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
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'm trying to open an Abaqus GUI on a cluster. So far I've done this using:
I log in on the cluster using MobaXterm
I start a job using:
qsub -I - X -l nodes=1:ppn=1,mem=32gb
I load Abaqus:
module load abaqus/2019
I call the Abaqus GUI:
abaqus cae
As said, this used to work until the day before yesterday. Now I get the following error when I try this:
Abaqus License Manager checked out the following license:
"cae" from Flexnet server the_server
<15 out of 30 licenses remain available>
FXApp::openDisplay: unable to open display :0.0
Fatal Exception: connect
Abaqus Error: Abaqus/CAE Kernel excited with an error
I've looked around and it seems that somebody else had a very similar problem here, with solutions being posted here (see the figure below). However, the solution specifies '/etc/NetworkManager/nm-system-settings.conf', a file I cannot seem to find (I'm using Windows).
Does anybody know how to solve this issue?
The problem was that
qsub -I - X -l nodes=1:ppn=1,mem=32gb
should be
qsub -I -X -l nodes=1:ppn=1,mem=32gb
(removing the space between - and X)
I have been trying to pip install psycopg2 for some time now
I have just updated to python 3.7.4, before this problem started.
To set my path to a specific python version I used the code below.
nano .bash_profile
I thought that it would now be easy for my system to identify the path of the newly installed python, as to enable it to install psycopg2. Then the below started happening.
The second line of system terminal or python terminal is now always showing:
-bash: zzzzz#: command not found on my terminal
No matter what I type on my terminal, I am always getting command not found
This would mean you literally have "zzzzz" somewhere in the bash_profile. Bash is seeing "zzzzz" as just another command to run at startup like the rest of the profile script. As there is nothing in your PATH matching that string, bash reports the issue back to you.
Either remove the extra line from your .bash_profile. OR use a terribly wasteful work-around!
ln -s /bin/true /bin/zzzzz
This will create a symbolic link to the "true" binary (all it ever does is return true) from zzzzz. Now bash can find zzzzz and run it during start up, which does nothing. No more error and an absurd work around. You should fix the file.
I want to profile my Perl code by using Devel::DProf.
when I am running the profiler like
perl5.8 -d:DProf abc.pl # default version of Perl in my PC (Solaris) is 5.003
then it produces the tmon.out file in the current directory, but when I run
dprofpp
then it is not undertanding the command and giving error like command not found.
I know Devel::DProf - a DEPRECATED Perl code profiler, and should use Devel::NYTProf but just want to know why it is giving such an error, may be I am missing something.
How can I solve this?
Find out where you installed dprofpp and ensure that the directory is in your PATH, or call it with the full path.
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.