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

[Tony Travis]

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.
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