PCA on matrix with large M and N
There are a couple of things you can do.


Sample a representative, but small set of your data, which will allow you to compute PCA in memory. But seeing as you have 600,00 observations this will most likely not result in any meaningful results.
Use incremental PCA, here is a link: http://scikit-learn.org/stable/modules/generated/sklearn.decomposition.IncrementalPCA.html#sklearn.decomposition.IncrementalPCA


But the main problem you have is that a number of samples are less than the amount of observations you have. I would recommend a different approach to dimensionality reduction. Autoencoders would be my recommendation to you. Autoencoders can be trained in an iterative fashion, circumventing your memory issue, and can learn more complicated projections than PCA (which is a linear transform). In case you want a linear projection you can have an autoencoder with one hidden layer, and the solution found by the neural network will be equal to the solution found by PCA.

Here are a couple of links you will find helpful:


http://ai.stanford.edu/~quocle/tutorial2.pdf
https://www.quora.com/How-is-autoencoder-compared-with-other-dimensionality-reduction-algorithms
https://www.cs.toronto.edu/~hinton/science.pdf