Beagle 2.1 Mc OSX 10.8

[Christopher Blair]

HI all, 

I am desperately trying to get Beagle up and running on my Mac. I have tried both downloading and installing the .pgk file and installing from source, but to no avail. When I open BEAST and test Beagle it simply crashes BEAST with no warning. If I try and run BEAST from the command line via beast -beagle I get the following error:

nable to load CPU plugin!

Please check for proper libhmsbeagle installation.

CUDA error: "Driver not initialized" from file <GPUInterfaceCUDA.cpp>, line 169.

I just downloaded and installed the CUDA 5.5 toolkit for OSX. Any thoughts?

Chris

--

Christopher Blair, Ph.D.
Postdoctoral Associate
Department of Biology
Duke University, Box 90338
BioSci 130 Science Drive
Durham, NC 27708
ph: 919-613-8727
Christopher.Blair@duke.edu

Website: https://sites.google.com/site/christopherblairphd/home

[chris blair]

Also, I did receive errors when trying to install from source.

[chris blair]

So apparently my graphics card is not supported, but I should still be able to use Beagle by selecting use CPU correct? Any thoughts about why it crashes BEAST when I test it?

[Andrew Rambaut]

That is correct. However, I have not heard of anyone having problems with BEAGLE on Mac OS X using the PKG installer.

If you run BEAST in the command line do you see any error messages?

Andrew

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Andrew Rambaut 

Institute for Evolutionary Biology | Centre for Infection, Immunity & Evolution 

Ashworth Laboratories, University of Edinburgh, Edinburgh, EH3 9JT, UK

contact – a.ra...@ed.ac.uk | http://tree.bio.ed.ac.uk | tel +44 131 6508624

[Christopher Blair]

HI Andrew, 

This is the error I receive:

unable to load CPU plugin!

Please check for proper libhmsbeagle installation.

CUDA error: "Driver not initialized" from file <GPUInterfaceCUDA.cpp>, line 169.

Perhaps this is because I downloaded the CUDA toolkit and that my GPU is not supported?

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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[Andrew Rambaut]

Can you try removing the libraries installed and then reinstalling from the installer. You fill find the libraries in:

/usr/local/lib/libhmsbeagle*

and:

/Library/Java/Extensions/libhmsbeagle-jni.jnilib

Andrew

[Marc Suchard]

Hi Chris,

It sounds like your CUDA driver is not properly installed.  If you have a CUDA-enabled GPU installed, then first try to reinstall/update the device driver from your System Preferences.  If you do not have a CUDA device, then (1) compile BEAGLE without CUDA-support or (2) install BEAGLE for the Mac OS X installer package.

What appears most awkward to me is the error "Unable to load CPU plugin" (and not GPU plugin).  This sounds like you have a botched compilation/installation of BEAGLE.  Certainly delete all the installed libraries first as Andrew suggests.

best, Marc

[Santiago Sanchez]

A quick thought,

If he just reinstalls BEAGLE command-line without cuda, wouldn't this overwrite older, previously installed libraries?

Santiago

Santiago Sanchez-Ramirez

Ecology and Evolutionary Biology, University of Toronto

Natural History (Mycology), Royal Ontario Museum

100 Queen's Park

Toronto, ON

M5S 2C6

Canada

--

[Christopher Blair]

Thanks everyone for the suggestions. After the holidays I will tinker a bit more and see I'd I can figure it out.

Chris

[Christopher Blair]

HI all, 

I am coming back to this issue, but to no avail. I did as Andrew suggested and removed the libraries and reinstalled via the installer for OSX. When I try to test Beagle it still crashes BEAST. I am selecting CPU and not GPU.

Chris

[Nicola de maio]

Hi all,
I am having the same exact problem as Chris described.
I have a NVIDIA GeForce GT 750M graphics processor, and OSX 10.8.5.

Nicola

[Francisco V.]

Hi everyone, I am having the same problem as Chris and Nicola. I am running a species tree analysis on Beast 2 and I got the following error even though I am not specifying to use Beagle: CUDA error: "Driver not initialized" from file <GPUInterfaceCUDA.cpp>, line 169.

It is curious that when I run Beast 1.8  I can run a similar analysis and only get the same error when specifying to use Beagle.

I have tried several times uninstalling the beagle libraries, re-installing beagle using the installer, and compiling beagle manually (getting some errors - in the make step and make check).

I would really appreciate to get feedback to solve this issue.

Cheers!

[Nick Matzke]

Hi all,

I am having this problem also.  The BEAST GUI crashes while running the primates-mtDNA.xml example.  I can see the error by running it from command line:

sw_vers
ProductName: Mac OS X
ProductVersion: 10.9.2
BuildVersion: 13C1021

The error:

=========

java -Xms512m -Xmx512m -jar /Applications/BEAST_2.1.2/lib/beast.jar -seed 12345 -overwrite /Applications/BEAST_2.1.2/examples/testYuleCalibrated.xml

                  BEAST v2.1.2, 2002-2014

       Bayesian Evolutionary Analysis Sampling Trees

                 Designed and developed by

Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard

                              

               Department of Computer Science

                   University of Auckland

                  re...@cs.auckland.ac.nz

                  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://beast2.cs.auckland.ac.nz

                              

Source code distributed under the GNU Lesser General Public License:

              http://code.google.com/p/beast2

                              

                     BEAST developers:

Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, 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 Strimmer

Random number seed: 12345

File: testYuleCalibrated.xml seed: 12345 threads: 1

Element data found with idref='alignment'. All other attributes are ignored.

Element parameter found with idref='clockRate.c:alignment'. All other attributes are ignored.

Element tree found with idref='Tree.t:alignment'. All other attributes are ignored.

Element distribution found with idref='posterior'. All other attributes are ignored.

Element distribution found with idref='likelihood'. All other attributes are ignored.

Element distribution found with idref='prior'. All other attributes are ignored.

Element distribution found with idref='treeLikelihood.alignment'. All other attributes are ignored.

Element parameter found with idref='kappa.s:alignment'. All other attributes are ignored.

Element distribution found with idref='CalibratedYuleModel.t:alignment'. All other attributes are ignored.

Element parameter found with idref='birthRateY.t:alignment'. All other attributes are ignored.

Element distribution found with idref='chimpgroup.prior'. All other attributes are ignored.

Element parameter found with idref='clockRate.c:alignment'. All other attributes are ignored.

Element parameter found with idref='freqParameter.s:alignment'. All other attributes are ignored.

Element distribution found with idref='posterior'. All other attributes are ignored.

Element distribution found with idref='likelihood'. All other attributes are ignored.

Element distribution found with idref='prior'. All other attributes are ignored.

human: 768 4

chimp: 768 4

bonobo: 768 4

gorilla: 768 4

orangutan: 768 4

siamang: 768 4

6 taxa

768 sites

69 patterns

CUDA error: "Driver not initialized" from file <GPUInterfaceCUDA.cpp>, line 169.

=========

I have updated CUDA (to 6, the newest version) and reinstalled BEAST and BEAGLE from the package installers...still the same error.  Any hints/advice from people who've seen this?  The only reference to this problem on the internet seems to be this thread...

Cheers,

Nick

[Remco Bouckaert]

Hi Nick,

By default, BEAST 2 attempts to load BEAGLE, and it should fall back on the Java TreeLikelihood implementation if it cannot load BEAGLE. Apparently something goes wrong in that it manages to load BEAGLE, but then the CUDA driver is not properly initialised.

To force BEAST to ignore BEAGLE, you can use the -java flag, so if you run

java -Xms512m -Xmx512m -jar /Applications/BEAST_2.1.2/lib/

beast.jar -java -seed 12345 -overwrite /Applications/BEAST_2.1.2/examples/testYuleCalibrated.xml

you should be able to run the file. I am not sure how to solve the CUDA driver problem unfortunately.

Cheers,

Remco

[Nick Matzke]

Looks like my GPU is not beagle-compatible so I will try compiling BEAST without BEAGLE on this machine...cheers!

Nick

For more options, visit https://groups.google.com/d/optout.

[Nick Matzke]

Ah -- just saw this -- the -java flag fixed it!  

Thanks!

Nick

[Andrew Rambaut]

Running with the -java flag will make BEAST much slower. BEAGLE doesn't require CUDA to run (it will use the processors by preference). I suggest you uninstall CUDA and then reinstall BEAGLE. 

A. 

[Nick Matzke]

Thanks for tip!  I'm not sure why this computer has CUDA installed in the first place, actually, since it appears to be pointless.  So yeah, I'll uninstall it.

Cheers, Nick