[Bio-linux-dev] "bamm" - problems with pthreads

[Tim Booth]

Hi Tony,

Try this:

unzip bamm-2.2.0.zip
cd bamm-2.2.0 
cmake .
make
sed 's/$/ -pthread -std=c++11/' CMakeFiles/bamm.dir/link.txt | sh

In other words, I think you had the right idea, but CMake defeated you
because CMake is a confusing, obfuscating and poorly documented pile of
****.

Cheers,

TIM

On Thu, 2014-09-11 at 15:52 +0100, Tony Travis wrote:
> Hi,
> 
> We're having problems running "bamm" under Bio-Linux 8 / Ubuntu 14.04
> LTS. I've compiled the program from source (obtained from GitHub) but
> when I run it, "bamm" throws an exception. I've tried recompiling using
> this bug-fix for G++ and tried using "clang" instead, but the problem
> was not resolved - Any ideas?
> 
> Thanks,
> 
>   Tony.
> 
> diff --git a/CMakeLists.txt b/CMakeLists.txt
> index 9f27da2..10d19ca 100644
> --- a/CMakeLists.txt
> +++ b/CMakeLists.txt
> @@ -10,7 +10,7 @@ SET(BAMM_VERSION_DATE 2014-09-05)
> 
> # Set compiler flags
> IF(NOT WIN32)
> 
>     SET(CXX_LANGUAGE_FLAGS "-std=c++11")
>     SET(CXX_LANGUAGE_FLAGS "-Wl,--no-as-needed -std=c++11 -pthread")
> SET(CXX_DEBUG_FLAGS "-g") SET(CXX_WARNING_FLAGS "-Wall -Wextra")
> SET(CXX_OPTIMIZATION_FLAGS "-O3")
> 
> soi696 at wildcat:~/Desktop/BAMM2$ bamm -c ControlFileAmoAspeciation.txt
> BAMM 2.2.0 (2014-09-05)
> Copyright (C) 2012-2014 Daniel Rabosky
> BAMM is distributed under the GNU General Public License.
> See http://bamm-project.org for more information.
> 
> Random seed: 1410445448
> 
> Model type: Speciation/Extinction
> 
> Reading tree from file .
> Tree contains 370 taxa.
> 
> Initial log-likelihood: -1285.74
> 
> Reading tree from file .
> Tree contains 370 taxa.
> 
> Initial log-likelihood: -1285.74
> 
> Reading tree from file .
> Tree contains 370 taxa.
> 
> Initial log-likelihood: -1285.74
> 
> Reading tree from file .
> Tree contains 370 taxa.
> 
> Initial log-likelihood: -1285.74
> 
> Running 4 chains for 80000000 generations.
> 
> terminate called after throwing an instance of 'std::system_error'
> what(): Enable multithreading to use std::thread: Operation not permitted
> Aborted
> 
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
> 
> 
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
> Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705