From 053bf2d0eefd42fe1247189fb8470f08b27885f8 Mon Sep 17 00:00:00 2001
From: Rayne Liu <rl746@cornell.edu>
Date: Thu, 13 Aug 2020 17:39:20 -0400
Subject: [PATCH] Finally found the bug with the pool but did not understand it
 - but PyCBC pool also worked with ptemcee

---
 code/RDGW150914_ptemcee.py           | 27 ++++++++++++---------------
 code/RDGW150914_ptemcee1.py          |  7 +++++--
 code/RDGW150914_ptemcee2.py          |  6 +++++-
 code/RDGW150914_ptemcee3.py          |  6 +++++-
 code/RDGW150914_ptemcee4.py          |  6 +++++-
 code/condor_submit_RdownPtemcee.sub  |  4 ++--
 code/condor_submit_RdownPtemcee1.sub |  4 ++--
 code/condor_submit_RdownPtemcee2.sub |  4 ++--
 code/condor_submit_RdownPtemcee3.sub |  4 ++--
 code/condor_submit_RdownPtemcee4.sub |  4 ++--
 10 files changed, 42 insertions(+), 30 deletions(-)

diff --git a/code/RDGW150914_ptemcee.py b/code/RDGW150914_ptemcee.py
index e27eae7..58cb04a 100755
--- a/code/RDGW150914_ptemcee.py
+++ b/code/RDGW150914_ptemcee.py
@@ -16,6 +16,8 @@ from matplotlib import rc
 plt.rcParams.update({'font.size': 16.5})
 
 import ptemcee
+from pycbc.pool import choose_pool
+#from multiprocessing import Pool
 import math
 import h5py
 import inspect
@@ -32,18 +34,19 @@ from scipy.optimize import minimize
 #tshift: time shift after the strain peak
 #vary_fund: whether you vary the fundamental frequency. Works in the model_dv function.
 
-rootpath="/work/rayne.liu" #"/Users/RayneLiu"
+rootpath="/Users/RayneLiu"# "/work/rayne.liu" 
 nmax=1
 tshift=19
 vary_fund = True
 
 #sampler parameters
 npoints=101 
-nwalkers = 32
+nwalkers = 42
 ntemps=12
 ndim = int(4*(nmax+1))
 burnin = 10 #How many points do you burn before doing the corner plot. You need to watch the convergence of the chain plot a bit.
             #This is trivial but often forgotten: this cannot be more than npoints! Usually 1/5~1/4 npoints is what I observe.
+
 numbins = 21 #corner plot parameter - how many bins you want
 datacolor = '#105670' #'#4fa3a7'
 pkcolor = '#f2c977' #'#ffb45f'
@@ -160,8 +163,8 @@ def log_likelihood(theta):
 # The evidence is just a normalization factor
 def log_probability(theta):
     lp = log_prior(theta)
-    print('lp:')
-    print(lp)
+    #print('lp:')
+    #print(lp)
     if not np.isfinite(lp):
         return -np.inf
     return lp + log_likelihood(theta)
@@ -170,6 +173,9 @@ def log_probability(theta):
 
 
 #Fit with ptemcee
+#Set the number of cores of your processors
+pool = choose_pool(4)
+pool.size = 4
 vary_param = float(vary_fund)
 pos = np.array([[random.uniform(-0.1,0.1), random.uniform(-0.1,0.1), 4.28313743e-01, random.uniform(2.5, 2.6) + (1-vary_param) * np.pi]])
 for i in range (1,nmax+1):
@@ -180,7 +186,8 @@ pos = pos.T.flatten()
 pos = list(pos)
 pos += 1e-5 * np.random.randn(ntemps, nwalkers, ndim)
 #print(pos)
-sampler = ptemcee.Sampler(nwalkers, ndim, log_likelihood, log_prior, ntemps=ntemps)
+
+sampler = ptemcee.Sampler(nwalkers, ndim, log_likelihood, log_prior, ntemps=ntemps, pool=pool)
 sampler.run_mcmc(pos,npoints)
 
 
@@ -291,13 +298,3 @@ plt.xlabel("t")
 plt.ylabel("h")
 
 figband.savefig(rootpath+'/git/rdstackingproject/plotsmc/vary'+str(vary_fund)+'nmax='+str(nmax)+'_tshift='+str(tshift)+'_'+str(npoints)+'pt_band.pdf', format = 'pdf')
-"""
-
-
-
-
-
-
-
-
-"""
diff --git a/code/RDGW150914_ptemcee1.py b/code/RDGW150914_ptemcee1.py
index bde6934..e491c3d 100755
--- a/code/RDGW150914_ptemcee1.py
+++ b/code/RDGW150914_ptemcee1.py
@@ -16,6 +16,7 @@ from matplotlib import rc
 plt.rcParams.update({'font.size': 16.5})
 
 import ptemcee
+from pycbc.pool import choose_pool
 import math
 import h5py
 import inspect
@@ -170,6 +171,9 @@ def log_probability(theta):
 
 
 #Fit with ptemcee
+#Set the number of cores of your processors
+pool = choose_pool(4)
+pool.size = 4
 vary_param = float(vary_fund)
 pos = np.array([[random.uniform(-0.1,0.1), random.uniform(-0.1,0.1), 4.28313743e-01, random.uniform(2.5, 2.6) + (1-vary_param) * np.pi]])
 for i in range (1,nmax+1):
@@ -180,12 +184,11 @@ pos = pos.T.flatten()
 pos = list(pos)
 pos += 1e-5 * np.random.randn(ntemps, nwalkers, ndim)
 #print(pos)
-sampler = ptemcee.Sampler(nwalkers, ndim, log_likelihood, log_prior, ntemps=ntemps)
+sampler = ptemcee.Sampler(nwalkers, ndim, log_likelihood, log_prior, ntemps=ntemps, pool=pool)
 sampler.run_mcmc(pos,npoints)
 
 
 
-
 #Define labels and start plotting
 paramlabels_a = [r'$\alpha_'+str(i)+'$' for i in range (nmax+1)]
 paramlabels_b = [r'$\beta_'+str(i)+'$' for i in range (nmax+1)]
diff --git a/code/RDGW150914_ptemcee2.py b/code/RDGW150914_ptemcee2.py
index 3d29a78..19f8eea 100755
--- a/code/RDGW150914_ptemcee2.py
+++ b/code/RDGW150914_ptemcee2.py
@@ -16,6 +16,7 @@ from matplotlib import rc
 plt.rcParams.update({'font.size': 16.5})
 
 import ptemcee
+from pycbc.pool import choose_pool
 import math
 import h5py
 import inspect
@@ -170,6 +171,9 @@ def log_probability(theta):
 
 
 #Fit with ptemcee
+#Set the number of cores of your processors
+pool = choose_pool(4)
+pool.size = 4
 vary_param = float(vary_fund)
 pos = np.array([[random.uniform(-0.1,0.1), random.uniform(-0.1,0.1), 4.28313743e-01, random.uniform(2.5, 2.6) + (1-vary_param) * np.pi]])
 for i in range (1,nmax+1):
@@ -180,7 +184,7 @@ pos = pos.T.flatten()
 pos = list(pos)
 pos += 1e-5 * np.random.randn(ntemps, nwalkers, ndim)
 #print(pos)
-sampler = ptemcee.Sampler(nwalkers, ndim, log_likelihood, log_prior, ntemps=ntemps)
+sampler = ptemcee.Sampler(nwalkers, ndim, log_likelihood, log_prior, ntemps=ntemps, pool=pool)
 sampler.run_mcmc(pos,npoints)
 
 
diff --git a/code/RDGW150914_ptemcee3.py b/code/RDGW150914_ptemcee3.py
index 6e2f096..c49e4c2 100755
--- a/code/RDGW150914_ptemcee3.py
+++ b/code/RDGW150914_ptemcee3.py
@@ -16,6 +16,7 @@ from matplotlib import rc
 plt.rcParams.update({'font.size': 16.5})
 
 import ptemcee
+from pycbc.pool import choose_pool
 import math
 import h5py
 import inspect
@@ -170,6 +171,9 @@ def log_probability(theta):
 
 
 #Fit with ptemcee
+#Set the number of cores of your processors
+pool = choose_pool(4)
+pool.size = 4
 vary_param = float(vary_fund)
 pos = np.array([[random.uniform(-0.1,0.1), random.uniform(-0.1,0.1), 4.28313743e-01, random.uniform(2.5, 2.6) + (1-vary_param) * np.pi]])
 for i in range (1,nmax+1):
@@ -180,7 +184,7 @@ pos = pos.T.flatten()
 pos = list(pos)
 pos += 1e-5 * np.random.randn(ntemps, nwalkers, ndim)
 #print(pos)
-sampler = ptemcee.Sampler(nwalkers, ndim, log_likelihood, log_prior, ntemps=ntemps)
+sampler = ptemcee.Sampler(nwalkers, ndim, log_likelihood, log_prior, ntemps=ntemps, pool=pool)
 sampler.run_mcmc(pos,npoints)
 
 
diff --git a/code/RDGW150914_ptemcee4.py b/code/RDGW150914_ptemcee4.py
index 759575a..af162ee 100755
--- a/code/RDGW150914_ptemcee4.py
+++ b/code/RDGW150914_ptemcee4.py
@@ -16,6 +16,7 @@ from matplotlib import rc
 plt.rcParams.update({'font.size': 16.5})
 
 import ptemcee
+from pycbc.pool import choose_pool
 import math
 import h5py
 import inspect
@@ -170,6 +171,9 @@ def log_probability(theta):
 
 
 #Fit with ptemcee
+#Set the number of cores of your processors
+pool = choose_pool(4)
+pool.size = 4
 vary_param = float(vary_fund)
 pos = np.array([[random.uniform(-0.1,0.1), random.uniform(-0.1,0.1), 4.28313743e-01, random.uniform(2.5, 2.6) + (1-vary_param) * np.pi]])
 for i in range (1,nmax+1):
@@ -180,7 +184,7 @@ pos = pos.T.flatten()
 pos = list(pos)
 pos += 1e-5 * np.random.randn(ntemps, nwalkers, ndim)
 #print(pos)
-sampler = ptemcee.Sampler(nwalkers, ndim, log_likelihood, log_prior, ntemps=ntemps)
+sampler = ptemcee.Sampler(nwalkers, ndim, log_likelihood, log_prior, ntemps=ntemps, pool=pool)
 sampler.run_mcmc(pos,npoints)
 
 
diff --git a/code/condor_submit_RdownPtemcee.sub b/code/condor_submit_RdownPtemcee.sub
index ced2df3..478b6f8 100755
--- a/code/condor_submit_RdownPtemcee.sub
+++ b/code/condor_submit_RdownPtemcee.sub
@@ -12,8 +12,8 @@ initialdir = .
 notify_user = rl746@cornell.edu
 notification = Complete
 arguments  = "-processid $(Process)" 
-request_memory = 16GB
-request_cpus = 1
+request_memory = 8GB
+request_cpus = 4
 on_exit_remove = (ExitBySignal == False) || ((ExitBySignal == True) && (ExitSignal != 11))
 accounting_group = aei.dev.test_dynesty
 queue 1
diff --git a/code/condor_submit_RdownPtemcee1.sub b/code/condor_submit_RdownPtemcee1.sub
index 34bcd92..0358c84 100755
--- a/code/condor_submit_RdownPtemcee1.sub
+++ b/code/condor_submit_RdownPtemcee1.sub
@@ -12,8 +12,8 @@ initialdir = .
 notify_user = rl746@cornell.edu
 notification = Complete
 arguments  = "-processid $(Process)" 
-request_memory = 16GB
-request_cpus = 1
+request_memory = 8GB
+request_cpus = 4
 on_exit_remove = (ExitBySignal == False) || ((ExitBySignal == True) && (ExitSignal != 11))
 accounting_group = aei.dev.test_dynesty
 queue 1
diff --git a/code/condor_submit_RdownPtemcee2.sub b/code/condor_submit_RdownPtemcee2.sub
index 218ef23..f780e1f 100755
--- a/code/condor_submit_RdownPtemcee2.sub
+++ b/code/condor_submit_RdownPtemcee2.sub
@@ -12,8 +12,8 @@ initialdir = .
 notify_user = rl746@cornell.edu
 notification = Complete
 arguments  = "-processid $(Process)" 
-request_memory = 16GB
-request_cpus = 1
+request_memory = 8GB
+request_cpus = 4
 on_exit_remove = (ExitBySignal == False) || ((ExitBySignal == True) && (ExitSignal != 11))
 accounting_group = aei.dev.test_dynesty
 queue 1
diff --git a/code/condor_submit_RdownPtemcee3.sub b/code/condor_submit_RdownPtemcee3.sub
index de8eda0..f9e3d38 100755
--- a/code/condor_submit_RdownPtemcee3.sub
+++ b/code/condor_submit_RdownPtemcee3.sub
@@ -12,8 +12,8 @@ initialdir = .
 notify_user = rl746@cornell.edu
 notification = Complete
 arguments  = "-processid $(Process)" 
-request_memory = 16GB
-request_cpus = 1
+request_memory = 8GB
+request_cpus = 4
 on_exit_remove = (ExitBySignal == False) || ((ExitBySignal == True) && (ExitSignal != 11))
 accounting_group = aei.dev.test_dynesty
 queue 1
diff --git a/code/condor_submit_RdownPtemcee4.sub b/code/condor_submit_RdownPtemcee4.sub
index b337b63..2780f90 100755
--- a/code/condor_submit_RdownPtemcee4.sub
+++ b/code/condor_submit_RdownPtemcee4.sub
@@ -12,8 +12,8 @@ initialdir = .
 notify_user = rl746@cornell.edu
 notification = Complete
 arguments  = "-processid $(Process)" 
-request_memory = 16GB
-request_cpus = 1
+request_memory = 8GB
+request_cpus = 4
 on_exit_remove = (ExitBySignal == False) || ((ExitBySignal == True) && (ExitSignal != 11))
 accounting_group = aei.dev.test_dynesty
 queue 1
-- 
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