From e2da94fcd14dd6f45547b11e3b44e0ca52309e7f Mon Sep 17 00:00:00 2001
From: jsnelgro <johnny.snelgrove@gmail.com>
Date: Sun, 9 Aug 2015 14:04:38 -0400
Subject: [PATCH 1/2] annealing runs should be running in parallel now

---
 runAnnealBayes.m | 38 ++++++++++++++++++++++++++++----------
 1 file changed, 28 insertions(+), 10 deletions(-)

diff --git a/runAnnealBayes.m b/runAnnealBayes.m
index 83c950d92..74e747991 100644
--- a/runAnnealBayes.m
+++ b/runAnnealBayes.m
@@ -26,26 +26,44 @@
     end
 end
 
-for t = 1:T
+erdosAnnealRes = cell(I, J, T);
+wishAnnealRes = cell(J, T);
+
+parfor t = 1:T
     disp(['cur t:' num2str(t) '     out of    ' num2str(T)]);
     for j = 1:J
-        load(files{(t-1)*J+j});
+        da = load(files{(t-1)*J+j});
+        data = da.data;
+        dslice = erdosAnnealRes(:,:,t);
         for k=1:length(erdosPs)
             [covMat bestLP] = simAnnealErdos(@erdosPost,data,numOptRuns,erdosPs(k),.4);
+            dslice{j,k} = covMat;
+            erdosAnnealRes(:,:,t) = dslice;
+        end
+        if runWish
+            [wishCovMat bestLP] = simAnneal(@wishPost,data,numOptRuns,b,10*eye(N));
+            wishAnnealRes{j,t} = wishCovMat;
+        end
+    end
+end
+
+% add to bayesSigs
+disp('processing annealing results...');
+for t = 1:T
+    for j = 1:J
+        for k = 1:length(erdosPs)
+            covMat = erdosAnnealRes{k,j,t};
             bayesSigs{k,j}(:,:,t) = reshape(covMat, [ N N 1]);
             tBDists(k,j,t) = covMatDist(reshape(bayesSigs{k,j}(:,:,t), [N N]), ...
-                                        reshape(trueSigs{j}(:,:,t), [N N]));
+                reshape(trueSigs{j}(:,:,t), [N N]));
         end
         if runWish
-            [covMat bestLP] = simAnneal(@wishPost,data,numOptRuns,b,10*eye(N));
-            bayesSigs{length(erdosPs)+1,j}(:,:,t) = reshape(covMat, [N N 1]);
+            wishCovMat = wishAnnealRes{j,t};
+            bayesSigs{length(erdosPs)+1,j}(:,:,t) = reshape(wishCovMat, [N N 1]);
             
             tBDists(length(erdosPs)+1,j,t) = covMatDist(reshape(bayesSigs{length(erdosPs)+1,j}(:,:,t), [N N]), ...
-                                        reshape(trueSigs{j}(:,:,t), [N N]));
+                reshape(trueSigs{j}(:,:,t), [N N]));
         end
     end
 end
-
-
-end
-
+disp('finished processing annealing runs');

From 9bf91cad4ba318c110a395c6ff1fa72cda674e8c Mon Sep 17 00:00:00 2001
From: jsnelgro <johnny.snelgrove@gmail.com>
Date: Fri, 4 Sep 2015 18:28:32 -0400
Subject: [PATCH 2/2] add matlabpool to actually use workers

---
 README.md        | 2 +-
 runAnnealBayes.m | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 3511db7f2..a8573e0c6 100644
--- a/README.md
+++ b/README.md
@@ -42,4 +42,4 @@ from the command line:
 
 3. `sh install_<your os>.sh`
 
-4. `matlab2011 -nodesktop -nosplash -nojvm -r runFullSims` *(if you're on brie. Otherwise it's just `matlab -nodesktop -nosplash -r runFullSims`)*
+4. `matlab2011 -nodesktop -nosplash -r runFullSims` *(if you're on brie. Otherwise it's just `matlab -nodesktop -nosplash -r runFullSims`)*
diff --git a/runAnnealBayes.m b/runAnnealBayes.m
index 74e747991..9a0b11cf6 100644
--- a/runAnnealBayes.m
+++ b/runAnnealBayes.m
@@ -28,7 +28,7 @@
 
 erdosAnnealRes = cell(I, J, T);
 wishAnnealRes = cell(J, T);
-
+matlabpool(4)
 parfor t = 1:T
     disp(['cur t:' num2str(t) '     out of    ' num2str(T)]);
     for j = 1:J
@@ -45,7 +45,9 @@
             wishAnnealRes{j,t} = wishCovMat;
         end
     end
+    disp(['t:' num2str(t) ' finished.']);
 end
+matlabpool close
 
 % add to bayesSigs
 disp('processing annealing results...');