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

[Ketan Maheshwari]

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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