I'm trying to circumvent using MEX to link to MATLAB and just call a binary using "!" as in:
>> !template_image_rigid -args ....
template_image_rigid: /opt/MatlabR2010a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib/libboost_program_options.so.1.40.0)
template_image_rigid: /opt/MatlabR2010a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib/libdirac_encoder.so.0)
Is there a way to easily fix this dynamic link issue from within MATLAB? I know I can recompile the source with MATLAB and use a MEX call, but since it takes a while to run the solver I just want to run it as shell command and import text data later into MATLAB.
If it helps, the source & CMakeLists.txt can be found here: https://github.com/pkarasev3/nlmagick/tree/master/samples
Grr, community = fail.
Diagnoising: do !gnome-terminal from within matlab and look at "env":
env | grep Matlab
which gives
XKEYSYMDB=/opt/MatlabR2010a/X11/app-defaults/XKeysymDB
MATLABPATH=/opt/MatlabR2010a/toolbox/local
XAPPLRESDIR=/opt/MatlabR2010a/X11/app-defaults
LD_LIBRARY_PATH=/opt/MatlabR2010a/sys/os/glnxa64:/opt/MatlabR2010a/bin/glnxa64:/opt/MatlabR2010a/extern/lib/glnxa64:/opt/MatlabR2010a/runtime/glnxa64:/opt/MatlabR2010a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/opt/MatlabR2010a/sys/java/jre/glnxa64/jre/lib/a md64/server:/opt/MatlabR2010a/sys/java/jre/glnxa64/jre/lib/amd64
OSG_LD_LIBRARY_PATH=/opt/MatlabR2010a/sys/openscenegraph/lib/glnxa64
TOOLBOX=/opt/MatlabR2010a/toolbox
XFILESEARCHPATH=/opt/MatlabR2010a/sys/java/jre/glnxa64/jre/lib/locale/%L/%T/%N%S::/usr/dt/app-defaults/%L/Dt
MATLAB=/opt/MatlabR2010a
Ok so the LD_LIBRARY_PATH is bad.
Trick: write a poltergeist script and run it from gnome-terminal, Launch it from Matlab with:
!./hack.sh RunStuffThatLinksElsewhere
where hack.sh is a script with something like:
#!/bin/bash
source ~/.bashrc
export LD_LIBRARY_PATH=''
gnome-terminal --command="${1}"
so an easy test is to try it with "eog", this hack gets around the link issue and lets you run it from within matlab...
Simpler:
setenv('foo',num2str(some_value) )
!LD_LIBRARY_PATH="" && ./my_binary -f $foo
disp('done with external program!')
I solved this problem by replacing the version of libstdc++.so.6 with a newer version from my system (I use ubuntu 12.04).
First find the system version of libstdc++.so.6.
From the command line type:
locate libstdc++.so.6
My system version of libstdc was
/usr/lib/i386-linux-gnu/libstdc++.so.6
Then replace the matlab libstdc version with a link to the system libstdc.
From the command line type (replace [....] with you settings):
cd [matlab_dir]/sys/os/glnx86
mv libstdc++.so.6 libstdc++.so.6-OLD
ln -s [your_system_version_of_libstdc] libstdc++.so.6
I recently ran into the same problem. My solution also uses a poltergeist script like other answers. The script is as follows (poltergeist.sh):
#!/bin/bash
export LD_LIBRARY_PATH=''
eval "$#"
It basically resets the library path and subsequently evaluates the call given by the arguments to the script. From within matlab I then call in this manner:
system([pwd,'/poltergeist.sh echo hello world!']);
The advantage to this approach is that you can dynamically modify the call command within matlab. As far as I know this is not possible using the bang syntax in the currently provided answers.
Related
I get the following error:
Can't load '...\AppData\Local\Temp\par-6e72616f\cache-20221205133501\5743946b.xs.dll' for module GD:
load_file:
The specified module could not be found at <embedded>/DynaLoader.pm line 193.
at <embedded>/PAR/Heavy.pm line 140.
(Line breaks added for readability.)
Here is the file t2.pl:
use GD;
Here is the command to convert it to an exe (I use a batch file that timestamps it):
pp -T 20221205133501 -o t2_20221205133501.exe t2.pl
On my laptop, the exe works, but on a barebones Citrix environment it fails.
My environment:
Strawberry Perl v5.32.1 built for MSWin32-x86-multi-thread-64int
GD v2.73
I know the file is simple, but that one line is enough to cause the crash.
The file it complains about exists and is located where it is looking.
I have looked and is looks like I need to add -m GD, or -l xxx to make it work. I tried adding all the dll files I could find for GD, but failed.
I have a corporate environment so I can't really use anything that depends on external programs not in Windows 10. pp_simple depends on wxpar which I do not have. I have used:
objdump -x C:\Strawberry\perl\vendor\lib\auto\GD\GD.xs.dll | find "DLL"
which got me a list of DLLs, and I did try using them with -l.
From Re: Par with strawberry-Perl
There are likely missing DLLs that need to be added to the pp call
using the --link option.
Finding these manually can be a pain, so have a look at pp_autolink or
pp_simple (the former is mine, but adapted from the latter).
https://github.com/shawnlaffan/perl-pp-autolink
https://www.perlmonks.org/?node_id=1148802
I use the system/unix command on Matlab in order to run an external program via the command line. I want to execute it via an alias define in .zshrc on my computer. Unfortunately, the alias seems to be not available.
Example with ll
on a terminal: which ll gives ll: aliased to ls -lh
on Matlab: unix('ll') gives zsh:1: command not found: ll
I check if I used the right shell: unix('echo $SHELL') gives /usr/local/bin/zsh.
I have add setopt aliases in my .zshrc but it changes nothing. Is it possible to check which startup files is used when you open a non interactive shell?
The ~/.zshrc seems to be not loaded in the non interactive case. The solution consists in loaded aliases and added setopt aliases in ~/.zshenv. See this for instance.
The dexy documentation states than any language may be used. The tutorial use the py filter to run Python file, but I didn't find any filter to run Perl file.
I try to execute a very simple Perl file
I've tried to use the bash or sh filter, but with no luck, and didn't find any execute-or-like filter.
Am I missing something obvious ?
Ok, here are the different solutions I found about this.
1. A perl filter now exist
Ok, Ana is the owner of this project and is very reactive. I asked her the question about dexy and perl on IRC, and tada ! Less than 1 hour later, there was a commit on the repository with perl support.
So, if you just get latest version and install it this way :
git clone https://github.com/dexy/dexy
cd dexy
sudo pip install -e .
You should have a perl filter.
If you want to pass arguments to a script, just use the scriptargs setting.
2. Use a bash script
Another very simple solution is to embed the launch of a perl script into a sh/bash script, and use the sh/shint/bash filter that already exist.
3. Use bash script without additional files
If you fear that the latest solution will makes you add a lot of tiny scripts in your directories, you may use the contents feature of dexy. That way, the required one-liners are defined in dexy.yaml only.
Something like :
- shell-myscript.sh|sh:
- contents: "perl ./perl/myscript.pl --any-parameter"
- perl/myscript.pl
is doing the job just fine for me.
After I setup fish as the main shell chsh -s /usr/local/bin/fish, I've tried to use ls command in MATLAB, but I got the following error:
??? Error using ==> ls at 36
/usr/local/bin/fish: /opt/MATLAB/R2011a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.15'
not found (required by /usr/local/bin/fish)
Someone knows why it happens? My actual solution is to reset bash as the main shell and always run fish to use it.
Matlab uses its own glibc librarires, and it's often a big mess because of that.
You can look at my answer there for one way to solve that:
GLIBCXX not found when compiling vtk example under mex
I am trying to run a Matlab script from Windows command prompt but I can't execute it sometimes. The script runs fine when manually launched. Matlab version is 2011a and Windows is Server 2003 SP2. Details:
Script mytask.m is located inside say E:\Production\Project. This is SAVED on Matlab's path.
When I place mytask.m inside bin folder, it executes fine by the command:
`C:\Program Files\MATLAB\R2011a\bin>matlab -r mytask`
If you delete it and try to access it at its original location, the script doesn't run although Matlab editor window is launched:
`C:\Program Files\MATLAB\R2011a\bin>matlab -r "E:\Production\Project\mytask"
Any suggestions please? Thanks.
The syntax for matlab -r is
matlab -r "statement"
In other words, you need to provide some executable commands as the statement. For example:
matlab -r "run E:\Production\Project\mytask"
However, it seems that matlab does not load the customized paths in this way. If you have some customized paths, you probably have to define them in startup.m and place this startup.m in the directory where you invoke matlab.
I didn't check myself, but if you define E:\Production\Project\ as the path in startup.m, you probably can run matlab -r mytask without problem, as mytask will be recognized as a user function/script.
A simple example of startup.m
path(path, 'E:\Production\Project\');