In this paper, we improve the algorithms of Lauder-Wan \cite{LW} and Harvey \cite{Ha} to compute the zeta function of a system of $m$ polynomial equations in $n$ variables over the finite field $\FF_q$ of $q$ elements, for $m$ large. The dependence on $m$ in the original algorithms was exponential in $m$. Our main result is a reduction of the exponential dependence on $m$ to a polynomial dependence on $m$. As an application, we speed up a doubly exponential time algorithm from a software verification paper \cite{BJK} (on universal equivalence of programs over finite fields) to singly exponential time. One key new ingredient is an effective version of the classical Kronecker theorem which (set-theoretically) reduces the number of defining equations for a "large" polynomial system over $\FF_q$ when $q$ is suitably large.

Suppose $q$ is a prime power and $f\in\mathbb{F}_q[x]$ is a univariate polynomial with exactly $t$ monomial terms and degree $

Suppose $p$ is a prime, $t$ is a positive integer, and $f\!\in\!\mathbb{Z}[x]$ is a univariate polynomial of degree $d$ with coefficients of absolute value $<\!p^t$. We show that for any fixed $t$, we can compute the number of roots in $\mathbb{Z}/(p^t)$ of $f$ in deterministic time $(d+\log p)^{O(1)}$. This fixed parameter tractability appears to be new for $t\!\geq\!3$. A consequence for arithmetic geometry is that we can efficiently compute Igusa zeta functions $Z$, for univariate polynomials, assuming the degree of $Z$ is fixed.