[ExM Users] mkstatic questions

Fri May 30 11:09:25 CDT 2014

Yes, the TCL related error message appeared on the stdout and the
accompanying stderr message was about insufficient procs for Turbine.
Increasing the proccount on qsub fixed it.

On Fri, May 30, 2014 at 10:54 AM, Tim Armstrong <tim.g.armstrong at gmail.com>
wrote:

>  That the generic error that happens when any error occurs running a Tcl
> script.  It would usually be caused by an error in the Tcl code.  It will
> dump any Tcl error info.  Was there anything else reported?
>
>  - Tim
>
>
> On Fri, May 30, 2014 at 10:34 AM, Ketan Maheshwari <ketan at mcs.anl.gov>
> wrote:
>
>> Hi,
>>
>>  At runtime, on Cetus, I am getting the following:
>>
>>  Error while loading Tcl code originally from file
>> /home/ketan/rosetta/flexpep_docking/user-code.tcl:
>> Error while loading Tcl code originally from file
>> /home/ketan/rosetta/flexpep_docking/user-code.tcl:
>> Error executing compiled in main script (source
>> /home/ketan/rosetta/flexpep_docking/user-code.tcl): turbine error
>> TURBINE_ERROR_UNKNOWN (15)
>> Error executing compiled in main script (source
>> /home/ketan/rosetta/flexpep_docking/user-code.tcl): turbine error
>> TURBINE_ERROR_UNKNOWN (15)
>>
>>  My qsub line is as follows:
>>
>>  qsub --env BG_COREDUMPONEXIT=1:BG_SHAREDMEMSIZE=32MB -t 50 -n 3
>> --proccount 2 --mode c1 ./static_leaf_main
>>
>>  Any ideas on how I can further debug this or probable causes?
>>
>>  Thanks,
>> Ketan
>>
>>
>>
>>
>>  On Thu, May 29, 2014 at 12:03 PM, Tim Armstrong <
>> tim.g.armstrong at gmail.com> wrote:
>>
>>>   Yeah, with static linking it wants everything to be available as a .a
>>> archive.  It's a pain, since if you're static linking, everything needs to
>>> be static, but if you're using any dynamic linking, it defaults to using
>>> the .so and it's difficult to override.
>>>
>>>  - Tim
>>>
>>>
>>>  On Thu, May 29, 2014 at 10:11 AM, Justin M Wozniak <wozniak at mcs.anl.gov
>>> > wrote:
>>>
>>>>
>>>> I just fixed the perms on libtclturbine.a
>>>>
>>>> For Tcl, there is currently no static archive in that directory- I will
>>>> try to make one.
>>>>
>>>> On 05/29/2014 09:59 AM, Ketan Maheshwari wrote:
>>>>
>>>> Thanks! Trying to link with the following:
>>>>
>>>>  /soft/compilers/wrappers/xl/mpixlcxx -o static_leaf_main
>>>> static_leaf_main.o /home/ketan/rosetta/flexpep_docking/leaf_main.a \
>>>>  -pg -qsmp=omp -g -O0 -qarch=qp -qtune=qp -qhot
>>>> -Wl,--allow-multiple-definition \
>>>>  /projects/ExM/ketan/openmp-gnu-july16-mini/build/src/debug/linux/2.6/64/ppc64/xlc/static-mpi/apps/public/flexpep_docking/FlexPepDocking.o
>>>> \
>>>>  -L$TCL_HOME/lib -L$TURBINE_HOME/lib
>>>> -L/projects/ExM/ketan/openmp-gnu-july16-mini/external/lib \
>>>>  -L/projects/ExM/ketan/openmp-gnu-july16-mini/build/src/debug/linux/2.6/64/ppc64/xlc/static-mpi
>>>> \
>>>>  -Lsrc
>>>> -L/projects/ExM/ketan/openmp-gnu-july16-mini/build/external/debug/linux/2.6/64/ppc64/xlc/static-mpi
>>>> \
>>>>  -Lexternal -L/home/vsachde/ROSETTA/zlib/lib -ldevel -lprotocols.7
>>>> -lprotocols.6 -lprotocols_f.5 -lprotocols_e.5 \
>>>>  -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5
>>>> -lprotocols_h.4 -lprotocols_g.4 -lprotocols_f.4 \
>>>>  -lprotocols_e.4 -lprotocols_d.4 -lprotocols_c.4 -lprotocols_b.4
>>>> -lprotocols_a.4 -lprotocols.3 -lprotocols_b.2 \
>>>>  -lprotocols_a.2 -lprotocols.1 -lcore.5 -lcore.4 -lcore.3 -lcore.2
>>>> -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL \
>>>>  -lz -lcppdb -lsqlite3 -lz -ltclstub8.5 -ltcl8.5 -ltclturbine
>>>> -ltclturbinestatic -ltclturbinestaticres
>>>>
>>>>  Getting the error message:
>>>>  /bgsys/drivers/ppcfloor/gnu-linux/powerpc64-bgq-linux/bin/ld: cannot
>>>> find -ltcl8.5
>>>> /bgsys/drivers/ppcfloor/gnu-linux/powerpc64-bgq-linux/bin/ld: cannot
>>>> find -ltclturbine
>>>>
>>>>
>>>>  $TCL_HOME is /home/wozniak/Public/sfw/ppc64/tcl-8.5.12
>>>> $TURBINE_HOME is /home/wozniak/Public/sfw/ppc64/turbine/lib
>>>>
>>>>  and the libs that ld is complaining about does seem to be available
>>>> at the above locations. Any suggestions?
>>>>
>>>>  Thanks,
>>>> Ketan
>>>>
>>>>
>>>> On Thu, May 29, 2014 at 9:09 AM, Tim Armstrong <
>>>> tim.g.armstrong at gmail.com> wrote:
>>>>
>>>>>
>>>>>  Forgot to send this to the list.
>>>>>
>>>>>
>>>>>  On Thu, May 29, 2014 at 8:06 AM, Tim Armstrong <
>>>>> tim.g.armstrong at gmail.com> wrote:
>>>>>
>>>>>>   Another thing I should mention is that you can source the
>>>>>> turbine-build-config,sh script under turbine to get many of the variables
>>>>>> you need e.g. install dirs, tcl version, linker flags.
>>>>>>
>>>>>>  - Tim
>>>>>>
>>>>>>
>>>>>>  On Wed, May 28, 2014 at 9:40 AM, Tim Armstrong <
>>>>>> tim.g.armstrong at gmail.com> wrote:
>>>>>>
>>>>>>>   main_script lets you specify the Tcl script that's run on
>>>>>>> application startup.  To run a compiled Swift program, you set main_script
>>>>>>> to point to the Tcl output file.  mkstatic.tcl doesn't need Swift source
>>>>>>> files.
>>>>>>>
>>>>>>>  Note that you only need to fill in the fields in the "Manifest
>>>>>>> info" section to generate the C main program.  You probably only need the
>>>>>>> follow to generate the C code:
>>>>>>>
>>>>>>> # Name and version of Tcl package
>>>>>>> pkg_name=flex_pep_docking_or_whatever
>>>>>>> pkg_version=0.0
>>>>>>>
>>>>>>> # C function names to initialise Tcl modules
>>>>>>> # These follow the Tcl naming convention, e.g., Userlib_Init
>>>>>>> # Use nm on your extension object code to find this symbol
>>>>>>> lib_init=_Z24FlexPepDocking_wrap_InitP10Tcl_Interp
>>>>>>>
>>>>>>> # lib scripts are executed in specified order, before main_script and
>>>>>>> # after lib_inits
>>>>>>> lib_script=../flexpep_docking/user-code.tcl
>>>>>>>
>>>>>>> # headers for user Tcl code, e.g. lib_init functions
>>>>>>> lib_include=../flexpep_docking/FlexPepDocking_wrap.h
>>>>>>>
>>>>>>> # main script (generated by STC).
>>>>>>> # If provided, always runs this main script.
>>>>>>> # Otherwise, the script file is specified at run time as the
>>>>>>> # first command line argument (like tclsh)
>>>>>>> main_script = stc_output_file.tcl
>>>>>>>
>>>>>>>
>>>>>>>  - Tim
>>>>>>>
>>>>>>>
>>>>>>>  On Wed, May 28, 2014 at 9:17 AM, Ketan Maheshwari <
>>>>>>> ketan at mcs.anl.gov> wrote:
>>>>>>>
>>>>>>>> Thanks. One more question:
>>>>>>>>
>>>>>>>>  I am not sure where should I provide the application source file
>>>>>>>> in the manifest files?
>>>>>>>>
>>>>>>>>  Thanks,
>>>>>>>> Ketan
>>>>>>>>
>>>>>>>>
>>>>>>>>  On Tue, May 27, 2014 at 2:14 PM, Tim Armstrong <
>>>>>>>> tim.g.armstrong at gmail.com> wrote:
>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>  On Tue, May 27, 2014 at 1:50 PM, Ketan Maheshwari <
>>>>>>>>> ketan at mcs.anl.gov> wrote:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>>  Trying to get the Rosetta application static build for Turbine
>>>>>>>>>> using mkstatic.tcl.
>>>>>>>>>>
>>>>>>>>>>  I am a bit confused about the entries in the manifest file:
>>>>>>>>>>
>>>>>>>>>>  1. The purpose of lib_script option is not very clear to me.
>>>>>>>>>> What scripts are supposed to go in there? The template lists
>>>>>>>>>> user_stuff1.tcl, user_stuff2.tcl.
>>>>>>>>>>
>>>>>>>>>>    Any Tcl scripts that you want to run when the library loads.
>>>>>>>>> E.g. if you set pkg_name=the_pkg and lib_script=the_pkg.tcl, then pkg.tcl
>>>>>>>>> will be included in the executable.  It's run when the Tcl user script does
>>>>>>>>> a "package require the_pkg".
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>  2. The lib_include entry: does it accept both include dirs and
>>>>>>>>>> header files?
>>>>>>>>>>
>>>>>>>>>  It has to be a header file - it will just add a #include at the
>>>>>>>>> top of the C main file.  You have to provide any include directory flags to
>>>>>>>>> the C compiler later when you compile it.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>  3. From the documentation
>>>>>>>>>> http://www.mcs.anl.gov/exm/local/guides/swift.html#mkstatic, I
>>>>>>>>>> see that there are options at commandline such as --include-lib and
>>>>>>>>>> --include-system-lib. Are these in lieu of the ones in the manifest?
>>>>>>>>>>
>>>>>>>>>  These let you link in entire library directories.
>>>>>>>>>
>>>>>>>>> --include-system-lib is for the Tcl standard library directory
>>>>>>>>> that is always loaded on startup - it links the files into the executable
>>>>>>>>> so that it doesn't need to load them off disk.  It's mainly for
>>>>>>>>> performance, but it can help build entirely self-contained executables.
>>>>>>>>>
>>>>>>>>>  --include-lib  lets you link in an external library, e.g. a
>>>>>>>>> directory of Tcl files, or a directory with a pkgIndex.tcl file.  These are
>>>>>>>>> set up to to be loaded on demand with "package require".  --include-lib
>>>>>>>>> <dir> is essentially an alternative to setting TURBINE_USER_LIB=<dir>.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>  Thanks,
>>>>>>>>>> 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
>>>>
>>>>
>>>
>>
>
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