Cosmological parameter estimation with the MCMC Hammer, please use https://cosmo-gitlab.phys.ethz.ch/cosmo/CosmoHammer, this repository is outdated ! Docs at http://cosmo-docs.phys.ethz.ch/cosmoHammer/
License: GNU General Public License v3.0
My machine runs into a memory limit exceeded error when trying to run the sampler for a long number of iteration with lots of walkers. I looked at the code for the source of the error and it looks like Emcee needs to create the entire array with dimension (nwalker, niteration, ndim) at initiation and then concatenates that array to some other array which requires twice the amount of memory needed to store the entire chain. I am thinking to circumvent this issue by running the chain for smaller number of iterations, then storing the chain into hard disk, then resuming sampling from last iteration state, and doing this repetitively until the desired chain length is achieved. Is it possible to resume sampling from the last iteration state and automatically save the newly sampled states at the end of the already saved output files? If so, how can this be done?
Below is the error that I received (Python: 3.6.1, openmpi: 1.4).
Traceback (most recent call last):
File "/u/home/a/ajshajib/mybin/lenstronomy/lenstronomy/Sampling/sampler.py", line 67, in pso
for swarm in pso.sample(n_iterations):
File "/u/home/a/ajshajib/mybin/CosmoHammer/cosmoHammer/pso/ParticleSwarmOptimizer.py", line 78, in sample
self._get_fitness(self.swarm)
File "/u/home/a/ajshajib/mybin/CosmoHammer/cosmoHammer/pso/MpiParticleSwarmOptimizer.py", line 51, in _get_fitness
results = mapFunction(self.func, pos)
File "/u/home/a/ajshajib/mybin/CosmoHammer/cosmoHammer/util/MpiUtil.py", line 43, in map
self.mapFunction(function, splitList(sequence,size)[rank])))
File "mpi4py/MPI/Comm.pyx", line 1272, in mpi4py.MPI.Comm.allgather
File "mpi4py/MPI/msgpickle.pxi", line 770, in mpi4py.MPI.PyMPI_allgather
File "mpi4py/MPI/msgpickle.pxi", line 104, in mpi4py.MPI.Pickle.dump
File "mpi4py/MPI/msgpickle.pxi", line 91, in mpi4py.MPI.Pickle.cdumps
TypeError: can't pickle module objects
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