.cosmo'
data.cosmo_out = open(data.cosmo_out_name, 'w')

@ThomasTram ThomasTram Feb 15, 2023

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I don't think it is particularly nice to leave files open like this, but I acknowledge that this is how MontePython is coded. (This is why the last line of chain files are sometimes corrupted!)
In a perfect world, you always open files using a context manager (i.e. using with)

@EBHolm EBHolm Feb 15, 2023

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I agree! But I think, for readability, it's better to keep it like how the usual .txt files are written.

print('Creating %s\n' % data.cosmo_out_name)

@ThomasTram ThomasTram Feb 15, 2023

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This is kinda old school; why not do something like this:

python
print(f'Creating {data.cosmo_out_name}\n')

@EBHolm EBHolm Feb 15, 2023

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I just copied the print statement for the .txt files ;) but yes I agree that's nicer.


# in case of a restart, copying the whole thing in the new file
if command_line.restart is not None:
# Construct filename of old chain from input.
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3 changes: 3 additions & 0 deletions montepython/mcmc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -784,6 +784,9 @@ def chain(cosmo, data, command_line):
# multiplicity of the point and start the loop again
if get_new_position(
data, sigma_eig, U, k, Cholesky, Rotation) is True:
# Prints the position even if it is not accepted
if command_line.print_cosmo:
io_mp.print_vector([data.cosmo_out], 1, 0.0, data)

@ThomasTram ThomasTram Feb 15, 2023

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If you did not store a file handle before, what you can do is simply to open the file in append mode:

with open(data.cosmo_out_name, 'a') as fid:
    io_mp.print_vector([fid], 1, 0.0, data)

@EBHolm EBHolm Feb 15, 2023

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That's much nicer. I wonder why MontePython doesn't already do this? Maybe it's slow to re-open the each time?

newloglike = sampler.compute_lkl(cosmo, data)
else: # reject step
rej += 1
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8 changes: 8 additions & 0 deletions montepython/parser_mp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -566,6 +566,9 @@ def create_parser():
<**>--display-each-chi2<**> : bool
<++>Shows the effective chi2 from each likelihood and the total.<++>
Useful e.g. if you run at the bestfit point with -f 0 (flag)<++>
<**>--print-cosmo<**> : bool
<++>Prints CLASS inputs before each loglkl evaluation.<++>
Inputs are printed in a separate file from the chains. (flag)<++>
<**>--parallel-chains<**> : bool
<++>Option for when running parallel without MPI<++>.
Informs the code you are running parallel chains. This
Expand Down Expand Up @@ -809,6 +812,11 @@ def create_parser():
# display option
runparser.add_argument('--display-each-chi2', help=helpdict['display-each-chi2'],
dest='display_each_chi2', action='store_true')

# print cosmo inputs before evaluating loglkl
runparser.add_argument('--print-cosmo', help=helpdict['print-cosmo'],
dest='print_cosmo', action='store_true')

# -- parallel chains without MPI (OPTIONAL)
runparser.add_argument('--parallel-chains', help=helpdict['parallel-chains'],
action='store_true')
Expand Down