[ExM Users] debugging suggestions for non-static main-wrap segfault

[Ketan Maheshwari]

I expect it to run the application or crash on segfault. Nothing happens.



On Tue, Jul 29, 2014 at 1:39 PM, Tim Armstrong <tim.g.armstrong at gmail.com>
wrote:

>  That looks right, it should run dock_wrap.tcl fine.  And it runs
> successfully to completion with no output?  Is that what you expected it to
> do?
>
>  Backtracking to your original problem, if you could work out which
> "package require" statement was failing and provide some info about that
> package it might help understand the issue.
>
>  - Tim
>
>
> On Tue, Jul 29, 2014 at 1:32 PM, Ketan Maheshwari <ketan at mcs.anl.gov>
> wrote:
>
>>  I run tclsh as follows:
>>
>>  /home/ketan/tcl-install/bin/tclsh8.5 dock_wrap.tcl -i rigid.in
>>
>>  and
>>
>>  mpiexec -n 3 /home/ketan/tcl-install/bin/tclsh8.5 dock_wrap.tcl -i
>> rigid.in
>>
>>
>>  On Tue, Jul 29, 2014 at 1:28 PM, Tim Armstrong <
>> tim.g.armstrong at gmail.com> wrote:
>>
>>>   I forgot to reply all earlier, re-including the list.
>>>
>>>  How are you running tclsh?
>>>
>>>
>>> On Tue, Jul 29, 2014 at 11:53 AM, Ketan Maheshwari <ketan at mcs.anl.gov>
>>> wrote:
>>>
>>>> when I try tclsh, it does not do anything. Just returns with an exit
>>>> status 0.
>>>>
>>>>
>>>>  On Tue, Jul 29, 2014 at 11:02 AM, Tim Armstrong <
>>>> tim.g.armstrong at gmail.com> wrote:
>>>>
>>>>>   You can run it directly with tclsh or mpiexec tclsh, which is what
>>>>> turbine eventually does after setting up environment variables, etc.
>>>>>
>>>>>  - Tim
>>>>>
>>>>>
>>>>> On Tue, Jul 29, 2014 at 10:57 AM, Ketan Maheshwari <ketan at mcs.anl.gov>
>>>>> wrote:
>>>>>
>>>>>> Is it possible to run the dock_wrap.tcl outside of turbine just as in
>>>>>> the case of static build?
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>  On Tue, Jul 29, 2014 at 10:45 AM, Wozniak, Justin M. <
>>>>>> wozniak at mcs.anl.gov> wrote:
>>>>>>
>>>>>>>
>>>>>>> Ok, it's in.  The Swift/K SVN is apparently down so it's not on the
>>>>>>> web yet but see the asciidoc.
>>>>>>>
>>>>>>> On 07/29/2014 10:21 AM, Justin M Wozniak wrote:
>>>>>>>
>>>>>>>
>>>>>>> I thought VALGRIND was in the manual already but it isn't.  I will
>>>>>>> add it now.  I will also talk about our GDB feature.
>>>>>>>
>>>>>>> On 07/29/2014 10:17 AM, Ketan Maheshwari wrote:
>>>>>>>
>>>>>>> Thanks! Seems turbine script already had a placeholder for Valgrind
>>>>>>> so I tried that and from the output, it seems tcl libraries are causing
>>>>>>> segfault but I may be wrong. Attached is the Valgrind output.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Tue, Jul 29, 2014 at 10:05 AM, Tim Armstrong <
>>>>>>> tim.g.armstrong at gmail.com> wrote:
>>>>>>>
>>>>>>>>  I don't have any particular insight into the cause of the
>>>>>>>> segfault, I can help with the debugger though.
>>>>>>>>
>>>>>>>> You need to point gdb at the tclsh that is being used by turbine
>>>>>>>> (which is just a shell script).  You can locate the correct tclsh by
>>>>>>>> looking at TCLSH in scripts/turbine-config.sh in the turbine install
>>>>>>>> directory.
>>>>>>>>
>>>>>>>>  - TIm
>>>>>>>>
>>>>>>>>
>>>>>>>>  On Tue, Jul 29, 2014 at 10:00 AM, Ketan Maheshwari <
>>>>>>>> ketan at mcs.anl.gov> wrote:
>>>>>>>>
>>>>>>>>>  Hi,
>>>>>>>>>
>>>>>>>>>  Trying to main-wrap DOCK 6.6 application for ATPESC, I get the
>>>>>>>>> build right (seems) but things fail at runtime giving segfault:
>>>>>>>>>
>>>>>>>>>  $ turbine -n 4 user-code.tcl
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ===================================================================================
>>>>>>>>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>>>>>> =   EXIT CODE: 139
>>>>>>>>> =   CLEANING UP REMAINING PROCESSES
>>>>>>>>> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>>>>>
>>>>>>>>> ===================================================================================
>>>>>>>>> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation
>>>>>>>>> fault (signal 11)
>>>>>>>>> This typically refers to a problem with your application.
>>>>>>>>> Please see the FAQ page for debugging suggestions
>>>>>>>>>
>>>>>>>>>  This is on MCS machine. Any suggestion to debug this? I tried
>>>>>>>>> gdb but it gives:
>>>>>>>>>
>>>>>>>>>   "/nfs2/ketan/exm-install/turbine/bin/turbine": not in
>>>>>>>>> executable format: File format not recognized
>>>>>>>>>
>>>>>>>>>  With strace, I see some signs of missing files but not sure if
>>>>>>>>> that is the cause of segfault. Attached is the strace output of:
>>>>>>>>>
>>>>>>>>>  strace -o strace.out turbine -n 4 user-code.tcl
>>>>>>>>>
>>>>>>>>>  The code has some MPI and pthread elements but does not use them
>>>>>>>>> as far as I understand.
>>>>>>>>>
>>>>>>>>>  Thanks for any suggestions.
>>>>>>>>>
>>>>>>>>>  --
>>>>>>>>> Ketan
>>>>>>>>>
>>>>>>>>>  _______________________________________________
>>>>>>>>> ExM-user mailing list
>>>>>>>>> ExM-user at lists.mcs.anl.gov
>>>>>>>>> https://lists.mcs.anl.gov/mailman/listinfo/exm-user
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> ExM-user mailing listExM-user at lists.mcs.anl.govhttps://lists.mcs.anl.gov/mailman/listinfo/exm-user
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>   --
>>>>>>> Justin M Wozniak
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Justin M Wozniak
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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