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

[Tim Armstrong]

I don't see any reason why that invocation of tclsh would silently fail to
run the tcl script.  Have you attempted to confirm your hypothesis that
it's not running the script, for example by modifying the script to print
something at the beginning or end?


On Tue, Jul 29, 2014 at 1:42 PM, Ketan Maheshwari <ketan at mcs.anl.gov> wrote:

> 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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