Software

Run MrBayes Along With Beagle-lib

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MrBayes 3 is a program for Bayesian inference and model choice across a large space of phylogenetic and evolutionary models. And BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. BEAGLE is able to accelerate MrBayes analyses very much.

This post introduces the way to run MrBayes along with BEAGLE.

Install beagle-lib for NVidia Tesla V100 on Debian buster

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BEAGLE is a high-performance library to accelerate the calculations of Bayesian and Maximun Likelihood phylogenetics analyses. The latest version of beagle-lib was released on Dec 4, 2018.

When compiled for NVidia Tesla V100 on Debian buster 10.9, an error was encountered:

nvcc fatal   : Value 'compute_30' is not defined for option 'gpu-architecture'

Install hdf5r package in R 4.0.2

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While installing the R package “hdf5r” version 1.3.3, I encountered the error:

fatal error: hdf5.h: No such file or directory
 #include <hdf5.h>
          ^~~~~~~~
compilation terminated.

My OS is Debian buster/10.6, and the package “libhdf5-dev” has been installed. It looks R cannot find the path of hdf5 header and library files.

Install conda compiler tools

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Conda is quite convenient for non-root users to install softwares in Linux system. But sometimes there is no packages available in anaconda repository and we have to install these softwares from source. This post introduces the way to compile and install softwares from source, use the Kyoto Cabinet Perl module as an example.