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Table 4 Memory usage in GB for the computations summarized in Table  3

From: A roadmap for the computation of persistent homology

Data set (a) Computations on cluster
eleg Klein HIV drag 2 random genome
Size of complex 4.4 × 106 1.1 × 107 2.1 × 108 1.3 × 109 3.1 × 109 4.5 × 108
Max. dim. 2 2 2 2 8 2
javaPlex (st) <5 <15 >64 >64 >64 >64
Dionysus (st) 1.3 11.6 - - - -
DIPHA (st) 0.1 0.2 2.7 4.9 - 4.8
Perseus 5.1 12.7 - - - -
Dionysus (d) 0.5 1.1 - - - -
DIPHA (d) 0.1 0.2 1.8 13.8 9.6 6.3
Gudhi 0.2 0.5 8.5 62.8 - 21.5
Ripser 0.007 0.02 0.06 0.2 24.7 0.07
Data set (b) Computations on shared-memory system
eleg Klein HIV drag 2 genome fract r
Size of complex 3.2 × 108 1.1 × 107 2.1 × 108 1.3 × 109 4.5 × 108 2.8 × 109
Max. dim. 3 2 2 2 2 3
javaPlex (st) <600 <15 <700 >700 <700 >700
Perseus - 11.7 - - - -
Dionysus (d) - 1.1 16.8 134.2 - 268.5
DIPHA (d) 31.2 0.9 17.7 109.5 37.3 276.1
Gudhi 15.4 0.5 10.2 62.8 21.4 134.8
Ripser 0.2 0.03 0.07 0.2 0.07 155
  1. For javaPlex, we indicate the value of the maximum heap size that was sufficient to perform the computation. The value that we give is an upper bound to the memory usage. For DIPHA, we indicate the maximum memory used by a single core (considering all cores). See Table 3 for details on the number of cores used.