Wednesday, March 14, 2018

PYMC3 Reports "WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions"

When I run PYMC3 on Ubuntu 16.04 LTS, I encounter an error,

WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.

This went after I installed,

sudo apt-get install libblas-dev liblapack-dev libatlas-base-dev gfortran  

I also notice that the problem persists when I only install the mkl and mkl-service as suggested in the theano documentation and the discussion here

Tuesday, March 6, 2018

Old Bug in open-vm-tools and Git Commit Problem.

There is a known bug in open-vm-tools that can interference with a number of applications when we operate on a vmhgfs-fuse file system. This bug is documented as issue #90, and there are a few other discussion about this, in particular, a discussion on how to install recent release of open-vm-tools on Ubuntu 16.04 LTS since Ubuntu 16.04 LTS at this moment still ships open-vm-tools version 10.0.7 that carries this bug.

You may check your open-vm-tools version with one of many methods, such as,

vmware-toolbox-cmd -v


apt-show-versions open-vm-tools

If the output indicates that you have a version of earlier than 10.1.0, your version of open-vm-tools may have this bug. It causes serious problems in a few rather frequently used applications. In my case, when I use do a git commit, I would observe the following,

$ git commit -m "done something trivial"
error: bad index file sha1 signature
fatal: index file corrupt

After 5 seconds, when I try it again, the git commit is successful. As discussed in issue #90, this is the result that the tools cache file attributes and entries and causes a cache inconsistency. The 5-second delay is the waiting time before the cached items get updated.

Some also observed that this bug causes the npm install to fail.

Perhaps, the more important issue is how we may address this issue before the Linux distributors have a new version of the tools for us to upgrade to. Suggested in the discussions cited is to use a Ubuntu test PPA repository since it does not appear to be problem-free to build the tools from the source. The steps to install from the test PPA are as follows,

sudo add-apt-repository ppa:ci-train-ppa-service/3152
sudo apt-get update
sudo apt-get upgrade open-vm-tools open-vm-tools-desktop open-vm-tools-dkms

In my case, these steps lead to the successful installation of the open-vm-tools version (build-7253323), and it seems to work fine although some seem to observe some issues, such as, a race condition.