install problem on Mac running OS 10.10.5

[mcg...@gmail.com]

I'm new to the program and trying to install Mac version 2.5.2.21. I have loaded gcc version 5.0 but I still get the following error. I suspect that this is a simple path or permissions issue but could use some guidance.

Thanks!

Jim

dyld: Symbol not found: __ZTTNSt7__cxx1118basic_stringstreamIcSt11char_traitsIcESaIcEEE
Referenced from: /Applications/fsc_mac64/./fsc25
Expected in: /usr/local/lib/libstdc++.6.dylib
in /Applications/fsc_mac64/./fsc25
Trace/BPT trap: 5

[Anne-Laure Ferchaud]

Hi Jim,

Have you tried to install a recent version of gcc, as sugggested on fastsimocal website ? see below

It should solve your problem about the stdc++.6.dylib library...

Anne-Laure

"
I have realized (thanks to MelissaWilson Sayre) that the plain version of fsc25 will not run on mac osX unless you have installed a recent version of gcc.

This is because fsc25 is multithreaded and it uses intel's libraries based on openMP, which are not distributed anymore with recent versions of mac OSX.

So to be able to run fsc25 on your mac, you need to first install a recent version of gcc.

To do so, follow these steps:

1. Download gcc-5.1-bin.tar.gz
2. Open a terminal
   
3. cd to the download folder
4. Extract the tar archive with the command 
   gunzip gcc-5.1-bin.tar.gz
5. Install gcc ver 5.1 in /usr/local with the command
   sudo tar -xvf gcc-5.1-bin.tar -C
   

"

[mcg...@gmail.com]

Yes, I loaded gcc-5.0 but I continue to get the same error. I would not be surprised if the compiler is still the problem. Perhaps I need an older gcc compiler for multithreading?

[mcg...@gmail.com]

OK, looks like no one on this user group can help me solve my installation problem. I've spent hours trying to figure out how to resolve a dynamic library issue. Lots of people dealing with other software run into similar dynamic library issues but they are usually writing their own code and can localize the problematic coding issues (usually , but the fixes when posted are not clearly transferable to my situation. Hopefully, I'm the only person who has encountered such a problem and I can chalk it up to 'bad luck.'

Just to restate the problem - I downloaded the mac64 version of fastsimcoal. Because it would not execute and following advice on the software website, I loaded the latest gcc compiler (gcc 5.0.0 20141005). Following advice on-line, I did not set this as my default compiler, but its in my path. I'm no programmer, but it is difficult for me to understand why having the gcc compiler matters when the program is distributed pre-compiled. In any event, loading gcc did not solve my problem.

When I attempt to execute the program, I get the following error string.

dyld: Symbol not found: __ZTTNSt7__cxx1118basic_stringstreamIcSt11char_traitsIcESaIcEEE
Referenced from: /Applications/fsc_mac64/./fsc25
Expected in: /usr/local/lib/libstdc++.6.dylib
in /Applications/fsc_mac64/./fsc25
Trace/BPT trap: 5

Sadly, I'm in over my head with this error. It could have something to do with setting symbolic links, but I'm not sure how I would implement this here. If anyone stumbles across this post and has a suggestion to resolve this issue, I'd be grateful for advice. I'd really like to try fastsimcoal.

Jim

[Laurent Excoffier]

try to download gcc 5.1 or 5.2, not 5.0

laurent

[Andrea Thomaz]

Hi!

Im having exactly the same issue as reported above and Im wondering if somebody was able to figure it out.
I already downloaded the gcc 5.0 (link from fastsimcoal website), gcc 5.1, 5.2 and 5.3 and still does not work.
I already ran fastsimcoal (previous version) in my computer (with previous OS version too) and at that time was working just fine.
Any suggestion would be great!

Thanks

[ma...@bristol.ac.uk]

I had this problem and was unwilling to resolve it as I already had a valid version of gcc5.2 running on my machine, but installed through brew. Instead of breaking both versions, I used "vagrant" (https://www.vagrantup.com) to install a version of ubuntu as a virtual machine, on which execution can be done via "vagrant ssh -c". So the execution pipeline stays mac friendly and you don't need to know a VM was involved.

Its a useful solution to be aware of, though doesn't address the underlying issue.

[Laurent Excoffier]

okay, I'll try to have a look at that installation problem. Just need to get a hand on another mac.

Which version of the OS do you have?

best

laurent

[Andrea Thomaz]

Hi!

The version Im having the issue is the OS El Capitan 10.11.1
For the previous OS versions was working just fine.

Thanks much!
Andrea

[ashotm...@gmail.com]

Hi everyone,

This is the first time I am running arlequin on Mac but seems that I am having the same problem when running arlecore:

dyld: Symbol not found: __ZTTNSt7__cxx1118basic_stringstreamIcSt11char_traitsIcESaIcEEE

Referenced from: /Users/ashotmargaryan/Desktop/mt_arm/arlequin/./arlecoremac_64bit
Expected in: /usr/lib/libstdc++.6.dylib
in /Users/ashotmargaryan/Desktop/mt_arm/arlequin/./arlecoremac_64bit
Trace/BPT trap: 5

the OSX is the same as Andrea's: OS El Capitan 10.11.1

Thanks!.

Ashot

[ashotm...@gmail.com]

Hi everyone,

I probably did something wrong before, but now I've installed gcc-6.0-bin.tar and both arlecore and fastsimcoal2 seem to be working just fine !!!

Best
Ashot

[nkl...@gmail.com]

Hi all,

I have just installed an updated (v6.1.0) gcc in a Mac running OS v.10.11.6 (El Capitan), which I have confirmed via:

Last login: Sat Jul 23 12:30:48 on ttys000
Nathans-MacBook-Pro:~ aurantiacus$ gcc --version
gcc (MacPorts gcc6 6.1.0_0) 6.1.0
Copyright (C) 2016 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.

Yet I am still getting the following dynamic libraries error when I attempt to open fsc25. Any additional recommendations for how this might be resolved would be appreciated.

Last login: Sat Jul 23 12:31:02 on ttys000
/Applications/Phylogenetics/fastsimcoal2.5/fsc25 ; exit;
Nathans-MacBook-Pro:~ aurantiacus$ /Applications/Phylogenetics/fastsimcoal2.5/fsc25 ; exit;
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Applications/Phylogenetics/fastsimcoal2.5/fsc25
Reason: image not found
Trace/BPT trap: 5
logout
Saving session...
...copying shared history...
...saving history...truncating history files...
...completed.

Thanks, Nathan

[sara.d.n...@gmail.com]

Jim, was this ever resolved for you? I'm running into the same error - have now tried every version of gcc from 5.0-6.2, nothing seems to work for me.

[Pablo G Goikoetxea]

HI

It seems fsc25 does not find the openmp installation. My recommendation:

1- Uninstall gcc6.1

2- brew install gcc --without-multilib

3- It seems a symlink to libgomp.1.dylib should be created in /usr/local/lib. In my case it wasn't. Try to find somewhere in /usr/local/Cellar/gcc/6.1.x/lib/gcc/6/ (or similar) the libgomp.1.dylib and copy it to /usr/local/lib/.

4- That solved thet error (other solutions in "stackoverflow.com/questions/35134681/installing-openmp-on-mac-os-x-10-11", but did not work for me)

....

5- Now I am stucked with another error:

yld: Symbol not found: __ZTTNSt7__cxx1118basic_stringstreamIcSt11char_traitsIcESaIcEEE

  Referenced from: /Applications/1-MyApps/abctoolbox2.0/fsc25

  Expected in: /usr/lib/libstdc++.6.dylib

 in /Applications/1-MyApps/abctoolbox2.0/fsc25

(sic, problems started with me unconsciously upgrading to Mac OSX Sierra)

Pablo

[Pablo G Goikoetxea]

Hi

Sorry I have first answered an older post (23/7/16), related to fsc25 not finding libgomp.1.dylib.

As I indicated there, the brew gcc-6.3.0 install doesn't seem to create the necessary symlinks in /usr/local/lib. However, my installation contains the libstdc++.6.dylib symlink in /usr/lib/

As the error reports

------------------------------

yld: Symbol not found: __ZTTNSt7__cxx1118basic_stringstreamIcSt11char_traitsIcESaIcEEE

  Referenced from: /Applications/1-MyApps/abctoolbox2.0/fsc25

  Expected in: /usr/lib/libstdc++.6.dylib

 in /Applications/1-MyApps/abctoolbox2.0/fsc25

-------------------------------

the problem does not seem related to finding the dylib, but seems related to "yld" (whatever it is...). I'm not expert at all... but could it be related to compilation with different libstdc++.X.dylib versions?

Using "Sierra" 10.12.2 and gcc-6.3.0 (brew install, as I also needed the isl library)

Cheers

Pablo

[Pablo G Goikoetxea]

Hi again

Shame on me!!

I pasted the error wrong, without the first d. And this led me to some nonsense..... Sorry to abuse your time.

In any case, my Mac set up has the libstdc++.6.dylib in the correct place, but I get the same error as above when trying to run fsc25.

Pablo

[kcha...@gmail.com]

Hi Pablo,
Did you ever get this figured out? I am getting the same error message when trying to run arlecore, and I am also using Sierra. Tried upgrading to the most recent version of gcc, and I noticed it is specified as being for El Capitan, so I'm wondering if this is the problem. On the verge of just giving up and just using the arlequin GUI on a PC...

[carlos.m...@gmail.com]

I'm running Sierra 10.13.4 and the problem is exactly the same. I wonder whether somebody have resolved this issue.

[raheleh....@gmail.com]

I am running Sierra 10.13.4 too and got the same error!Could you resolve that?
I installed gcc and get the same error:
gcc --version
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 8.1.0 (clang-802.0.42)
Target: x86_64-apple-darwin17.5.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
_________________________________________
But when I type gcc, I get this error:
gcc
clang: error: no input files

[gln.co...@gmail.com]

I have been experiencing the same problem with arlecoremac_64bit. Then I tried to run my analysis using the 32bit architecture of the program, and it runs smoothly.

I have no idea why, but maybe it can help others to get going with their analysis.

Cheers

[Angela McDonnell]

Hi everyone,

I am having issues getting fastsimcoal2 to work on Mac High Sierra. I have updated gcc using xcode and I still get the same error as before:

AngJMcD:fsc26_mac64 angelarein$ ./fsc26 -i test.par -n 100

dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib

  Referenced from: /Applications/fastsimcoal2/fsc26_mac64/./fsc26

  Reason: image not found

Abort trap: 6

I would love to use fastsimcoal2... but I'm kind of at a loss for what to do next. It seems this is a common error, but updating gcc hasn't helped yet. 

Angela

[Luc]

Hello, I also have a similar problem. I have an OS 10.10.5 Yosemite.

I have followed the instructions given in the fastsimcoal webpage for gcc:
Download gcc-7.1-bin.tar.gz

Open a terminal
cd to the download folder
Extract the tar archive with the command

gunzip gcc-7.1-bin.tar.gz

Install gcc ver 5.1 in /usr/local with the command

sudo tar -xvf gcc-7.1-bin.tar -C /.

When executing the last line I get many messages like this:
x usr/local/lib/gcc/x86_64-apple-darwin15.6.0/7.1.0/plugin/include/input.h: Cannot extract through symlink usr/local/lib/gcc

At the end line I get:
tar: Error exit delayed from previous errors.

Could someone please give me any suggestion?. I am new to fastsimcoal and to popgen in general. Thanks very much, Luc

[mountain...@gmail.com]

Hey all,

I'm getting a similar error when trying to run the precompiled version on my Mac (10.13.6):

dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib

Referenced from: /Applications/fastsimcoal2/./fsc26

Reason: image not found
Abort trap: 6

Has anyone figured out how to solve this? I got the error, re-installed gcc with 'brew install gcc' (now version 8.x I believe), and still the same error.

Thanks!

[Anne Riley]

I am having the same or similar problem. I have followed the directions for downloading gcc 7.1 but am getting the following when I try to open fsc26:

 exit;

dyld: Symbol not found: __ZTTNSt7__cxx1118basic_stringstreamIcSt11char_traitsIcESaIcEEE

  Referenced from: /Users/anneriley/Downloads/fsc26_mac64/fsc26
  Expected in: /usr/local/lib/libstdc++.6.dylib
 in /Users/anneriley/Downloads/fsc26_mac64/fsc26
Abort trap: 6

When executing the last line I get several messages that look like this:

x usr/local/include/c++/7.1.0/backward/strstream

and the last line reads:

tar: Error exit delayed from previous errors.

Has anyone found a solution to this problem? It appears it is common. Any suggestions?

Thank you,

Anne