Issue with using the system-command - matlab

when I use in a terminal session
curl -help
I get the help list. When I use in MATLAB
system ('curl -help')
I get the error:
System Lookup error, curl : undefined symbol:curl_url_cleanup. Linux is Fedora based Solus 4.0
In my understanding the system command should work like this. How can I get the help file?

MATLAB modifies the LD_LIBRARY_PATH environment variable, so that its own libraries can be found. However, MATLAB comes with tons of external libraries, and usually these are older versions.
So it happens at times that a command executed through system links to a version of a library that comes with MATLAB, rather than the one that comes with the OS.
The solution is to execute the command in a "clean environment", such as the one provided by env -i:
system('env -i curl -help')

Related

cross-compile postgresql for ARM Sitara AM335x

I'm having trouble cross compiling PostgreSQL for my TI Sitara AM335x EVM SK. My host system is an i386 machine running Ubuntu 12.04.
My application is written in C++ using Qt. When I try and compile, I get the error that libpq.so is incompatible. I believe this is because the cross compiler is trying to use the host libpq.so instead of one for the target system (which as I have found out, doesn't exist).
I've downloaded the source for PostgreSQL with the intention of cross compiling that in order to give me the libpq.so library that will be compatible with my target system, however there is virtually no information on how to do this.
I have tried using the CC argument with the configure file to change my compiler to the following: CC=/home/tim/ti-sdk-am335x-evm-06.00.00.00/linux-devkit/sysroots/i686-arago-linux/usr/bin/arm-linux-gnueabihf-gcc but the configure script gives me this error: configure: error: cannot run C compiled programs. If you meant to cross compile, use --host.
The configure file makes a small reference to the --host option, but the only information in the file that I could find is in reference to mingw and windows, which isn't what I want.
I've done some quick searching through the configure file, and it references the --host option, but with no explanation of what is a valid host. I'm assuming that with --host option there will be an associated --target.
What arguments can I give the configure script so that it will cross compile with the correct compiler to generate a library that my target device can use? Are there any resources out there that I haven't found in regards to how the --host/--target works or how to use them?
OK, so after fiddling around for a little while, I think I was actually able to cross compile PostgreSQL and answer my own question.
Before I went any further, I had realized I had forgotten to add the path to my cross compiler to the PATH environment variable. I used the command export PATH=/path/to/cross/compiler:$PATH to insert the compiler path to the PATH environment variable.
Next, I did some experimenting with the --host option. To start off with I tried using ./configure --host=arm-linux-gnueabihf and running the configure script. The configure script seemed to accept this as the host argument. I then went to the next step of running the makefile. Running this makefile resulted in errors being generated. The errors were selected processor does not support Thumb mode. I did a quick search to see what information I could find about this error and came to this webpage: http://www.postgresql.org/message-id/E1Ra1sk-0000Pq-EL#wrigleys.postgresql.org.
This webpage gave me a bit more information since it seemed like the person was trying to do something very similar to me. One of the responders to the post mentioned that --disable-spinlocks is intended for processors that aren't supported by default by PostgreSQL. I emulated the arguments that were used in the website listed above and used the command: ./configure --host=arm-linux CC=arm-linux-gnueabihf-gcc AR=arm-linux-gnueabihf-ar CPP=arm-linux-gnueabihf-cpp --without-readline --without-zlib --disable-spinlocks to generate my makefile. This makefile actually generated all of the files, including the libpq.so library file I was needing.
Hope this helps somebody else in the future!

Calling pdftops does not work in Matlab

I want to use the export_fig package for Matlab. At one point this worked, but now it's broken. The error occurs here:
>> system('pdftops -h')
dyld: Library not loaded: /opt/local/lib/libtiff.5.dylib
Referenced from: /opt/local/bin/pdftops
Reason: Incompatible library version: pdftops requires version 8.0.0 or later, but libtiff.5.dylib provides version 6.0.0
pdftops -h: Trace/breakpoint trap
But when I call pdftops from my own bash terminal everything works fine. I suppose it must be because Matlab has some bad library paths or something, but I don't know where to go from here?
Some relevant environmental vars used by matlab:
>> system('env')
SHELL=/bin/bash
OSG_LD_LIBRARY_PATH=/Applications/MATLAB_R2013b.app/sys/openscenegraph/lib/maci64
PATH=/usr/bin:/bin:/usr/sbin:/sbin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/texbin
__CHECKFIX1436934=1
XFILESEARCHPATH=/Applications/MATLAB_R2013b.app/sys/java/jre/maci64/jre/lib/locale/%L/%T/%N%S:
DYLD_FRAMEWORK_PATH=/Applications/MATLAB_R2013b.app/sys/os/maci64:/Applications/MATLAB_R2013b.app/bin/maci64/../../Contents/MacOS:/Applications/MATLAB_R2013b.app/bin/maci64:/Applications/MATLAB_R2013b.app/extern/lib/maci64:/Applications/MATLAB_R2013b.app/sys/java/jre/maci64/jre/lib/./native_threads:/Applications/MATLAB_R2013b.app/sys/java/jre/maci64/jre/lib/./server:/Applications/MATLAB_R2013b.app/sys/java/jre/maci64/jre/lib/./lib/jli
SHLVL=1
__KMP_REGISTERED_LIB_33586=0x124404710-cafeb339-libiomp5.dylib
DYLD_LIBRARY_PATH=/Applications/MATLAB_R2013b.app/sys/os/maci64:/Applications/MATLAB_R2013b.app/bin/maci64/../../Contents/MacOS:/Applications/MATLAB_R2013b.app/bin/maci64:/Applications/MATLAB_R2013b.app/extern/lib/maci64:/Applications/MATLAB_R2013b.app/sys/java/jre/maci64/jre/lib/./native_threads:/Applications/MATLAB_R2013b.app/sys/java/jre/maci64/jre/lib/./server:/Applications/MATLAB_R2013b.app/sys/java/jre/maci64/jre/lib/./lib/jli
If you take a look at the error message, MATLAB uses libtiff to call pdftops, but only has version 6.0.0. It says it needs version 8.0.0 or later. There has been a case where this happened before here on StackOverflow. Someone was trying to install mexopencv and has encountered the same error that you're talking about: Compiling mexopencv in OS X 10.9 with Xcode 5 and Matlab R2013b
Though this is unrelated to what you're doing, they encountered the libtiff error that you speak of. They provide two solutions how to fix this error:
Go into MATLAB's root directory, then go bin/os directory where os is the directory of the operating system you are using (in my case, it's maci64). To get into the root directory, in the command prompt do this: cd/(matlabroot). Once you're here, locate the libtiff.5.dylib file and rename it to something like libtiff.5.dylib.bak so that the libtiff libraries that are used are the ones that are default to your system rather than what MATLAB is using internally in the program.
Force MATLAB to point to the library that is part of the system rather than using the one built into MATLAB. As such, in MATLAB's command prompt, run this command:
setenv('DYLD_INSERT_LIBRARIES','/opt/local/lib/libtiff.5.dylib');
Once you do this, you may get further errors that are similar but are with other libraries. As such, you need to keep appending these libraries in the second parameter of setenv and colon-delimiting them until you resolve the issues. You need to make sure that you're pointing to the ones on your system rather than the ones installed with MATLAB. In your case, you have to do:
setenv('DYLD_INSERT_LIBRARIES', ...
'/opt/local/lib/libtiff.5.dylib:/opt/local/lib/l‌​ibcurl.4.dylib');
Glad this helped!

memory command is not available even after compiled with TCL_MEM_DEBUG flag

I have memory related problem in my application on solaris9 environment where Tcl_DeleteInterp() function calls lot of free() and mutex_unlock() functions. To debug the problem i followed the below steps to compile tcl on solaris server (with TCL_MEM_DEBUG flag) but still i couldn't use the 'memory' command in my interpreter.
Ran configure script on server (./configure –prefix=<directory needs to be installed> --enable-symbols=mem)
Make clean all
Make install (tcl libraries and tlcsh exe is copied to the path specified in step1)
Compilation generated two libraries (libtcl8.4g.so and libtclstub8.4g.a), I copied libtcl8.4g.so as libtcl8.4.so to my app
Copied tcl8.4 directory as well.
I also copied the tclsh8.4 to $PROVHOME/bin and created soft link as tclsh-> tclsh8.4.
From my application i linked the debug symbol enabled libraries to the place where exactly i created the Tcl interpreter.
Initialized the Tcl interpreter to using Tcl_InitMemory() function (so that the memory command will be registered in the supplied(arg) interpreter.
When i used the interpreter exe (tclsh) separately i could execute the memory command, but when i used the same exe on my application its not working. Can someone help me what could be the possible reason for this problem ?
Also help me how can i cross verify the libraries that they are compiled with TCL_MEM_DEBUG flag.
Will the Tcl source code tar file contain Solaris directory where i have to build the libraries or should i use the unix source code for solaris platform as well ?
Thanks
Are you using [mem] interactively (which does expansion of unambiguous short command names) and forgetting to use the full name ([memory]) in your scripts?
You're using Tcl embedded in your code? You need to call Tcl_InitMemory (passing in the handle to the interpreter where you want the memory command created) after creation of the interpreter and before you run user scripts, i.e., straight after the Tcl_CreateInterp gives you the handle (which should in turn come after the Tcl_FindExecutable call that initializes the shared parts of the library).
You must also make sure that everything is built with that flag set so that the correct memory allocation APIs are used in both your code when it integrates with Tcl, and you must make sure that you are linking against the debugging build. It's probably the linking that has gone wrong, but I've not done that level of development on Solaris for many years.
I think you'll find that “Getting a list of used libraries by a running process (unix)” is relevant to your problems.

Can't load 'C:/strawberry/perl/site/lib/auto/XML/LibXML/LibXML.dll' for module XML::LibXML

I have downloaded strawberry PERL and writing one application with CGI Perl Apache on Winxp sp3).
One of the libraries (written by someone else) which I using uses XML::LibXML. When i load the page it gives Internal Server Error. From Apache error log i can see this error:
Can't load 'C:/strawberry/perl/site/lib/auto/XML/LibXML/LibXML.dll' for module XML::LibXML: load_file:The specified module could not be found at C:/strawberry/perl/lib/DynaLoader.pm line 190.
C:/strawberry/perl/site/lib/auto/XML/LibXML/LibXML.dll exists with all permissions.
Also this library works properly on Linux. My application also works fine if I remove all code that needs LibXML.
Can anyone tell me when can be possible issue here.
If you peek into the source for DynaLoader you'll find
Many dynamic extension loading problems will appear to come from
this section of code: XYZ failed at line 123 of DynaLoader.pm.
Often these errors are actually occurring in the initialisation
C code of the extension XS file. Perl reports the error as being
in this perl code simply because this was the last perl code
it executed.
You should have also gotten (but may not have noticed) the following dialog, which provides a more accurate error message:
The problem isn't that perl can't find LibXML.dll; it's that LibXML.dll can't find the real libxml. (The former is just a wrapper that provides Perl bindings for the latter.) To fix that you need to ensure that Strawberry Perl's c\bin folder is in your PATH. In your case, that would be C:\strawberry\c\bin.
You might have to check the environment variable settings in the windows,
make sure that the installation path of the module is present in the PATH variable.
The reason it works in linux is that make files usually set the environment variables for you in linux in windows it may not have set properly.
For eg;
go to Control Panel\System and Security\System click change settings then advanced tab in user variable section see if there is a variable called perl5lib.
if not create an new perl5lib variable and add the path of your library ( usuall C:\Perl\site\lib but may be different in your case)
I had the same issue after installing Strawberry perl. It was working fine when I run the script from server, but not remotely from a automation tool. The issue was because of the Environment variables not updated when we run it remotely. So I did server reboot, which resolved the issue.
I encountered the same problem recently, in my case it was not related to PATH variable (it was already correct). The thing is I was executing my script from Git Bash console and as it turned out git-bash perl was being used instead of Strawberry (see git-bash perl should not be first in path). Switching to standard Windows CMD terminal helped.

Runtime error for MCC compiled program using parfor

I have problems running a program compiled with MCC that uses parfor. The non-compiled .m version works (no bug). When I run the compiled version, I get
"distcomp.remoteparfor" is undefined. I believe I exactly have the error described in
the following link.
http://www.mathworks.com/support/solutions/en/data/1-PAHWE/index.html?product=CO&solution=1-PAHWE
However, since MCR is not installed on my machine (got Matlab and MCC),
I am wondering what the pathes $APPNAME_mcr/java/jar/toolbox and
$MCR/MATLAB Component Runtime/v70/java/jar/toolbox correspond to. I found
the distcomp.jar file in C:\Program Files\MATLAB\R2011b\java\jar\toolbox, but I don't know where to put it since see any path corresponding to $MCR/MATLAB Component Runtime/v70/java/jar/toolbox since MCR is not installed.
Thanks a lot!
Fred
No need to install the MCR if you are simply trying to run the application on the same machine that has MATLAB. The question to ask is, HOW are you launching the compiled application? From a DOS command window? From within MATLAB using the SYSTEM command?
If you are launching the application from a DOS / UNIX command line, then the important thing to keep in mind is that the MATLAB binaries need to be on your system path i.e. just make sure:
$MATLABROOT\bin\$ARCH
is on your system path. Where $MATLABROOT is the matlab installation folder, and $ARCH is your system architecture. For example:
c:\work\matlab\bin\win64
on my machine since my installation folder which contains MATLAB is:
c:\work
and i am on a win64 machine.
The problem is solved. The solution is to make the program
a function instead of a script :
http://www.mathworks.com/matlabcentral/answers/22825-parfor-errors-when-file-is-compiled