matlab-emacs-discuss

[Matlab-emacs-discuss] How to debug MEX files (C code) from Emacs?

[Dong T. <ti...@me...>]

Hello,

Could anyone provide a pointer on how to debug MEX files from Emacs?
E.g. using gdb?

I am familiar with the procedure of debugging pure c/c++ code or .m code
from Emacs using gdb, but I don't know a good way to debug MEX file coded
in C from Emacs.

Thanks in advance,
Dong

Re: [Matlab-emacs-discuss] How to debug MEX files (C code) from Emacs?

[Eric L. <Eri...@ma...>]

Hi Dong,

You can fire up GDB from within Emacs and "attach" to a process.   Using this to attach to a process running MATLAB inside Emacs' matlab-shell will let you debug through MATLAB code and into your C++ code.

I haven't done this in a few years, and not with Mex (I was debugging MATLAB directly) but I'm guessing the principle is the same.

Eric

-----Original Message-----
From: Dong Tian [mailto:ti...@me...] 
Sent: Wednesday, July 19, 2017 1:56 PM
To: mat...@li...
Subject: [Matlab-emacs-discuss] How to debug MEX files (C code) from Emacs?

Hello,

Could anyone provide a pointer on how to debug MEX files from Emacs?
E.g. using gdb?

I am familiar with the procedure of debugging pure c/c++ code or .m code from Emacs using gdb, but I don't know a good way to debug MEX file coded in C from Emacs.

Thanks in advance,
Dong

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Re: [Matlab-emacs-discuss] How to debug MEX files (C code) from Emacs?

[Dong T. <ti...@me...>]

Hi Eric, all,

Thanks for replying.

It is non-trivial to attach the matlab process to gdb.

Matlab provides a command line option -Dgdb to associate the Matlab process
for gdb debugging. Would it be easier to launch "matlab-shell" with -Dgdb
as option? Maybe your or someone else could put lights on this approach?

Thanks,
Dong

On Wed, Jul 19, 2017 at 09:01:56PM +0000, Eric Ludlam wrote:
> Hi Dong,
> 
> You can fire up GDB from within Emacs and "attach" to a process.   Using this to attach to a process running MATLAB inside Emacs' matlab-shell will let you debug through MATLAB code and into your C++ code.
> 
> I haven't done this in a few years, and not with Mex (I was debugging MATLAB directly) but I'm guessing the principle is the same.
> 
> Eric
> 
> -----Original Message-----
> From: Dong Tian [mailto:ti...@me...] 
> Sent: Wednesday, July 19, 2017 1:56 PM
> To: mat...@li...
> Subject: [Matlab-emacs-discuss] How to debug MEX files (C code) from Emacs?
> 
> Hello,
> 
> Could anyone provide a pointer on how to debug MEX files from Emacs?
> E.g. using gdb?
> 
> I am familiar with the procedure of debugging pure c/c++ code or .m code from Emacs using gdb, but I don't know a good way to debug MEX file coded in C from Emacs.
> 
> Thanks in advance,
> Dong
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________
> Matlab-emacs-discuss mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matlab-emacs-discuss

Re: [Matlab-emacs-discuss] How to debug MEX files (C code) from Emacs?

[Dennis O. <do...@pu...>]

You can use Python as a scripting language in gdb to find the PID of a currently running MATLAB process and attach to it. I remember doing this a while back. The code was something around the lines of:

<code>

# debugging MEX files in emacs on linux

import sys
pythondir = '/usr/share/gcc-6.2.1/python'
sys.path.append(pythondir)

from libstdcxx.v6 import register_libstdcxx_printers
from subprocess import check_output

try:
    register_libstdcxx_printers(None)
except Exception as e:
    pass

# find the PID of the MATLAB process
def get_pid(name):
    return list(map(int, check_output(["pidof", name]).split()))

# set a new breakpoint, deleting any breakpoints referring to the same location
def new_bp(loc):
    bps = gdb.breakpoints()
    if bps:
        for bp in bps:
            if bp.location == loc:
                gdb.execute("d " + str(bp.number))
    # set the dummy breakpoint
    return gdb.Breakpoint(loc)

# attach to the MATLAB process. if gdb attach fails, do
#    sudo sh -c "echo 0 > /proc/sys/kernel/yama/ptrace_scope"
pids = get_pid("MATLAB")
gdb.execute("attach {:d}".format(pids[0]))

<end code>

an alternative approach is to launch matlab from gdb:

<code>

run_matlab = True

if run_matlab:
    # spawn a new MATLAB process
    matlab_dir = "/path/to/MATLAB/R2016b/bin/glnxa64/MATLAB"
    gdb.execute("file " + matlab_dir)

    # set the MATLAB_DEBUG env
    gdb_loc = "/usr/bin/gdb"
    gdb.execute("set environment MATLAB_DEBUG = " + gdb_loc)

    # need to execute this according to
    # https://www.mathworks.com/help/matlab/matlab_external/debugging-on-linux-platforms.html
    gdb.execute("handle SIGSEGV SIGBUS nostop noprint")

    # set the breakpoint at the mexFunction
    mex_Bp = new_bp("mexFunction")

    # run matlab
    gdb.execute("run -nojvm -r debug_encoder -singleCompThread")

<end code>

Dennis

Dong Tian <ti...@me...> writes:

> Hi Eric, all,
>
> Thanks for replying.
>
> It is non-trivial to attach the matlab process to gdb.
>
> Matlab provides a command line option -Dgdb to associate the Matlab process
> for gdb debugging. Would it be easier to launch "matlab-shell" with -Dgdb
> as option? Maybe your or someone else could put lights on this approach?
>
> Thanks,
> Dong
>
> On Wed, Jul 19, 2017 at 09:01:56PM +0000, Eric Ludlam wrote:
>> Hi Dong,
>>
>> You can fire up GDB from within Emacs and "attach" to a process.   Using this to attach to a process running MATLAB inside Emacs' matlab-shell will let you debug through MATLAB code and into your C++ code.
>>
>> I haven't done this in a few years, and not with Mex (I was debugging MATLAB directly) but I'm guessing the principle is the same.
>>
>> Eric
>>
>> -----Original Message-----
>> From: Dong Tian [mailto:ti...@me...]
>> Sent: Wednesday, July 19, 2017 1:56 PM
>> To: mat...@li...
>> Subject: [Matlab-emacs-discuss] How to debug MEX files (C code) from Emacs?
>>
>> Hello,
>>
>> Could anyone provide a pointer on how to debug MEX files from Emacs?
>> E.g. using gdb?
>>
>> I am familiar with the procedure of debugging pure c/c++ code or .m code from Emacs using gdb, but I don't know a good way to debug MEX file coded in C from Emacs.
>>
>> Thanks in advance,
>> Dong
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://secure-web.cisco.com/1ujKNEvoZ9nB-3MswM8yQpeWgC6aSas93lzT8a00GA11SdB5SpQ6CVRIOx-heKXnqKECDVK85FoUunZq98vpNfzj9z-dAEXYdTSCYMo17rGews2sXFe04QVklpkIgysqCMwIaoJQltBgN0vzTKcyy6uH42EmnOZN9d_7d6GI8HTluD2CTM_kIvO0I4ApdEW1uyzzeVHPDe01AEhL8z1lCXCd9Ls5JK37FPBnlqU-vHsqgajNbrh54-xMsjRMjU-khdIzpnhQOzvN53aQbsoH_mYU759kv1n9L6l97WEaazGtUV61gkLrwcRmPqtZUkz2IU_aA6HkROB1JRv1L63MCOuGFFTjdNrbynGp78WL3jRQ/http%3A%2F%2Fsdm.link%2Fslashdot _______________________________________________
>> Matlab-emacs-discuss mailing list
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>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
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Re: [Matlab-emacs-discuss] How to debug MEX files (C code) from Emacs?

[Dong T. <ti...@me...>]

Hi Dennis,

Your input is very useful to me, thanks! The method to attach a running
MATLAB process fits my need better.

After some tests on your scripts, I just realized that a secondary emacs
instance is preferred, given that a first emacs instance is running
matlab-shell.

A bit of summary of what I do:

Put Dennis' first piece of code in matalb-attach.py

Launch the first emacs, using emacsclient, to run matlab-shell.

Launch the second emacs, using emacsclient, to run gdb.
M-x: gdb
gdb -i=mi -x matalb-attach.py
(gdb) break mexFunction

In the first emacs,
(matlab-shell) K>> *some commands to call mexFunction*

In the second emacs,
(gdb) window will grab the control on MATLAB and show the source code of
mexFunction. Make sure using -g when compiling the mex function.

Thank you,
Dong

On Mon, Jul 24, 2017 at 02:12:34PM -0400, Dennis Ogbe wrote:
> You can use Python as a scripting language in gdb to find the PID of a
> currently running MATLAB process and attach to it. I remember doing this
> a while back. The code was something around the lines of:
> 
> <code>
> 
> # debugging MEX files in emacs on linux
> 
> import sys
> pythondir = '/usr/share/gcc-6.2.1/python'
> sys.path.append(pythondir)
> 
> from libstdcxx.v6 import register_libstdcxx_printers
> from subprocess import check_output
> 
> try:
>     register_libstdcxx_printers(None)
> except Exception as e:
>     pass
> 
> # find the PID of the MATLAB process
> def get_pid(name):
>     return list(map(int, check_output(["pidof", name]).split()))
> 
> # set a new breakpoint, deleting any breakpoints referring to the same location
> def new_bp(loc):
>     bps = gdb.breakpoints()
>     if bps:
>         for bp in bps:
>             if bp.location == loc:
>                 gdb.execute("d " + str(bp.number))
>     # set the dummy breakpoint
>     return gdb.Breakpoint(loc)
> 
> # attach to the MATLAB process. if gdb attach fails, do
> #    sudo sh -c "echo 0 > /proc/sys/kernel/yama/ptrace_scope"
> pids = get_pid("MATLAB")
> gdb.execute("attach {:d}".format(pids[0]))
> 
> <end code>
> 
> an alternative approach is to launch matlab from gdb:
> 
> <code>
> 
> run_matlab = True
> 
> if run_matlab:
>     # spawn a new MATLAB process
>     matlab_dir = "/path/to/MATLAB/R2016b/bin/glnxa64/MATLAB"
>     gdb.execute("file " + matlab_dir)
> 
>     # set the MATLAB_DEBUG env
>     gdb_loc = "/usr/bin/gdb"
>     gdb.execute("set environment MATLAB_DEBUG = " + gdb_loc)
> 
>     # need to execute this according to
>     # https://www.mathworks.com/help/matlab/matlab_external/debugging-on-linux-platforms.html
>     gdb.execute("handle SIGSEGV SIGBUS nostop noprint")
> 
>     # set the breakpoint at the mexFunction
>     mex_Bp = new_bp("mexFunction")
> 
>     # run matlab
>     gdb.execute("run -nojvm -r debug_encoder -singleCompThread")
> 
> <end code>
> 
> Dennis
> 
> Dong Tian <ti...@me...> writes:
> 
> > Hi Eric, all,
> >
> > Thanks for replying.
> >
> > It is non-trivial to attach the matlab process to gdb.
> >
> > Matlab provides a command line option -Dgdb to associate the Matlab process
> > for gdb debugging. Would it be easier to launch "matlab-shell" with -Dgdb
> > as option? Maybe your or someone else could put lights on this approach?
> >
> > Thanks,
> > Dong
> >
> > On Wed, Jul 19, 2017 at 09:01:56PM +0000, Eric Ludlam wrote:
> >> Hi Dong,
> >>
> >> You can fire up GDB from within Emacs and "attach" to a process.
> >> Using this to attach to a process running MATLAB inside Emacs'
> >> matlab-shell will let you debug through MATLAB code and into your C++
> >> code.
> >>
> >> I haven't done this in a few years, and not with Mex (I was debugging
> >> MATLAB directly) but I'm guessing the principle is the same.
> >>
> >> Eric
> >>
> >> -----Original Message-----
> >> From: Dong Tian [mailto:ti...@me...]
> >> Sent: Wednesday, July 19, 2017 1:56 PM
> >> To: mat...@li...
> >> Subject: [Matlab-emacs-discuss] How to debug MEX files (C code) from Emacs?
> >>
> >> Hello,
> >>
> >> Could anyone provide a pointer on how to debug MEX files from Emacs?
> >> E.g. using gdb?
> >>
> >> I am familiar with the procedure of debugging pure c/c++ code or .m
> >> code from Emacs using gdb, but I don't know a good way to debug MEX
> >> file coded in C from Emacs.
> >>
> >> Thanks in advance,
> >> Dong
> >>
> >> ------------------------------------------------------------------------------
> >> Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://secure-web.cisco.com/1ujKNEvoZ9nB-3MswM8yQpeWgC6aSas93lzT8a00GA11SdB5SpQ6CVRIOx-heKXnqKECDVK85FoUunZq98vpNfzj9z-dAEXYdTSCYMo17rGews2sXFe04QVklpkIgysqCMwIaoJQltBgN0vzTKcyy6uH42EmnOZN9d_7d6GI8HTluD2CTM_kIvO0I4ApdEW1uyzzeVHPDe01AEhL8z1lCXCd9Ls5JK37FPBnlqU-vHsqgajNbrh54-xMsjRMjU-khdIzpnhQOzvN53aQbsoH_mYU759kv1n9L6l97WEaazGtUV61gkLrwcRmPqtZUkz2IU_aA6HkROB1JRv1L63MCOuGFFTjdNrbynGp78WL3jRQ/http%3A%2F%2Fsdm.link%2Fslashdot _______________________________________________
> >> Matlab-emacs-discuss mailing list
> >> Mat...@li...
> >> https://secure-web.cisco.com/10eOO6rYM1RqFCHmlXsWS1TYTfQt0mblS7KZvYNUIxTp-ZGg9Gb7geEfnffV5gC9W3jjN5jlZyDrKFrGw14cD9PgfSBzm5qQ_6jbAPG5AQ61KZoTDufZTTsMhvlc7k-8mkewh3PKUPkO-9wtKK_ayCNqBB37kEYCLOH673oZPhzvewWVdd2KYIRf8sWleZLty8CyehfWXIWwMAX6yxqj9reri0LJu_hSOjSDE7bqwujPw_GaFGbRLesA4iu9JVaGg--IWyW7nW0t2ki22_ESPWiRYdGq7hqiMg7EYsAtkPymllsorUJDO3-uBqjP-SI1ky0GgTCRGnzpyoe5id6tfPy19K959g_PDiyGSEevC8Us/https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fmatlab-emacs-discuss
> >
> > ------------------------------------------------------------------------------
> > Check out the vibrant tech community on one of the world's most
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> > _______________________________________________
> > Matlab-emacs-discuss mailing list
> > Mat...@li...
> > https://secure-web.cisco.com/10eOO6rYM1RqFCHmlXsWS1TYTfQt0mblS7KZvYNUIxTp-ZGg9Gb7geEfnffV5gC9W3jjN5jlZyDrKFrGw14cD9PgfSBzm5qQ_6jbAPG5AQ61KZoTDufZTTsMhvlc7k-8mkewh3PKUPkO-9wtKK_ayCNqBB37kEYCLOH673oZPhzvewWVdd2KYIRf8sWleZLty8CyehfWXIWwMAX6yxqj9reri0LJu_hSOjSDE7bqwujPw_GaFGbRLesA4iu9JVaGg--IWyW7nW0t2ki22_ESPWiRYdGq7hqiMg7EYsAtkPymllsorUJDO3-uBqjP-SI1ky0GgTCRGnzpyoe5id6tfPy19K959g_PDiyGSEevC8Us/https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fmatlab-emacs-discuss