Trouble Installing BEAGLE on Mac Big Sur (zsh)

[Janvi A]

Hi everyone! 

I was wondering if someone could help with a BEAST/BEAGLE installation problem that has been really difficult to resolve. 

So far we have tried to

• Updated the zshrc profile 
• Download BEAGLE using the source code and the installer. Interestingly, with the installer, none of the libhms files download. However, even after getting BEAGLE from the source code things don’t seem to work 
• Set the JAVA_HOME path

Some information on my laptop:

• macOS Big Sur Version 11.4 20F71

What we think looks like a problem:

• Not loading CPU plug-in
  • "Unable to load CPU plugin!"
• Looking for plug-ins in the wrong place
  • "Looking for plugins in /Users/janviahuja/Documents/TEST_BEAST/pluginsRead"

This is what the error looks like:

(base) janviahuja@Janvis-MacBook-Pro ~ % cd Documents/TEST_BEAST 
(base) janviahuja@Janvis-MacBook-Pro TEST_BEAST % /Applications/BEASTv1104/bin/beast -beagle_AUTO test.xml
Unable to load CPU plugin!
Please check for proper libhmsbeagle installation.    BEAST v1.10.4 Prerelease #bc6cbd9, 2002-2018
    Bayesian Evolutionary Analysis Sampling Trees
         Designed and developed by
  Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard        Department of Computer Science
          University of Auckland
         ale...@cs.auckland.ac.nz       Institute of Evolutionary Biology
         University of Edinburgh
           a.ra...@ed.ac.uk       David Geffen School of Medicine
      University of California, Los Angeles
           msuc...@ucla.edu        Downloads, Help & Resources:
          http://beast.communitySource code distributed under the GNU Lesser General Public License:
      http://github.com/beast-dev/beast-mcmc           BEAST developers:
Alex Alekseyenko, Guy Baele, Trevor Bedford, Filip Bielejec, Erik Bloomquist, Matthew Hall,
Joseph Heled, Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li,
Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel,
      Oliver Pybus, Chieh-Hsi Wu, Walter Xie             Thanks to:
   Roald Forsberg, Beth Shapiro and Korbinian StrimmerUsing BEAGLE library v3.2.0 (PRE-RELEASE) for accelerated, parallel likelihood evaluation
2009-, BEAGLE Working Group - https://beagle-dev.github.io/
Citation: Ayres et al (2012) Systematic Biology 61: 170-173 | doi:10.1093/sysbio/syr100Random number seed: 1625055340514Loading additional development parsers from development_parsers.properties, which is additional set of parsers only available for development version ...
Parsing XML file: test.xml
 File encoding: UTF8
Looking for plugins in /Users/janviahuja/Documents/TEST_BEAST/pluginsRead alignment: alignment
 Sequences = 40
   Sites = 29903
  Datatype = nucleotide
Site patterns 'CP1+2.patterns' created by merging 2 pattern lists
 pattern count = 95
Site patterns 'CP3.patterns' created from positions 3-29903 of alignment 'alignment'
 only using every 3 site
 unique pattern count = 57Creating the tree model, 'treeModel'
 taxon count = 40
 tree height = 1.178117857036102Using strict molecular clock model.Creating state frequencies model 'frequencies': Initial frequencies = {0.25, 0.25, 0.25, 0.25}Creating HKY substitution model. Initial kappa = 2.0Creating state frequencies model 'frequencies': Initial frequencies = {0.25, 0.25, 0.25, 0.25}Creating HKY substitution model. Initial kappa = 2.0Creating site rate model: 
 with initial relative rate = 0.5 with weight: 1.4999498394863564
 4 category discrete gamma with initial shape = 0.5Creating site rate model: 
 with initial relative rate = 0.5 with weight: 3.000200662185211
 4 category discrete gamma with initial shape = 0.5Running benchmarks to automatically select fastest BEAGLE resource for analysis... 
Fatal exception: null
java.lang.NullPointerException
at java.base/java.util.Objects.requireNonNull(Objects.java:208)
at java.base/java.util.Arrays$ArrayList.<init>(Arrays.java:4136)
at java.base/java.util.Arrays.asList(Arrays.java:4121)
at beagle.BeagleFactory.getBenchmarkedResourceDetails(Unknown Source)
at dr.evomodel.treedatalikelihood.MultiPartitionDataLikelihoodDelegate.<init>(Unknown Source)
at dr.evomodelxml.treedatalikelihood.TreeDataLikelihoodParser.createTreeDataLikelihood(Unknown Source)
at dr.evomodelxml.treedatalikelihood.TreeDataLikelihoodParser.parseXMLObject(Unknown Source)
at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)
at dr.xml.XMLParser.convert(Unknown Source)
at dr.xml.XMLParser.convert(Unknown Source)
at dr.xml.XMLParser.parse(Unknown Source)
at dr.app.beast.BeastMain.<init>(Unknown Source)
at dr.app.beast.BeastMain.main(Unknown Source)
(base) janviahuja@Janvis-MacBook-Pro TEST_BEAST % 

[Marc Suchard]

I can report that other users have also experienced a similar issue on Big Sur.  One solution that has worked for others is to build BEAGLE from source off of the `v4_release` branch and install.  Then things work again.

We should be providing a new `pre-release` Mac installer for BEAGLE v4 soon.   Email me directly if you'd like to try it out as an beta-tester.

best, Marc

[Matthew Green]

Hi Marc,

Can you provide a link to BEAGLE v4? I, too, am having issues installing BEAGLE from source code.

Thanks,

Matt Green.

[Atanas Demirev]

Hi Marc,

When is the BEAGLE v4 going to be available?

I think this issue is persistent on the Big Sur and Monterey OS.

I also would like to try the beta test and see if it solves the problem.

Let us know.

Thanks 

Atanas