updated benchmark results

14 files changed, 131 insertions, 106 deletions

diff --git a/benchmarks/Dockerfile b/benchmarks/Dockerfile
index cead00d..92bbb2c 100644
--- a/benchmarks/Dockerfile
+++ b/benchmarks/Dockerfile
@@ -55,13 +55,13 @@ RUN curl -LO https://raw.githubusercontent.com/Ripser/ripser/dev/benchmarks/sphe
 
 COPY o3_1024.txt .
 COPY o3_4096.txt .
-COPY clifford_torus_50000.points.csv .
+COPY clifford_torus_50000.points.txt .
 
 RUN (echo "OFF\n2000 0 0" && cat dragon_vrip.ply.txt_2000_.txt) >dragon_vrip.ply.txt_2000_.off \
 && (echo "OFF\n50 0 0" && cat random_point_cloud_50_16_.txt) >random_point_cloud_50_16_.off \
 && (echo "OFF\n1024 0 0" && cat o3_1024.txt) >o3_1024.off \
 && (echo "OFF\n4096 0 0" && cat o3_4096.txt) >o3_4096.off \
-&& (echo "nOFF\n4 50000 1 0" && cat clifford_torus_50000.points.csv) >clifford_torus_50000.points.off
+&& (echo "nOFF\n4 50000 0 0" && cat clifford_torus_50000.points.txt) >clifford_torus_50000.points.off
 
 
 FROM benchmark-setup as benchmark-ripser
@@ -77,7 +77,7 @@ WORKDIR /benchmark
 RUN time -v -o sphere_3_192.ripser.txt    ripser sphere_3_192.distance_matrix --dim 2
 RUN time -v -o o3_1024.ripser.txt    ripser o3_1024.txt --format point-cloud --dim 3 --threshold 1.8 --ratio 2
 RUN time -v -o o3_4096.ripser.txt    ripser o3_4096.txt --format point-cloud --dim 3 --threshold 1.4 --ratio 2
-RUN time -v -o clifford_torus_50000.ripser.txt    ripser clifford_torus_50000.points.csv --format point-cloud --dim 2 --threshold .11 --ratio 2
+RUN time -v -o clifford_torus_50000.ripser.txt    ripser clifford_torus_50000.points.txt --format point-cloud --dim 2 --threshold .15 --ratio 2
 
 RUN time -v -o random.ripser.txt    ripser random_point_cloud_50_16_.txt --format point-cloud --dim 7
 RUN time -v -o fractal-r.ripser.txt    ripser fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt --dim 2
@@ -104,11 +104,11 @@ FROM benchmark-setup as benchmark-gudhi
 # RUN time -v -o sphere_3_192.gudhi.txt     rips_distance_matrix_persistence -d3 -p2 sphere_3_192.distance_matrix
 
 WORKDIR /benchmark
-RUN time -v -o sphere_3_192.gudhi.txt     gudhi-rips-distance-matrix-persistence -d3 -p2 sphere_3_192.distance_matrix
-# RUN time -v -o fractal-r.gudhi.txt     gudhi-rips-distance-matrix-persistence -d3 -p2 fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt
-RUN time -v -o o3_1024.gudhi.txt     gudhi-rips-persistence -d4 -p2 -r 1.8 o3_1024.off
-RUN time -v -o o3_4096.gudhi.txt     gudhi-rips-persistence -d4 -p2 -r 1.4 o3_4096.off
-RUN time -v -o clifford_torus_50000.gudhi.txt     gudhi-rips-persistence -d3 -p2 -r 0.11 clifford_torus_50000.off
+RUN time -v -o sphere_3_192.gudhi.txt     gudhi-rips-distance-matrix-persistence -d3 -p2 sphere_3_192.distance_matrix >sphere_3_192.gudhi.out.txt
+# RUN time -v -o fractal-r.gudhi.txt     gudhi-rips-distance-matrix-persistence -d3 -p2 fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt >fractal-r.gudhi.out.txt
+RUN time -v -o o3_1024.gudhi.txt     gudhi-rips-persistence -d4 -p2 -r 1.8 o3_1024.off >o3_1024.gudhi.out.txt
+RUN time -v -o o3_4096.gudhi.txt     gudhi-rips-persistence -d4 -p2 -r 1.4 o3_4096.off >o3_4096.gudhi.out.txt
+RUN time -v -o clifford_torus_50000.gudhi.txt     gudhi-rips-persistence -d3 -p2 -r 0.15 clifford_torus_50000.points.off >clifford_torus_50000.gudhi.out.txt
 
 
 FROM benchmark-setup as benchmark-dipha
@@ -127,13 +127,24 @@ ENV PATH="${PATH}:/dipha/dipha/build"
 WORKDIR /benchmark
 RUN time -v -o sphere_3_192.dipha.txt     dipha --dual --benchmark --upper_dim 3 sphere_3_192.complex sphere_3_192.dipha.diagram
 
+COPY o3_1024_1.8.dipha .
+RUN time -v -o o3_1024.dipha.txt     dipha --dual --benchmark --upper_dim 4 o3_1024_1.8.dipha o3_1024_1.8.dipha.diagram
 
+# COPY o3_4096_1.4.dipha .
+# RUN time -v -o o3_4096.dipha.txt     dipha --dual --benchmark --upper_dim 4 o3_4096_1.4.dipha o3_4096_1.4.dipha.diagram
 
-FROM benchmark-dipha as benchmark-dipha-multicore
+# COPY dragon_2000.dipha .
+# RUN time -v -o dragon-2.dipha.txt     dipha --dual --benchmark --upper_dim 2 dragon_2000.dipha dragon_2000.dipha.diagram
+
+
+
+# FROM benchmark-dipha as benchmark-dipha-multicore
 
 RUN time -v -o sphere_3_192.dipha-multicore.txt     mpiexec --allow-run-as-root --mca btl_vader_single_copy_mechanism none \
 dipha --dual --benchmark --upper_dim 3 sphere_3_192.complex sphere_3_192.dipha-multicore.diagram
 
+RUN time -v -o o3_1024.dipha-multicore.txt     mpiexec --allow-run-as-root --mca btl_vader_single_copy_mechanism none \
+dipha --dual --benchmark --upper_dim 4 o3_1024_1.8.dipha o3_1024_1.8.dipha-multicore.diagram
 
 
 ### FROM benchmark-setup as benchmark-eirene037
@@ -193,7 +204,13 @@ RUN time -v -o sphere_3_192.eirene.txt \
 	julia --eval 'maxdim = 2; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = readdlm("sphere_3_192.distance_matrix"); result = eirene(d, record="none", maxdim=maxdim))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end' >sphere_3_192.eirene.out.txt
 
 RUN time -v -o o3_1024.eirene.txt \
-	julia --eval 'maxdim = 2; maxrad = 1.8; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = transpose(readdlm("o3_1024.txt")); result = eirene(d, model="pc", record="none", maxdim=maxdim, maxrad=maxrad))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end' > o3_1024.eirene.out.txt
+	julia --eval 'maxdim = 3; maxrad = 1.8; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = transpose(readdlm("o3_1024.txt")); result = eirene(d, model="pc", record="none", maxdim=maxdim, maxrad=maxrad))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end' > o3_1024.eirene.out.txt
+
+RUN time -v -o o3_4096.eirene.txt \
+	julia --eval 'maxdim = 3; maxrad = 1.4; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = transpose(readdlm("o3_4096.txt")); result = eirene(d, model="pc", record="none", maxdim=maxdim, maxrad=maxrad))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end' > o3_4096.eirene.out.txt
+
+# RUN time -v -o clifford_torus_50000.points.eirene.txt \
+#	julia --eval 'maxdim = 2; maxrad = .15; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = transpose(readdlm("clifford_torus_50000.points.txt")); result = eirene(d, model="pc", record="none", maxdim=maxdim, maxrad=maxrad))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end' > clifford_torus_50000.eirene.out.txt
 
 RUN time -v -o dragon-2.eirene.txt \
 	julia --eval 'maxdim = 1; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = transpose(readdlm("dragon_vrip.ply.txt_2000_.txt")); result = eirene(d, model="pc", record="none", maxdim=maxdim))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end' >dragon-2.eirene.out.txt
@@ -243,9 +260,9 @@ FROM benchmark-setup as benchmark-output
 COPY --from=benchmark-ripser /benchmark /benchmark
 COPY --from=benchmark-gudhi /benchmark /benchmark
 COPY --from=benchmark-dipha /benchmark /benchmark
-COPY --from=benchmark-dipha-multicore /benchmark /benchmark
 COPY --from=benchmark-eirene /benchmark /benchmark
 # COPY --from=benchmark-eirene037 /benchmark /benchmark
 COPY --from=benchmark-dionysus2 /benchmark /benchmark
 
 RUN ls -l /benchmark
+
diff --git a/benchmarks/output/clifford_torus_50000.gudhi.txt b/benchmarks/output/clifford_torus_50000.gudhi.txt
index 4fc4e70..b64f9d0 100644
--- a/benchmarks/output/clifford_torus_50000.gudhi.txt
+++ b/benchmarks/output/clifford_torus_50000.gudhi.txt
@@ -1,21 +1,21 @@
-	Command being timed: "gudhi-rips-persistence -d3 -p2 -r .11 clifford_torus_50000.off"
-	User time (seconds): 0.00
-	System time (seconds): 0.00
-	Percent of CPU this job got: 0%
-	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.00
+	Command being timed: "gudhi-rips-persistence -d3 -p2 -r 0.15 clifford_torus_50000.points.off"
+	User time (seconds): 1082.97
+	System time (seconds): 35.21
+	Percent of CPU this job got: 195%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 9:31.03
 	Average shared text size (kbytes): 0
 	Average unshared data size (kbytes): 0
 	Average stack size (kbytes): 0
 	Average total size (kbytes): 0
-	Maximum resident set size (kbytes): 4628
+	Maximum resident set size (kbytes): 23804672
 	Average resident set size (kbytes): 0
-	Major (requiring I/O) page faults: 0
-	Minor (reclaiming a frame) page faults: 182
-	Voluntary context switches: 1
-	Involuntary context switches: 3
+	Major (requiring I/O) page faults: 11
+	Minor (reclaiming a frame) page faults: 5963234
+	Voluntary context switches: 143
+	Involuntary context switches: 20139
 	Swaps: 0
-	File system inputs: 0
-	File system outputs: 0
+	File system inputs: 1952
+	File system outputs: 2480
 	Socket messages sent: 0
 	Socket messages received: 0
 	Signals delivered: 0
diff --git a/benchmarks/output/clifford_torus_50000.ripser.txt b/benchmarks/output/clifford_torus_50000.ripser.txt
index 2ba3b3e..d803661 100644
--- a/benchmarks/output/clifford_torus_50000.ripser.txt
+++ b/benchmarks/output/clifford_torus_50000.ripser.txt
@@ -1,18 +1,18 @@
-	Command being timed: "ripser clifford_torus_50000.points.csv --format point-cloud --dim 2 --threshold .11 --ratio 2"
-	User time (seconds): 73.43
-	System time (seconds): 8.52
+	Command being timed: "ripser clifford_torus_50000.points.txt --format point-cloud --dim 2 --threshold .15 --ratio 2"
+	User time (seconds): 199.60
+	System time (seconds): 6.94
 	Percent of CPU this job got: 99%
-	Elapsed (wall clock) time (h:mm:ss or m:ss): 1:22.04
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 3:26.57
 	Average shared text size (kbytes): 0
 	Average unshared data size (kbytes): 0
 	Average stack size (kbytes): 0
 	Average total size (kbytes): 0
-	Maximum resident set size (kbytes): 8395660
+	Maximum resident set size (kbytes): 8395736
 	Average resident set size (kbytes): 0
 	Major (requiring I/O) page faults: 0
-	Minor (reclaiming a frame) page faults: 3697156
-	Voluntary context switches: 11
-	Involuntary context switches: 1647
+	Minor (reclaiming a frame) page faults: 4756609
+	Voluntary context switches: 5
+	Involuntary context switches: 1490
 	Swaps: 0
 	File system inputs: 0
 	File system outputs: 0
diff --git a/benchmarks/output/dragon-2.eirene.out.txt b/benchmarks/output/dragon-2.eirene.out.txt
index 4acc403..4bf0e4c 100644
--- a/benchmarks/output/dragon-2.eirene.out.txt
+++ b/benchmarks/output/dragon-2.eirene.out.txt
@@ -1,4 +1,4 @@
-95.041641248
+93.107345891
 dim 0: 2000×2 Array{Float64,2}:
  0.0    0.00324636 
  0.0    0.00309372 
diff --git a/benchmarks/output/dragon-2.eirene.txt b/benchmarks/output/dragon-2.eirene.txt
index 63938cb..9d5215b 100644
--- a/benchmarks/output/dragon-2.eirene.txt
+++ b/benchmarks/output/dragon-2.eirene.txt
@@ -1,21 +1,21 @@
 	Command being timed: "julia --eval maxdim = 1; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = transpose(readdlm("dragon_vrip.ply.txt_2000_.txt")); result = eirene(d, model="pc", record="none", maxdim=maxdim))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end"
-	User time (seconds): 123.00
-	System time (seconds): 3.60
+	User time (seconds): 120.08
+	System time (seconds): 3.74
 	Percent of CPU this job got: 100%
-	Elapsed (wall clock) time (h:mm:ss or m:ss): 2:06.26
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 2:03.45
 	Average shared text size (kbytes): 0
 	Average unshared data size (kbytes): 0
 	Average stack size (kbytes): 0
 	Average total size (kbytes): 0
-	Maximum resident set size (kbytes): 3361608
+	Maximum resident set size (kbytes): 3323332
 	Average resident set size (kbytes): 0
 	Major (requiring I/O) page faults: 4
-	Minor (reclaiming a frame) page faults: 3149520
-	Voluntary context switches: 39
-	Involuntary context switches: 408681
+	Minor (reclaiming a frame) page faults: 3296046
+	Voluntary context switches: 40
+	Involuntary context switches: 420401
 	Swaps: 0
 	File system inputs: 0
-	File system outputs: 4456
+	File system outputs: 4464
 	Socket messages sent: 0
 	Socket messages received: 0
 	Signals delivered: 0
diff --git a/benchmarks/output/fractal-r.eirene.out.txt b/benchmarks/output/fractal-r.eirene.out.txt
index 15d46b7..6752a19 100644
--- a/benchmarks/output/fractal-r.eirene.out.txt
+++ b/benchmarks/output/fractal-r.eirene.out.txt
@@ -1,4 +1,4 @@
-33.066562717
+32.240505053
 dim 0: 512×2 Array{Float64,2}:
  0.0    0.00042909
  0.0    0.0062596 
diff --git a/benchmarks/output/fractal-r.eirene.txt b/benchmarks/output/fractal-r.eirene.txt
index aef6677..cf36e8a 100644
--- a/benchmarks/output/fractal-r.eirene.txt
+++ b/benchmarks/output/fractal-r.eirene.txt
@@ -1,18 +1,18 @@
 	Command being timed: "julia --eval maxdim = 2; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = (m->(m+transpose(m))/2)(readdlm("fractal_9_5_2_random_edge_list.txt_0.19795_distmat.txt")); result = eirene(d, record="none", maxdim=maxdim))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end"
-	User time (seconds): 60.84
-	System time (seconds): 4.54
+	User time (seconds): 59.19
+	System time (seconds): 4.32
 	Percent of CPU this job got: 100%
-	Elapsed (wall clock) time (h:mm:ss or m:ss): 1:05.01
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 1:03.17
 	Average shared text size (kbytes): 0
 	Average unshared data size (kbytes): 0
 	Average stack size (kbytes): 0
 	Average total size (kbytes): 0
-	Maximum resident set size (kbytes): 5893804
+	Maximum resident set size (kbytes): 5896564
 	Average resident set size (kbytes): 0
 	Major (requiring I/O) page faults: 4
-	Minor (reclaiming a frame) page faults: 4231703
-	Voluntary context switches: 37
-	Involuntary context switches: 374724
+	Minor (reclaiming a frame) page faults: 4232730
+	Voluntary context switches: 39
+	Involuntary context switches: 306873
 	Swaps: 0
 	File system inputs: 0
 	File system outputs: 4336
diff --git a/benchmarks/output/o3_1024.eirene.out.txt b/benchmarks/output/o3_1024.eirene.out.txt
index 53d7b6d..0f646e4 100644
--- a/benchmarks/output/o3_1024.eirene.out.txt
+++ b/benchmarks/output/o3_1024.eirene.out.txt
@@ -1,4 +1,4 @@
-4.214078357
+7.418260614
 dim 0: 1024×2 Array{Float64,2}:
  0.0    0.597896 
  0.0    0.453623 
@@ -1618,7 +1618,6 @@ dim 2: 180×2 Array{Float64,2}:
  1.07051     1.10242 
  1.08178     1.08624 
  1.08745     1.11984 
- 1.09135     1.10587 
  1.11167     1.12898 
  1.11235     1.11326 
  1.13168     1.18629 
@@ -1631,13 +1630,11 @@ dim 2: 180×2 Array{Float64,2}:
  1.17817     1.18557 
  1.19721     1.24476 
  1.20064     1.24304 
- 1.20586     1.26559 
  1.20949     1.25367 
  1.21806     1.25246 
  1.2211      1.27057 
  1.22201     1.37283 
  1.22941     1.25137 
- 1.23464     1.2896  
  1.24477     1.28237 
  1.2468      1.24964 
  1.25496     1.31275 
@@ -1654,6 +1651,7 @@ dim 2: 180×2 Array{Float64,2}:
  1.29824     1.31844 
  1.306       1.31932 
  1.30903     1.31706 
+ 1.32116     1.35483 
  1.3253      1.34787 
  1.33955     1.35193 
  1.34057     1.38633 
@@ -1662,9 +1660,7 @@ dim 2: 180×2 Array{Float64,2}:
  1.34708     1.4347  
  1.35805     1.42945 
  1.36604     1.369   
- 1.36899     1.40239 
  1.37211     1.3941  
- 1.39525     1.56712 
  1.3996      1.51095 
  1.40043     1.43867 
  1.40056     1.40528 
@@ -1676,7 +1672,6 @@ dim 2: 180×2 Array{Float64,2}:
  1.44387     1.52606 
  1.45284     1.52627 
  1.45762     1.46176 
- 1.45849     1.53413 
  1.47179     1.55038 
  1.47397     1.52691 
  1.47405     1.48924 
@@ -1687,6 +1682,7 @@ dim 2: 180×2 Array{Float64,2}:
  1.56244     1.56745 
  1.61164     1.67463 
  1.61837     1.642   
+ 1.62103     1.74192 
  1.71663     1.72647 
  0.890155    0.896855
  0.953318    0.976321
@@ -1694,6 +1690,7 @@ dim 2: 180×2 Array{Float64,2}:
  1.07477     1.23625 
  1.07596     1.19538 
  1.07768     1.12849 
+ 1.09135     1.10587 
  1.09437     1.2226  
  1.10787     1.14724 
  1.14021     1.1637  
@@ -1706,11 +1703,12 @@ dim 2: 180×2 Array{Float64,2}:
  1.18087     1.21417 
  1.20487     1.45678 
  1.2051      1.41638 
+ 1.20586     1.26559 
  1.21066     1.27361 
  1.21467     1.40697 
  1.21773     1.40585 
  1.22489     1.28015 
- 1.22871     1.35926 
+ 1.23464     1.2896  
  1.23697     1.32803 
  1.23698     1.26564 
  1.23857     1.34364 
@@ -1731,32 +1729,35 @@ dim 2: 180×2 Array{Float64,2}:
  1.30245     1.48456 
  1.30931     1.40916 
  1.31497     1.46105 
- 1.32116     1.35483 
  1.32421     1.43489 
  1.32784     1.38146 
  1.32856     1.57685 
  1.34205     1.40855 
  1.35085     1.37159 
  1.36798     1.45972 
+ 1.36899     1.40239 
  1.36945     1.59246 
  1.37237     1.41415 
  1.37239     1.38953 
  1.37878     1.47392 
  1.38831     1.40355 
  1.39273     1.43421 
+ 1.39525     1.56712 
  1.40182     1.47944 
  1.40541     1.49948 
  1.44116     1.48188 
  1.44594     1.56423 
  1.45105     1.58574 
+ 1.45849     1.53413 
  1.49962     1.58932 
  1.55945     1.62818 
  1.56099     1.58856 
- 1.62103     1.74192 
+ 1.56396     1.62882 
  1.20782     1.37608 
  1.20966     1.37601 
  1.21942     1.3489  
  1.22483     1.62624 
+ 1.22871     1.35926 
  1.26439     1.52637 
  1.27318     1.54106 
  1.29315     1.50917 
@@ -1769,7 +1770,6 @@ dim 2: 180×2 Array{Float64,2}:
  1.37921     1.54764 
  1.42724     1.56933 
  1.529       1.66364 
- 1.56396     1.62882 
  1.20853     1.58866 
  1.28407     1.52212 
  1.34335     1.53171 
@@ -1782,3 +1782,11 @@ dim 2: 180×2 Array{Float64,2}:
  1.33526     1.6793  
  1.30651   Inf       
  1.28777   Inf       
+dim 3: 7×2 Array{Float64,2}:
+ 1.28671    1.32918
+ 1.50337    1.51256
+ 1.70403    1.7059 
+ 1.3017     1.32555
+ 1.52351    1.54091
+ 1.78632  Inf      
+ 1.75116  Inf      
diff --git a/benchmarks/output/o3_1024.eirene.txt b/benchmarks/output/o3_1024.eirene.txt
index b177843..99406b7 100644
--- a/benchmarks/output/o3_1024.eirene.txt
+++ b/benchmarks/output/o3_1024.eirene.txt
@@ -1,21 +1,21 @@
-	Command being timed: "julia --eval maxdim = 2; maxrad = 1.8; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = transpose(readdlm("o3_1024.txt")); result = eirene(d, model="pc", record="none", maxdim=maxdim, maxrad=maxrad))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end"
-	User time (seconds): 34.75
-	System time (seconds): 0.93
-	Percent of CPU this job got: 101%
-	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:35.23
+	Command being timed: "julia --eval maxdim = 3; maxrad = 1.8; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = transpose(readdlm("o3_1024.txt")); result = eirene(d, model="pc", record="none", maxdim=maxdim, maxrad=maxrad))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end"
+	User time (seconds): 36.76
+	System time (seconds): 1.09
+	Percent of CPU this job got: 100%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:37.52
 	Average shared text size (kbytes): 0
 	Average unshared data size (kbytes): 0
 	Average stack size (kbytes): 0
 	Average total size (kbytes): 0
-	Maximum resident set size (kbytes): 581060
+	Maximum resident set size (kbytes): 1111752
 	Average resident set size (kbytes): 0
-	Major (requiring I/O) page faults: 4
-	Minor (reclaiming a frame) page faults: 296062
-	Voluntary context switches: 45
-	Involuntary context switches: 475539
+	Major (requiring I/O) page faults: 5
+	Minor (reclaiming a frame) page faults: 564334
+	Voluntary context switches: 49
+	Involuntary context switches: 422007
 	Swaps: 0
-	File system inputs: 0
-	File system outputs: 4352
+	File system inputs: 512
+	File system outputs: 4384
 	Socket messages sent: 0
 	Socket messages received: 0
 	Signals delivered: 0
diff --git a/benchmarks/output/o3_1024.ripser.txt b/benchmarks/output/o3_1024.ripser.txt
index b4f43be..f68f3bb 100644
--- a/benchmarks/output/o3_1024.ripser.txt
+++ b/benchmarks/output/o3_1024.ripser.txt
@@ -1,18 +1,18 @@
 	Command being timed: "ripser o3_1024.txt --format point-cloud --dim 3 --threshold 1.8 --ratio 2"
-	User time (seconds): 2.56
-	System time (seconds): 0.06
+	User time (seconds): 2.31
+	System time (seconds): 0.08
 	Percent of CPU this job got: 99%
-	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.63
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.40
 	Average shared text size (kbytes): 0
 	Average unshared data size (kbytes): 0
 	Average stack size (kbytes): 0
 	Average total size (kbytes): 0
-	Maximum resident set size (kbytes): 151008
+	Maximum resident set size (kbytes): 151020
 	Average resident set size (kbytes): 0
 	Major (requiring I/O) page faults: 0
-	Minor (reclaiming a frame) page faults: 55726
+	Minor (reclaiming a frame) page faults: 55722
 	Voluntary context switches: 1
-	Involuntary context switches: 54
+	Involuntary context switches: 38
 	Swaps: 0
 	File system inputs: 0
 	File system outputs: 0
diff --git a/benchmarks/output/sphere_3_192.dipha.txt b/benchmarks/output/sphere_3_192.dipha.txt
index a52fc48..d12332b 100644
--- a/benchmarks/output/sphere_3_192.dipha.txt
+++ b/benchmarks/output/sphere_3_192.dipha.txt
@@ -1,18 +1,18 @@
 	Command being timed: "dipha --dual --benchmark --upper_dim 3 sphere_3_192.complex sphere_3_192.dipha.diagram"
-	User time (seconds): 47.37
-	System time (seconds): 5.09
-	Percent of CPU this job got: 99%
-	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:52.71
+	User time (seconds): 46.61
+	System time (seconds): 4.79
+	Percent of CPU this job got: 98%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:51.94
 	Average shared text size (kbytes): 0
 	Average unshared data size (kbytes): 0
 	Average stack size (kbytes): 0
 	Average total size (kbytes): 0
-	Maximum resident set size (kbytes): 5728596
+	Maximum resident set size (kbytes): 5728728
 	Average resident set size (kbytes): 0
 	Major (requiring I/O) page faults: 0
-	Minor (reclaiming a frame) page faults: 5510171
-	Voluntary context switches: 716
-	Involuntary context switches: 181
+	Minor (reclaiming a frame) page faults: 5510161
+	Voluntary context switches: 709
+	Involuntary context switches: 226
 	Swaps: 0
 	File system inputs: 0
 	File system outputs: 56
diff --git a/benchmarks/output/sphere_3_192.eirene.out.txt b/benchmarks/output/sphere_3_192.eirene.out.txt
index 898dd57..022f726 100644
--- a/benchmarks/output/sphere_3_192.eirene.out.txt
+++ b/benchmarks/output/sphere_3_192.eirene.out.txt
@@ -1,4 +1,4 @@
-11.746609248
+11.294754783
 dim 0: 192×2 Array{Float64,2}:
  0.0    0.0487061 
  0.0    0.131638  
diff --git a/benchmarks/output/sphere_3_192.eirene.txt b/benchmarks/output/sphere_3_192.eirene.txt
index 9b0bd5a..8a9d264 100644
--- a/benchmarks/output/sphere_3_192.eirene.txt
+++ b/benchmarks/output/sphere_3_192.eirene.txt
@@ -1,20 +1,20 @@
 	Command being timed: "julia --eval maxdim = 2; using Eirene; using DelimitedFiles; eirene([0 1; 1 0]); println(@elapsed (d = readdlm("sphere_3_192.distance_matrix"); result = eirene(d, record="none", maxdim=maxdim))); for i in 0:maxdim print("dim $(i): "); show(stdout, "text/plain", (barcode(result , dim = i))); println(); end"
-	User time (seconds): 42.89
-	System time (seconds): 1.35
-	Percent of CPU this job got: 100%
-	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:44.01
+	User time (seconds): 40.75
+	System time (seconds): 1.50
+	Percent of CPU this job got: 96%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:43.97
 	Average shared text size (kbytes): 0
 	Average unshared data size (kbytes): 0
 	Average stack size (kbytes): 0
 	Average total size (kbytes): 0
-	Maximum resident set size (kbytes): 1629496
+	Maximum resident set size (kbytes): 1624096
 	Average resident set size (kbytes): 0
-	Major (requiring I/O) page faults: 4
-	Minor (reclaiming a frame) page faults: 854253
-	Voluntary context switches: 33
-	Involuntary context switches: 299444
+	Major (requiring I/O) page faults: 888
+	Minor (reclaiming a frame) page faults: 818725
+	Voluntary context switches: 1690
+	Involuntary context switches: 346428
 	Swaps: 0
-	File system inputs: 0
+	File system inputs: 432720
 	File system outputs: 4272
 	Socket messages sent: 0
 	Socket messages received: 0
diff --git a/benchmarks/output/sphere_3_192.ripser.txt b/benchmarks/output/sphere_3_192.ripser.txt
index 711ef8e..29b2d3e 100644
--- a/benchmarks/output/sphere_3_192.ripser.txt
+++ b/benchmarks/output/sphere_3_192.ripser.txt
@@ -1,20 +1,20 @@
 	Command being timed: "ripser sphere_3_192.distance_matrix --dim 2"
-	User time (seconds): 1.11
-	System time (seconds): 0.07
-	Percent of CPU this job got: 99%
-	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.18
+	User time (seconds): 1.04
+	System time (seconds): 0.10
+	Percent of CPU this job got: 98%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.15
 	Average shared text size (kbytes): 0
 	Average unshared data size (kbytes): 0
 	Average stack size (kbytes): 0
 	Average total size (kbytes): 0
-	Maximum resident set size (kbytes): 185112
+	Maximum resident set size (kbytes): 185128
 	Average resident set size (kbytes): 0
-	Major (requiring I/O) page faults: 0
-	Minor (reclaiming a frame) page faults: 62824
-	Voluntary context switches: 1
-	Involuntary context switches: 106
+	Major (requiring I/O) page faults: 1
+	Minor (reclaiming a frame) page faults: 62823
+	Voluntary context switches: 2
+	Involuntary context switches: 28
 	Swaps: 0
-	File system inputs: 0
+	File system inputs: 40
 	File system outputs: 0
 	Socket messages sent: 0
 	Socket messages received: 0