fabian-paul

Hi Mamta, hi Frank, the continuous time estimator that is implemented in the pull request markovmodel/msmtools#57 is functional. To use the estimator as quick as possible, you could replace your...

I see. If we implement it as a Model with .timescales() and .propagate() we get much for free. Yes the PR is ready to merge. It was on halt for...

Hi Mamta, The comments above are a bit out-dated. We renamed the method in msmtools to `msmtools.estimation.rate_matrix`. Could you give that a try? Also msmtools doens't work with dtrajs directly...

Hi Mamta, apologies for the long delay. I had some time to dig into this error only now. I created a pull request with a tentative fix on https://github.com/markovmodel/msmtools/pull/98 There...

So what is the workaround that you would suggest for the moment to call methods from the superclass explicitly in a derived class? Just `SuperClassName.method(self)`? Should the same apply to...

I looked a bit deeper. This problem seems to be related to random number generation (see below). The problem only appeared with pyzmq 17.0.0. With version 16.0.2, the code worked...

I strongly suspect that the libsodium initialization hangs on the getrandom() call. If the entropy pool of the kernel runs low, getrandom() blocks. I've checked the entropy (following the [libsodium...

Let me add that likely there is also something wrong with the linux kernel that prevents it from collecting entropy. However I'm running ZMQ on a compute node on a...