Abort trap 6

[chris blair]

Hi all, 

I just wanted to pose a question to see if any users have had a similar issue. I am trying to run a sam file through pstacks and am getting an "Abort trap 6" error. After doing a bit of googling I came to realize that many users of OSX Mountain Lion get a similar error when running applications. I wanted to ask if there are any other OSX 10.8 users who have had a difficult time running pstacks. Thanks!

Chris

[Julian Catchen]

Hi Chris,

In Stacks 1.11 I fixed some bugs so that Stacks would build properly on
the native OS X compiler, clang. When you build Stacks on OS X, it
appears to be running g++ as the compiler, but it is really an alias for
clang. However, clang has not yet implemented OpenMP, so you still need
to disable that (--disable-openmp to the configure script). If you want
OpenMP you have to go through the process of installing a full version
of gcc using homebrew or macports (instructions on how to do this have
been posted previously on the list).

Anyway, you should make sure you have the newest install before we look
at any other "Abort" errors.

Best,

julian

[Christopher Blair]

Hi Julian, 

Thanks for the email. I downloaded 1.12, but am getting the following errors while building the program:

g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -MT src/ustacks-ustacks.o -MD -MP -MF src/.deps/ustacks-ustacks.Tpo -c -o src/ustacks-ustacks.o `test -f 'src/ustacks.cc' || echo './'`src/ustacks.cc

In file included from src/ustacks.cc:29:

src/ustacks.h:55:25: error: unordered_map: No such file or directory

In file included from src/ustacks.cc:29:

src/ustacks.h:56: error: ‘std::unordered_map’ has not been declared

In file included from src/ustacks.h:68,

                 from src/ustacks.cc:29:

src/kmers.h:44: error: ‘std::unordered_map’ has not been declared

In file included from src/ustacks.h:68,

                 from src/ustacks.cc:29:

src/kmers.h:79: error: expected initializer before ‘<’ token

src/kmers.h:80: error: expected initializer before ‘<’ token

src/kmers.h:86: error: ‘KmerHashMap’ has not been declared

src/kmers.h:87: error: ‘CatKmerHashMap’ has not been declared

src/kmers.h:88: error: ‘KmerHashMap’ was not declared in this scope

src/kmers.h:88: error: expected primary-expression before ‘,’ token

src/kmers.h:88: error: expected primary-expression before ‘&’ token

src/kmers.h:88: error: expected primary-expression before ‘)’ token

src/kmers.h:88: error: initializer expression list treated as compound expression

src/kmers.h:89: error: redefinition of ‘int free_kmer_hash’

src/kmers.h:88: error: ‘int free_kmer_hash’ previously defined here

src/kmers.h:89: error: ‘CatKmerHashMap’ was not declared in this scope

src/kmers.h:89: error: expected primary-expression before ‘,’ token

src/kmers.h:89: error: expected primary-expression before ‘&’ token

src/kmers.h:89: error: expected primary-expression before ‘)’ token

src/kmers.h:109: error: ‘KmerHashMap’ was not declared in this scope

src/kmers.h:109: error: expected primary-expression before ‘)’ token

In file included from src/ustacks.cc:29:

src/ustacks.h:100: error: expected initializer before ‘<’ token

src/ustacks.h:106: error: ‘DNASeqHashMap’ has not been declared

src/ustacks.h:108: error: ‘DNASeqHashMap’ was not declared in this scope

src/ustacks.h:108: error: expected primary-expression before ‘,’ token

src/ustacks.h:108: error: expected primary-expression before ‘&’ token

src/ustacks.h:108: error: expected primary-expression before ‘,’ token

src/ustacks.h:108: error: expected primary-expression before ‘&’ token

src/ustacks.h:108: error: expected primary-expression before ‘)’ token

src/ustacks.h:108: error: initializer expression list treated as compound expression

src/ustacks.h:109: error: ‘DNASeqHashMap’ was not declared in this scope

src/ustacks.h:109: error: expected primary-expression before ‘,’ token

src/ustacks.h:109: error: expected primary-expression before ‘&’ token

src/ustacks.h:109: error: expected primary-expression before ‘)’ token

src/ustacks.h:109: error: initializer expression list treated as compound expression

src/ustacks.cc: In function ‘int main(int, char**)’:

src/ustacks.cc:124: error: ‘DNASeqHashMap’ was not declared in this scope

src/ustacks.cc:124: error: expected `;' before ‘radtags’

src/ustacks.cc:130: error: ‘radtags’ was not declared in this scope

src/ustacks.cc:132: error: ‘reduce_radtags’ cannot be used as a function

src/ustacks.cc:134: error: ‘free_radtags_hash’ cannot be used as a function

src/ustacks.cc: In function ‘int merge_remainders(std::map<int, MergedStack*, std::less<int>, std::allocator<std::pair<const int, MergedStack*> > >&, std::map<int, Rem*, std::less<int>, std::allocator<std::pair<const int, Rem*> > >&)’:

src/ustacks.cc:219: error: ‘KmerHashMap’ was not declared in this scope

src/ustacks.cc:219: error: expected `;' before ‘kmer_map’

src/ustacks.cc:221: error: ‘kmer_map’ was not declared in this scope

src/ustacks.cc:316: error: ‘free_kmer_hash’ cannot be used as a function

src/ustacks.cc: In function ‘int merge_stacks(std::map<int, Stack*, std::less<int>, std::allocator<std::pair<const int, Stack*> > >&, std::map<int, Rem*, std::less<int>, std::allocator<std::pair<const int, Rem*> > >&, std::map<int, MergedStack*, std::less<int>, std::allocator<std::pair<const int, MergedStack*> > >&, std::set<int, std::less<int>, std::allocator<int> >&, int)’:

src/ustacks.cc:590: warning: iteration variable ‘index’ is unsigned

src/ustacks.cc: In function ‘int calc_kmer_distance(std::map<int, MergedStack*, std::less<int>, std::allocator<std::pair<const int, MergedStack*> > >&, int)’:

src/ustacks.cc:1028: error: ‘KmerHashMap’ was not declared in this scope

src/ustacks.cc:1028: error: expected `;' before ‘kmer_map’

src/ustacks.cc:1055: error: ‘kmer_map’ was not declared in this scope

src/ustacks.cc:1060: warning: iteration variable ‘i’ is unsigned

src/ustacks.cc:1124: error: ‘free_kmer_hash’ cannot be used as a function

src/ustacks.cc: At global scope:

src/ustacks.cc:1188: error: redefinition of ‘int reduce_radtags’

src/ustacks.h:108: error: ‘int reduce_radtags’ previously defined here

src/ustacks.cc:1188: error: ‘DNASeqHashMap’ was not declared in this scope

src/ustacks.cc:1188: error: ‘radtags’ was not declared in this scope

src/ustacks.cc:1188: error: expected primary-expression before ‘&’ token

src/ustacks.cc:1188: error: ‘unique’ was not declared in this scope

src/ustacks.cc:1188: error: expected primary-expression before ‘&’ token

src/ustacks.cc:1188: error: ‘rem’ was not declared in this scope

make[1]: *** [src/ustacks-ustacks.o] Error 1

make: *** [all] Error 2

Not sure what is causing these errors.

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

[Julian Catchen]

Hi Chris,

What type of system are you building Stacks on, and what version of g++ is
installed?

Executing

g++ --version

will tell you.

The unordered_map data structure is provided differently by different versions
of the C++ standard template library, the configure script should detect what
version you have and put in the right flag, but I don't see this flag in your
output. If your g++ is quite old, it won't have unordered_map. So, what was the
output of your configure script?

julian

> Christop...@duke.edu <mailto:peter....@duke.edu>
> <http://individual.utoronto.ca/chrisblair/index.html>
> Website: https://sites.google.com/site/christopherblairphd/home
>
> --
> Stacks website: http://creskolab.uoregon.edu/stacks/
> ---
> You received this message because you are subscribed to the Google Groups
> "Stacks" group.
> To unsubscribe from this group and stop receiving emails from it, send an email
> to stacks-users...@googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.

--
Julian M Catchen, Ph.D.
Institute of Ecology and Evolution
University of Oregon
--
jcat...@uoregon.edu
http://www.uoregon.edu/~jcatchen/

[Christopher Blair]

HI Julian, 

I am building Stacks on OSX 10.8.4.

Typing g++ --version yields:

i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)

Copyright (C) 2007 Free Software Foundation, Inc.

This is free software; see the source for copying conditions.  There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

After running configure I get the following output:

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... config/install-sh -c -d

checking for gawk... no

checking for mawk... no

checking for nawk... no

checking for awk... awk

checking whether make sets $(MAKE)... yes

checking for g++... g++

checking whether the C++ compiler works... yes

checking for C++ compiler default output file name... a.out

checking for suffix of executables... 

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C++ compiler... yes

checking whether g++ accepts -g... yes

checking for style of include used by make... GNU

checking dependency style of g++... gcc3

checking dependency style of g++... (cached) gcc3

checking for gcc... gcc

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking dependency style of gcc... gcc3

checking dependency style of gcc... (cached) gcc3

checking whether gcc and cc understand -c and -o together... yes

checking whether g++ supports C++11 features by default... no

checking whether g++ supports C++11 features with -std=gnu++11... no

checking whether g++ supports C++11 features with -std=gnu++0x... no

checking whether g++ supports C++11 features with -std=c++11... no

checking whether g++ supports C++11 features with -std=c++0x... no

configure: No compiler with C++11 support was found

checking for omp_set_num_threads in -lgomp... no

configure: WARNING: Unable to locate OpenMP library, you should probably specify '--disable-openmp'.

checking for gzread in -lz... yes

checking for dirent.h that defines DIR... yes

checking for library containing opendir... none required

checking how to run the C preprocessor... gcc -E

checking for grep that handles long lines and -e... /usr/bin/grep

checking for egrep... /usr/bin/grep -E

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

checking float.h usability... yes

checking float.h presence... yes

checking for float.h... yes

checking limits.h usability... yes

checking limits.h presence... yes

checking for limits.h... yes

checking for stdlib.h... (cached) yes

checking for string.h... (cached) yes

checking for stdbool.h that conforms to C99... no

checking for _Bool... yes

checking for an ANSI C-conforming const... yes

checking for size_t... yes

checking whether closedir returns void... no

checking for stdlib.h... (cached) yes

checking for GNU libc compatible malloc... yes

checking for stdlib.h... (cached) yes

checking for GNU libc compatible realloc... yes

checking for floor... yes

checking for memset... yes

checking for pow... yes

checking for sqrt... yes

configure: creating ./config.status

config.status: creating Makefile

config.status: creating config.h

config.status: config.h is unchanged

config.status: executing depfiles commands

-Chris

to stacks-users+unsubscribe@googlegroups.com.

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

--
Julian M Catchen, Ph.D.
Institute of Ecology and Evolution
University of Oregon
--
jcat...@uoregon.edu
http://www.uoregon.edu/~jcatchen/

--

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

[Christopher Blair]

I just noticed this error in configure:

configure: WARNING: Unable to locate OpenMP library, you should probably specify '--disable-openmp'

However, I did specify this (i.e. ./configure --disable-openmp).

[Julian Catchen]

Hi Chris,

When I run g++ --version on OS X Mavericks (10.9.1) I get:

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
--with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/c++/4.2.1
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
Target: x86_64-apple-darwin13.0.0
Thread model: posix

And I get the following in my configure output:

checking whether g++ supports C++11 features by default... no

checking whether g++ supports C++11 features with -std=gnu++11... yes

And it builds fine.

Finally, you'll still get the warning about openmp even when you give
the disable flag to configure, but it will build fine.

So, it's free to upgrade to OS X Mavericks or you can install a native
version of g++ as others have documented on the list and it will build
with OpenMP support as well.

Best,

julian

Christopher Blair wrote:
> I just noticed this error in configure:
>
> configure: WARNING: Unable to locate OpenMP library, you should probably
> specify '--disable-openmp'
>
> However, I did specify this (i.e. ./configure --disable-openmp).
>
>
> On Thu, Feb 20, 2014 at 2:18 PM, Christopher Blair <blai...@gmail.com
> <mailto:blai...@gmail.com>> wrote:
>
> HI Julian,
>
> I am building Stacks on OSX 10.8.4.
>
> Typing g++ --version yields:
>
> i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 (Based on Apple Inc.
> build 5658) (LLVM build 2336.11.00)
> Copyright (C) 2007 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions. There
> is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
> PURPOSE.
>
> After running configure I get the following output:
>

[Christopher Blair]

HI Julian, 

I would rather not install Mavericks if possible because of the many issues I have heard about. From reading the threads I was under the impression that g++ was required only if you want to run Stacks in parallel? 

If this is not the case, should I follow directions in this thread to delete my old compiler and install a new one (i.e. step 3)?

https://groups.google.com/forum/#!searchin/stacks-users/g$2B$2B/stacks-users/tbdDtpzQ4JI/tIw-OXcOibkJ

Chris

[Christopher Blair]

Julian, 

I installed gcc-4.8 on my system, which let me install Stacks 1.12 with no issues. I then tried to run pstacks with a sam file and no longer receive the Abort trap error. Thanks!

Chris