[ExM Users] mkstatic questions
Ketan Maheshwari
ketan at mcs.anl.gov
Fri May 30 10:52:48 CDT 2014
Please disregard the previous error, it was fixed. I am getting this one
now:
Abort(1) on node 3 (rank 3 in comm 1140850688): Fatal error in MPI_Recv:
Message truncated, error stack:
MPI_Recv(184)........: MPI_Recv(buf=0x13ffff8e60, count=29, MPI_BYTE,
src=0, tag=4, comm=0x84000000, status=0x13ffff8e80) failed
MPIDI_Buffer_copy(73): Message truncated; 33 bytes received but buffer size
is 29
Any ideas?
Thanks,
Ketan
On Fri, May 30, 2014 at 10:34 AM, Maheshwari, Ketan C. <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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