There are symmetric positive definite matrices $M$ for which Cholesky's algorithm will fail due to the limitations of floating point arithmetic.
A specific example is given here. Let $u \ll 1$ denote the unit round off error and consider the matrix
$$ M = \begin{bmatrix} 1 + 2u & 1 \\ 1 & 1 - u \end{bmatrix}.$$
This matrix is exactly representable. It is clear that $M$ is symmetric positive definite, for
$$ \text{Tr}(M) = 2 + u > 0$$
and
$$ \text{det}(M) = u - 2u^2 > 0.$$
Now let $\text{fl}(x)$ denote the floating point representation of the real number $x$. Since
$$1+2u = (1 + u)^2 - u^2$$
we have
$$ 1 < \sqrt{1 + 2 u} < 1 + u < 1 + 2u. $$
It follows that $\text{fl}(\sqrt{1+2u}) = 1$ as there are no floating point numbers in the open interval between $1$ and $1+2u$ and we must pick the option which has the smallest error. After processing the first column of $M$ and performing the linear update of the lower right corner, we are left with
$$ M^{(1)} = \begin{bmatrix} 1 & 1 \\ 1 & - u \end{bmatrix}.$$
The algorithm will now fail because the final pivot is strictly negative.
In general, if Cholesky's algorithm runs to completion, then it produces the exact factorization of a matrix $\hat{M} = \hat{L}\hat{L}^T $ which is close to $M$. This may very well be enough for your purposes, especially if you can establish that the smallest eigenvalue of $\hat{M}$ is not too small.