We calculate the contribution to the muon anomalous magnetic moment hadronic vacuum polarization from {the} connected diagrams of up and down quarks, omitting electromagnetism. We employ QCD gauge-field configurations with dynamical $u$, $d$, $s$, and $c$ quarks and the physical pion mass, and analyze five ensembles with lattice spacings ranging from $a approx 0.06$ to~0.15~fm. The up- and down-quark masses in our simulations have equal masses $m_l$. We obtain, in this world where all pions have the mass of the $pi^0$, $10^{10} a_mu^{ll}({rm conn.}) = 637.8,(8.8)$, in agreement with independent lattice-QCD calculations. We then combine this value with published lattice-QCD results for the connected contributions from strange, charm, and bottom quarks, and an estimate of the uncertainty due to the fact that our calculation does not include strong-isospin breaking, electromagnetism, or contributions from quark-disconnected diagrams. Our final result for the total $mathcal{O}(alpha^2)$ hadronic vacuum polarization to the muons anomalous magnetic moment is~$10^{10}a_mu^{rm HVP,LO} = 699(15)_{u,d}(1)_{s,c,b}$, where the errors are from the light-quark and heavy-quark contributions, respectively. Our result agrees with both {it ab-initio} lattice-QCD calculations and phenomenological determinations from experimental $e^+e^-$-scattering data. It is $1.3sigma$ below the no new physics value of the hadronic-vacuum-polarization contribution inferred from combining the BNL E821 measurement of $a_mu$ with theoretical calculations of the other contributions.
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