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Re: [Discuss-gnuradio] Building GNU Radio with previous Boost version

From: David Halls
Subject: Re: [Discuss-gnuradio] Building GNU Radio with previous Boost version
Date: Tue, 1 Sep 2015 11:17:58 +0000

​Dear All,


I have now had success building GNU Radio with previous Boost (1.49) version. Thanks for the help.


First you have to get boost 1.49 to build from source, download from


http://www.boost.org/users/history/version_1_49_0.html


then some edits are required as per


this involves find and replace of TIME_UTC with TIME_UTC_ in a number of files. Just do a find and replace in all of the source code, they are all shown in


https://svn.boost.org/trac/boost/changeset/78802


then do the install to a local directory somewhere...


./boostrap.sh --prefix=PATH_TO_LOCAL_DIRECTORY (i.e. not system folders, do not want to conflict with system boost)

./b2 install


then make GNU Radio with:


cmake -DBOOST_INCLUDEDIR=/PATH_TO_LOCAL_DIRECTORY/include -DBOOST_LIBRARYDIR=/PATH_TO_LOCAL_DIRECTORY​/lib ../


then make, install...


Finally at run-time one must point to the 1.49 libraries when launching GRC. I achieved this by adding the library path to /etc/ld.so.conf, but others may correct me and suggest a more suitable location for that change.


Thanks all for the help.


David


p.s. I will go on to create full documentation about how to call MATLAB shared libraries from GNU Radio, now the boost conflict has been resolved... 


From: David Halls
Sent: 19 August 2015 17:48
To: Marcus Müller; address@hidden
Subject: RE: [Discuss-gnuradio] Building GNU Radio with previous Boost version
 

​Marcus, Nathan, All,


Thanks Marcus I have tried building GNU Radio with Boost 1.49 (that required by MATLAB)


I've made a little progress, but it's slow going. I got the header files (not included with the MATLAB release) by downloading Boost 1.49, and building it and installing it to a home directory (not /usr/...).

cmake seems to run fine with

"cmake -DBOOST_INCLUDEDIR=/home/gnuradio/gnuradio_trlcode/boost_1_49/include -DBOOST_LIBRARYDIR=/usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/glnxa64 ../"

(so I am pointing to my header files for the INCLUDEDIR, and MATLABs libraries for the LIBRARYDIR) 

the output includes positive sounding things like
​
-- Boost version: 1.49.0
-- Found the following Boost libraries:
--   filesystem
--   system
--   unit_test_framework
--   program_options

and

-- Configuring gnuradio-runtime support...
--   Dependency Boost_FOUND = 1

​etc

but when I then try "make VERBOSE=1", there seem to be problems linking volk as pasted below. Can anyone help? Thanks!

David

make VERBOSE=1
/usr/bin/cmake -H/home/gnuradio/gnuradio_build/gnuradio -B/home/gnuradio/gnuradio_build/gnuradio/build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /home/gnuradio/gnuradio_build/gnuradio/build/CMakeFiles /home/gnuradio/gnuradio_build/gnuradio/build/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory `/home/gnuradio/gnuradio_build/gnuradio/build'
make -f volk/lib/CMakeFiles/volk.dir/build.make volk/lib/CMakeFiles/volk.dir/depend
make[2]: Entering directory `/home/gnuradio/gnuradio_build/gnuradio/build'
cd /home/gnuradio/gnuradio_build/gnuradio/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gnuradio/gnuradio_build/gnuradio /home/gnuradio/gnuradio_build/gnuradio/volk/lib /home/gnuradio/gnuradio_build/gnuradio/build /home/gnuradio/gnuradio_build/gnuradio/build/volk/lib /home/gnuradio/gnuradio_build/gnuradio/build/volk/lib/CMakeFiles/volk.dir/DependInfo.cmake --color=
make[2]: Leaving directory `/home/gnuradio/gnuradio_build/gnuradio/build'
make -f volk/lib/CMakeFiles/volk.dir/build.make volk/lib/CMakeFiles/volk.dir/build
make[2]: Entering directory `/home/gnuradio/gnuradio_build/gnuradio/build'
make[2]: Nothing to be done for `volk/lib/CMakeFiles/volk.dir/build'.
make[2]: Leaving directory `/home/gnuradio/gnuradio_build/gnuradio/build'
/usr/bin/cmake -E cmake_progress_report /home/gnuradio/gnuradio_build/gnuradio/build/CMakeFiles  95 96 97 98 99
[  5%] Built target volk
make -f volk/lib/CMakeFiles/test_all.dir/build.make volk/lib/CMakeFiles/test_all.dir/depend
make[2]: Entering directory `/home/gnuradio/gnuradio_build/gnuradio/build'
cd /home/gnuradio/gnuradio_build/gnuradio/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gnuradio/gnuradio_build/gnuradio /home/gnuradio/gnuradio_build/gnuradio/volk/lib /home/gnuradio/gnuradio_build/gnuradio/build /home/gnuradio/gnuradio_build/gnuradio/build/volk/lib /home/gnuradio/gnuradio_build/gnuradio/build/volk/lib/CMakeFiles/test_all.dir/DependInfo.cmake --color=
make[2]: Leaving directory `/home/gnuradio/gnuradio_build/gnuradio/build'
make -f volk/lib/CMakeFiles/test_all.dir/build.make volk/lib/CMakeFiles/test_all.dir/build
make[2]: Entering directory `/home/gnuradio/gnuradio_build/gnuradio/build'
make[2]: Nothing to be done for `volk/lib/CMakeFiles/test_all.dir/build'.
make[2]: Leaving directory `/home/gnuradio/gnuradio_build/gnuradio/build'
/usr/bin/cmake -E cmake_progress_report /home/gnuradio/gnuradio_build/gnuradio/build/CMakeFiles 
[  5%] Built target test_all
make -f volk/apps/CMakeFiles/volk-config-info.dir/build.make volk/apps/CMakeFiles/volk-config-info.dir/depend
make[2]: Entering directory `/home/gnuradio/gnuradio_build/gnuradio/build'
cd /home/gnuradio/gnuradio_build/gnuradio/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gnuradio/gnuradio_build/gnuradio /home/gnuradio/gnuradio_build/gnuradio/volk/apps /home/gnuradio/gnuradio_build/gnuradio/build /home/gnuradio/gnuradio_build/gnuradio/build/volk/apps /home/gnuradio/gnuradio_build/gnuradio/build/volk/apps/CMakeFiles/volk-config-info.dir/DependInfo.cmake --color=
make[2]: Leaving directory `/home/gnuradio/gnuradio_build/gnuradio/build'
make -f volk/apps/CMakeFiles/volk-config-info.dir/build.make volk/apps/CMakeFiles/volk-config-info.dir/build
make[2]: Entering directory `/home/gnuradio/gnuradio_build/gnuradio/build'
make[2]: Nothing to be done for `volk/apps/CMakeFiles/volk-config-info.dir/build'.
make[2]: Leaving directory `/home/gnuradio/gnuradio_build/gnuradio/build'
/usr/bin/cmake -E cmake_progress_report /home/gnuradio/gnuradio_build/gnuradio/build/CMakeFiles 
[  5%] Built target volk-config-info
make -f volk/apps/CMakeFiles/volk_profile.dir/build.make volk/apps/CMakeFiles/volk_profile.dir/depend
make[2]: Entering directory `/home/gnuradio/gnuradio_build/gnuradio/build'
cd /home/gnuradio/gnuradio_build/gnuradio/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/gnuradio/gnuradio_build/gnuradio /home/gnuradio/gnuradio_build/gnuradio/volk/apps /home/gnuradio/gnuradio_build/gnuradio/build /home/gnuradio/gnuradio_build/gnuradio/build/volk/apps /home/gnuradio/gnuradio_build/gnuradio/build/volk/apps/CMakeFiles/volk_profile.dir/DependInfo.cmake --color=
make[2]: Leaving directory `/home/gnuradio/gnuradio_build/gnuradio/build'
make -f volk/apps/CMakeFiles/volk_profile.dir/build.make volk/apps/CMakeFiles/volk_profile.dir/build
make[2]: Entering directory `/home/gnuradio/gnuradio_build/gnuradio/build'
Linking CXX executable volk_profile
cd /home/gnuradio/gnuradio_build/gnuradio/build/volk/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/volk_profile.dir/link.txt --verbose=1
/usr/bin/c++    -fvisibility=hidden -Wsign-compare -Wall -Wno-uninitialized -O3 -DNDEBUG    CMakeFiles/volk_profile.dir/volk_profile.cc.o CMakeFiles/volk_profile.dir/__/lib/qa_utils.cc.o  -o volk_profile -rdynamic ../lib/libvolk.so.0.0.0 -lboost_filesystem -lboost_system -lboost_unit_test_framework -lboost_program_options -ldl -lorc-0.4 -Wl,-rpath,/home/gnuradio/gnuradio_build/gnuradio/build/volk/lib: 
CMakeFiles/volk_profile.dir/volk_profile.cc.o: In function `main':
volk_profile.cc:(.text.startup+0x613b): undefined reference to `boost::filesystem3::path::wchar_t_codecvt_facet()'
volk_profile.cc:(.text.startup+0x6193): undefined reference to `boost::filesystem3::path::parent_path() const'
volk_profile.cc:(.text.startup+0x61a2): undefined reference to `boost::filesystem3::detail::status(boost::filesystem3::path const&, boost::system::error_code*)'
volk_profile.cc:(.text.startup+0x65b1): undefined reference to `boost::filesystem3::path::parent_path() const'
volk_profile.cc:(.text.startup+0x6613): undefined reference to `boost::filesystem3::path::parent_path() const'
volk_profile.cc:(.text.startup+0x6622): undefined reference to `boost::filesystem3::detail::create_directories(boost::filesystem3::path const&, boost::system::error_code*)'
collect2: error: ld returned 1 exit status
make[2]: *** [volk/apps/volk_profile] Error 1
make[2]: Leaving directory `/home/gnuradio/gnuradio_build/gnuradio/build'
make[1]: *** [volk/apps/CMakeFiles/volk_profile.dir/all] Error 2
make[1]: Leaving directory `/home/gnuradio/gnuradio_build/gnuradio/build'
make: *** [all] Error 2




From: Marcus Müller <address@hidden>
Sent: 17 August 2015 15:22
To: David Halls; address@hidden
Subject: RE: [Discuss-gnuradio] Building GNU Radio with previous Boost version
 
Hi David,

I think we can all agree that the community starting to run at the mention of Matlab is not a good thing - I think there might be frustration behind this flight instinct, so let's try to make this a success story.

I concur with the pretty detailed reply from mathworks; the reason is likely to be the binary/abi mismatch between the boost GNU Radio/your native runtime linker uses and the one that the Matlab library needs.

Now, you should be able to specify the boost that cmake uses when configuring the build process:
cmake -DBOOST_INCLUDEDIR=<matlab-shipped boost includes> -DBOOST_LIBRARY_DIR=<matlab-shipped library dir> ..
Also make sure to specify export LD_LIBRARY_DIR containing the same matlab library dir; otherwise, at runtime your system's boost will get linked in, and that will still result in segfaults.

Maybe there is also the option to statically link the Matlab library before loading it from GNU Radio, instead of doing it the other way around (which is option 2). To me, that sounds more logically sound, since it's Matlab that introduces library dependencies that are incompatible with your system libraries, because otherwise you might run into the same problem for other libraries that both Mathworks code and GNU Radio use and Mathworks ships their own version with. However, I don't know if that would even be possible, as I don't have Matlab around to test it.

All in all, I also like option 3 from Mathwork's reply, though I don't think the .mat method would work well for streaming like GNU Radio does;
you should be able to just open a file (fopen) and read from it (fread) in a loop, so that you can get what a file source in GNU Radio writes to a FIFO; basically, as Matlab pseudocode:

infile = fopen("/tmp/fifo_in");
outfile = fopen("/tmp/fifo_out", "w");
while 1
    datain = fread(infile, 1000, "float32");
    dataout = do_some_processing(datain);
    fwrite(outfile, dataout, "float32");
end

you'd have to

mkfifo /tmp/fifo_in /tmp/fifo_out

first and then use file sink/source to write/read to/from these.

Of course, a socket- or IPC-based solution might be cleaner, but I don't know much popular matlab tools that make it easy to write "real-world compatible" Matlab code (I think that lack of knowledge of high-quality well-known libraries might be what leads people to run away as soon as you mention Matlab).

Best regards,
Marcus


Am 17. August 2015 12:27:25 MESZ, schrieb David Halls <address@hidden>:

Hi Marcus,


I am calling MATLAB compiled code from within GNURadio C++ blocks. MATLAB compiled code uses a specific version of Boost, and they are still using 1.49, even with their latest release. I get a the trace below when I try to run the MATLAB code on newer GNURadio/Ubuntu/Boost though it works fine on my old (ancient) GNURadio/Ubuntu/Boost​ build where the Boost versions match. (Also included is MathWorks take on it).


I was reticent to give all the details because previous MATLAB questions have left the community running for the hills, saying I should write everything directly in C++ etc, but there are lots of reasons we can't do this, for now!


Thanks,


David





(python2:16446): IBUS-WARNING **: The owner of /home/gnuradio/.config/ibus/bus is not root!
Using Volk machine: avx_64_mmx_orc
Attempting to initialise the MCR application...
Attempting to initialise the libdla application...

------------------------------------------------------------------------
       Segmentation violation detected at Tue Jun 23 15:25:36 2015
------------------------------------------------------------------------

Configuration:
  Crash Decoding     : Disabled
  Default Encoding   : UTF-8
  GNU C Library      : 2.19 stable
  MATLAB Architecture: glnxa64
  MATLAB Root        : /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81
  MATLAB Version     : 8.1.0.604 (R2013a)
  Operating System   : Linux 3.13.0-32-generic #57-Ubuntu SMP Tue Jul 15 03:51:08 UTC 2014 x86_64
  Processor ID       : x86 Family 6 Model 60 Stepping 3, GenuineIntel

Fault Count: 1


Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX = 00000000049dd7f0  RBX = 00000000049dd820
  RCX = 0000000000000002  RDX = 0000000000000000
  RSP = 00007fff0de311e0  RBP = 0000000000000001
  RSI = 0000000000000000  RDI = 0000000000000001

   R8 = 00000000049dd820   R9 = 0000000000000000
  R10 = 000000000000069c  R11 = a3d70a3d70a3d70b
  R12 = 00000000ffffffff  R13 = 00007fff0de31450
  R14 = 000000000494e448  R15 = 000000000494e2f8

  RIP = 00007f1ee264a414  EFL = 0000000000010202

   CS = 0033   FS = 0000   GS = 0000

Stack Trace (from fault):
[  0] 0x00007f1ee264a414              /lib/x86_64-linux-gnu/libpthread.so.0+00042004 pthread_mutex_lock+00000004
[  1] 0x00007f1ede8b37fa /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.54.0+00047098 _ZN5boost6thread9interruptEv+00000074
[  2] 0x00007f1e9cec7b25 /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/glnxa64/libmwdservices.so+00146213
[  3] 0x00007f1e9ced7c76 /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/glnxa64/libmwdservices.so+00212086 _ZN10dsLockFileD1Ev+00000038
[  4] 0x00007f1e9cece93a /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/glnxa64/libmwdservices.so+00174394 _ZN5boost6detail17sp_counted_impl_pI10dsLockFileE7disposeEv+00000026
[  5] 0x00007f1ebc46e379 /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/glnxa64/libmat.so+00091001 _ZN5boost6detail12shared_countD1Ev+00000073
[  6] 0x00007f1e9ced3d40 /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/glnxa64/libmwdservices.so+00195904 _ZN24dsDirectoryExclusiveLock7releaseERKN5boost10posix_time13time_durationE+00000176
[  7] 0x00007f1e9ced3d9f /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/glnxa64/libmwdservices.so+00195999 _ZN24dsDirectoryExclusiveLock7releaseEv+00000031
[  8] 0x00007f1e9cecdf8c /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/glnxa64/libmwdservices.so+00171916 _ZN24dsDirectoryReadWriteLock8ReadLock4Impl7acquireERKN5boost10posix_time13time_durationEb+00001276
[  9] 0x00007f1e9cece3e6 /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/glnxa64/libmwdservices.so+00173030 _ZN24dsDirectoryReadWriteLock8ReadLock7acquireEb+00000038
[ 10] 0x00007f1e8d45c602 /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/glnxa64/libmwmclmcr.so+01230338
[ 11] 0x00007f1e8d3ee718 /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/glnxa64/libmwmclmcr.so+00780056
[ 12] 0x00007f1e8d3ef2d6 /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/glnxa64/libmwmclmcr.so+00783062 _ZN5boost6detail8function21function_obj_invoker0INS_3_bi6bind_tINS_10shared_ptrI21mclExtractedComponentEEPFS7_N6mclmcr12CtfExtractorEENS3_5list1INS3_5valueIS9_EEEEEES7_E6invokeERNS1_15function_bufferE+00000054
[ 13] 0x00007f1e8d42df95 /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/glnxa64/libmwmclmcr.so+01040277 _Z30mclInitializeComponentInstanceRKN5boost8functionIFiPKcEEES6_NS_9function0INS_10shared_ptrI21mclExtractedComponentEEEE+00000389
[ 14] 0x00007f1e8d3f9c0d /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/glnxa64/libmwmclmcr.so+00826381 mclInitializeComponentInstanceEmbedded+00000573
[ 15] 0x00007f1ec645c763 /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/runtime/glnxa64/libmwmclmcrrt.so.8.1+00124771 mclInitializeComponentInstanceEmbedded_proxy+00000067
[ 16] 0x00007f1ec5c2c1eb /home/gnuradio/gnuradio_trlcode/gr-trl/lib/libdla.so+00008683 libdlaInitializeWithHandlers+00000107
[ 17] 0x00007f1ec5c2c22b /home/gnuradio/gnuradio_trlcode/gr-trl/lib/libdla.so+00008747 libdlaInitialize+00000023
[ 18] 0x00007f1ec6c3393d                  /usr/local/lib/libgnuradio-trl.so+00493885
[ 19] 0x00007f1ec6c33e08                  /usr/local/lib/libgnuradio-trl.so+00495112 _ZN2gr3trl5dla_r4makeEiiibbfb+00000104
[ 20] 0x00007f1ec70bb740 /usr/local/lib/python2.7/dist-packages/trl/_trl_swig.so+02164544
[ 21] 0x000000000052c6d5                                   /usr/bin/python2+01230549 PyEval_EvalFrameEx+00001061
[ 22] 0x000000000055c594                                   /usr/bin/python2+01426836 PyEval_EvalCodeEx+00000676
[ 23] 0x000000000052ca8d                                   /usr/bin/python2+01231501 PyEval_EvalFrameEx+00002013
[ 24] 0x000000000056d0aa                                   /usr/bin/python2+01495210
[ 25] 0x00000000004d9854                                   /usr/bin/python2+00890964
[ 26] 0x00000000004d8379                                   /usr/bin/python2+00885625
[ 27] 0x00000000004f5d0b                                   /usr/bin/python2+01006859
[ 28] 0x000000000052cc20                                   /usr/bin/python2+01231904 PyEval_EvalFrameEx+00002416
[ 29] 0x000000000055c594                                   /usr/bin/python2+01426836 PyEval_EvalCodeEx+00000676
[ 30] 0x00000000005b7392                                   /usr/bin/python2+01799058 PyEval_EvalCode+00000050
[ 31] 0x0000000000469663                                   /usr/bin/python2+00431715
[ 32] 0x00000000004699e3                                   /usr/bin/python2+00432611 PyRun_FileExFlags+00000146
[ 33] 0x0000000000469f1c                                   /usr/bin/python2+00433948 PyRun_SimpleFileExFlags+00000750
[ 34] 0x000000000046ab81                                   /usr/bin/python2+00437121 Py_Main+00002910
[ 35] 0x00007f1ee229cec5                    /lib/x86_64-linux-gnu/libc.so.6+00138949 __libc_start_main+00000245
[ 36] 0x000000000057497e                                   /usr/bin/python2+01526142


If this problem is reproducible, please submit a Service Request via:

A technical support engineer might contact you with further information.

Thank you for your help.** This crash report has been saved to disk as /home/gnuradio/matlab_crash_dump.16446-1 **



MATLAB is exiting because of fatal error

>>> Done​



"The stack trace strongly suggests that the crash is related to a Boost library version conflict. MATLAB R2013a/MCR v8.1 includes and depends on Boost 1.49 libraries. In the stack trace we see that in practice your system's Boost 1.54 libraries are being accessed however.

These things may occur if you load a MATLAB Compiler Shared Library into an application which is already making use of this system Boost library.

There are no quick/easy workarounds for such issues other than:

1. Making sure that all components involved make use of the same Boost library versions, or

2. Making sure that the components which require Boost statically link against the Boost version which they prefer, or

3. Separating the different components which require Boost into separate applications.

In further detail:

Option 1: It looks like you are making use of GNU Radio from Python, I do believe that GNU Radio depends on Boost. You may be able to (re)compile GNU Radio to make it use Boost 1.49 and where you even specifically link it to the Boost libraries shipped with the MCR (these can be found in the bin/glnxa64 directory).

Option 2: If GNU Radio specifically requires a different Boost version you may be able to recompile it and statically link it against this version.

Option 3: Instead of compiling your MATLAB Code into a Shared Library, compile it into a standalone application which you can launch from your Python process. This separate standalone should be able to use its own Boost libraries without problems then. There are Python libraries which can read and write MAT-files so you can relatively efficiently pass in- and outputs from and to that standalone application through MAT-files."



From: discuss-gnuradio-bounces+address@hidden <discuss-gnuradio-bounces+address@hidden> on behalf of Marcus Müller <address@hidden>
Sent: 14 August 2015 17:59
To: address@hidden
Subject: Re: [Discuss-gnuradio] Building GNU Radio with previous Boost version
 
Hi David,

boost > 1.35 should work, but 1.49 is, if I remember correctly, an especially buggy version, especially in Ubuntu.
I guess you wouldn't ask if there wasn't a problem, so maybe you want to elaborate?

Best regards,
Marcus

On 08/14/2015 06:00 PM, David Halls wrote:

​Hi guys,


For a number of complicated reasons I would like to build GNU Radio with an older version of Boost. Specifically 1.49.


Thanks,


David



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