installed from source on mac osx 9 -- seg fault

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matthew.niemerg
Posts: 2
Joined: 25 Aug 2014, 06:39

installed from source on mac osx 9 -- seg fault

Postby matthew.niemerg » 25 Aug 2014, 06:59

Hello,

After carefully installing all of the dependencies for polymake and a successful build, I receive a seg fault when I run the 'polymake' command.

Running the lldb debugger with polymake, a la 'lldb polymake', the following error shows:

error: 'polymake' doesn't contain any 'host' platform architectures: x86_64, i386

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I use the gcc4.7.3 compiler, built from Mac's clang compiler (with no special flags on my end). I always compile by changing which compiler for any package with the CC=/path/to/gcc4.7.3/bin/gcc CXX=/path/to/gcc4.7.3/bin/g++ -- without any extra CFLAGS or CPPFLAGS or CXXFLAGS. Anyway, all the prereqs (i.e. perl, etc.) that would come on a pre-built osx system have been recompiled this way.

---

Here's my perl --version output:

This is perl 5, version 20, subversion 0 (v5.20.0) built for darwin-thread-multi-2level

Copyright 1987-2014, Larry Wall

Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl". If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.

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Here's my successful configure command (and output):

./configure --without-fink --with-gmp=/usr/local --with-mpfr=/usr/local --with-boost=/usr/local/boost_1_50_0_gcc4.7.3 --with-readline=/usr/local --with-java=/usr/bin/java --with-jni-headers=/System/Library/Frameworks/JavaVM.framework/Headers/ CC=/usr/local/gcc-4.7.3/bin/gcc CXX=/usr/local/gcc-4.7.3/bin/g++
checking C++ compiler ... ok (/usr/local/gcc-4.7.3/bin/g++ is GCC 4.7)
determining architecture ... ok (darwin.x86_64)
determining compiler flags ... ok
CFLAGS= -Wall ${ARCHFLAGS}
CXXFLAGS= -ftemplate-depth-200 -Wall -Wno-strict-aliasing -Wno-parentheses ${ARCHFLAGS}
checking gmp installation ... ok (/usr/local)
checking mpfr installation ... ok (/usr/local)
checking shared perl library ... ok
checking perl module XML::Writer ... ok
checking perl module XML::LibXML ... ok
checking perl module XML::LibXSLT ... ok
checking perl module Term::ReadLine ... ok
checking libxml2 installation ... ok

Configuring bundled extensions:
bundled extension libnormaliz ... ok (boost=/usr/local/boost_1_50_0_gcc4.7.3/include)
bundled extension java ... failed
bundled extension singular ... failed
bundled extension ppl ... failed
bundled extension javaview ... disabled because of unsatisfied prerequisite: java
bundled extension jreality ... disabled because of unsatisfied prerequisite: java
bundled extension bliss ... failed
bundled extension group ... ok (boost=/usr/local/boost_1_50_0_gcc4.7.3/include)
bundled extension nauty ... ok
* If you want to change the configuration of bundled extensions please see build.darwin.x86_64/bundled.log and try configure --help.

* Configuration successful. You should run 'make' now to build polymake.

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Also, when I ran valgrind on polymake, I get this:

valgrind polymake
==68729== Memcheck, a memory error detector
==68729== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
==68729== Using Valgrind-3.10.0.SVN and LibVEX; rerun with -h for copyright info
==68729== Command: /usr/local/bin/polymake
==68729==
arch: Unknown architecture: arch x86_64 /usr/bin/perl

(and some more stuff about memory on the heap)

---

Any thoughts?

Happy to provide any additional info.

Thanks,
Matt

User avatar
gawrilow
Main Author
Posts: 423
Joined: 25 Dec 2010, 17:40

Re: installed from source on mac osx 9 -- seg fault

Postby gawrilow » 25 Aug 2014, 15:38

polymake is a perl script, you can't run it directly under debugger or valgrind. You must run the executable /usr/bin/perl and supply the path to the main polymake script as an argument.

Regarding perl 5.20: it is only supported in the recent "perpetual betas". The release 2.13 is not compatible with it. From your post I can't recognize which polymake distribution are you trying to run. If it's in fact 2.13, then please check out the latest "perpetual beta" from GitHub.

matthew.niemerg
Posts: 2
Joined: 25 Aug 2014, 06:39

Re: installed from source on mac osx 9 -- seg fault

Postby matthew.niemerg » 25 Aug 2014, 19:02

ok. yes. i have 2.13 installed. i will git the latest of the perpetual beta off the repository.

thanks,
matt


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