Mesazhi #97 i Listës së E-mailave picongpu-users@hzdr.de
Nga: Huebl, Axel <a.huebl@hzdr.de>
Lënda: Running PIConGPU via tbg
Data: Tue, 9 Aug 2016 14:36:32 -0400
Për: <picongpu-users@hzdr.de>
Të dhëna të nënshkruara (Text SHA256)
Your simulation has not yet run.

Please check the output of the "tbg" command, the "queue" of your batch
system, etc.

if it would have run, a "simOutput" dir would exist in the directory you
listed.


Best,
Axel

On 09.08.2016 12:49, Alex Francisco wrote:
> which is the output of the example simulation "Laser Wakefield"?,.
>
> I can see is this in my folder ~/runs/testBatch01:
>
> alex@alex-Satellite-L635:~/runs/testBatch01$ ls
> picongpu  tbg
>
> Thank you very much
>
> Alex.
>
>
>
>
>
>
>
> 2016-08-09 11:27 GMT-05:00 René Widera <r.widera@hzdr.de
> <mailto:r.widera@hzdr.de>>:
>
>     Dear Alex,
>
>     `make install` for splash2txt copies the binary to the folder
>     defined in `CMAKE_INSTALL_PREFIX`.
>     It not creates a `bin` folder.
>
>     René
>
>     On 09.08.2016 17:48, Alex Francisco wrote:
>
>         When I execute: |make install, ||it is not copying the binaries
>         /bin to
>         this folder, |
>
>         alex@alex-Satellite-L635:~/paramSets/case001$ ls
>         cmakeFlags  include  splash2txt  submit
>
>         also when I am in the folder ~/src/picongpu, show me this, when I
>         execute cmake -L:
>
>         alex@alex-Satellite-L635:~/src/picongpu$ cmake -L
>         *CMake Error: The source
>         "/home/alex/src/picongpu/CMakeLists.txt" does
>         not match the source
>         "/home/alex/src/picongpu/src/tools/splash2txt/CMakeLists.txt"
>         used to
>         generate cache.  Re-run cmake with a different source directory.*
>         -- Cache values
>         ADIOS_CONFIG:FILEPATH=/usr/bin/adios_config
>         CMAKE_BUILD_TYPE:STRING=Debug
>         CMAKE_INSTALL_PREFIX:PATH=/home/alex/paramSets/case001
>         HDF5_DIR:PATH=HDF5_DIR-NOTFOUND
>         MPI_EXTRA_LIBRARY:STRING=/usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so
>         MPI_LIBRARY:FILEPATH=/usr/lib/libmpi_cxx.so
>         Splash_LIBRARIES:FILEPATH=/home/alex/lib/splash/lib/libsplash.a
>         Splash_ROOT_DIR:PATH=/home/alex/lib/splash
>
>
>         2016-08-08 15:41 GMT-05:00 Marco Garten <m.garten@hzdr.de
>         <mailto:m.garten@hzdr.de>
>         <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>:
>
>
>             Dear Alex,
>
>             the TBG command as you executed it uses the relative path
>         from inside
>             your paramSet. The config file is located inside
>             ~/paramSets/case001/submit - just like the hardware template
>         file
>             k20_profile.tpl is in ~/paramSets/case001/submit/hypnos/.
>             So either execute the command from ~/paramSets/case001 or
>         use the
>             absolute path.
>
>             Don't forget to delete the folder ~/runs/testBatch01/ before
>         because
>             otherwise TBG will tell you that the job name is already in
>         use. (The
>             run folders all contain a copy of the executable and the
>         parameter set
>             regardless if the job is running or not)
>
>             You seem to be using the config files and the architecture
>         template of
>             our home cluster on your local machine, though. That would
>         require you
>             to have 16 GPUs if you use the 0016gpus.cfg file. If you
>         want to do a
>             quick test whether the code is running at all you can just
>         execute:
>
>             cd ~/paramSets/case001/bin
>
>             ./picongpu -d 1 1 1 -g 64 128 64 -s 1000
>
>             This will run the code with one GPU on a grid of 64 x 128 x
>         64 cells for
>             1000 steps.
>             Please look at any of the *gpus.cfg files for additional
>         options to the
>             command that will generate output. I would recommend
>         something like:
>
>             --png_e.period 50 --png_e.axis yz --png_e.slicePoint 0.5
>         --png_e.folder
>             pngElectronsYZ --elec_cnt.period 50
>
>             This will give you the total count of electrons in the
>         simulation at
>             every 50th time step and also a PNG showing a YZ slice of
>         the electron
>             charge density. The output will now be created directly in
>         the "bin"
>             folder where your executable is.
>
>             Hope this works for you!
>
>             Best,
>
>             Marco
>
>             Am 08.08.2016 um 18:14 schrieb Alex Francisco:
>             > Thank you very much this worked!!!
>             >
>             > When I do execute this line of code in my terminal show this:
>             >
>             > alex@alex-Satellite-L635:~/src/picongpu$ tbg -s qsub -c
>             > submit/0016gpus.cfg -t
>         ~/paramSets/case001/submit/hypnos/k20_profile.tpl
>             > ~/runs/testBatch01/
>             >
>             > The given cfg file "submit/0016gpus.cfg" does not exist
>         (-c|--cfg).
>             >
>             >
>             > However, I turn to the folder case001 and there show me
>         the folder
>             > testBatch01, I ask to yours, if it can be showing me this
>         because I once
>             > create and do not need to recreate the subfolder
>         (testBatch01) ??
>             >
>             > alex@alex-Satellite-L635:~/runs$ ls
>             > testBatch01
>             >
>             > and in the folder testBatch01 show me this files:
>             >
>             > alex@alex-Satellite-L635:~/runs/testBatch01$ ls
>             > picongpu  tbg
>             >
>             >
>             > Furthermore, as I view the simulation output?
>             >
>             >
>             > I hope you can help me.
>             >
>             > Thank you very much.
>             >
>             > Alex Estupiñán.
>             >
>             >
>             > 2016-08-06 11:33 GMT-05:00 Huebl, Axel <a.huebl@hzdr.de
>         <mailto:a.huebl@hzdr.de> <mailto:a.huebl@hzdr.de
>         <mailto:a.huebl@hzdr.de>>
>              > <mailto:a.huebl@hzdr.de <mailto:a.huebl@hzdr.de>
>         <mailto:a.huebl@hzdr.de <mailto:a.huebl@hzdr.de>>>>:
>             >
>             >     I also fixed that compile problem in splash2txt by now.
>             >
>             >
>            
>         >https://github.com/ComputationalRadiationPhysics/picongpu/pull/1545
>         <https://github.com/ComputationalRadiationPhysics/picongpu/pull/1545>
>            
>         <https://github.com/ComputationalRadiationPhysics/picongpu/pull/1545
>         <https://github.com/ComputationalRadiationPhysics/picongpu/pull/1545>>
>             >  
>          <https://github.com/ComputationalRadiationPhysics/picongpu/pull/1545
>         <https://github.com/ComputationalRadiationPhysics/picongpu/pull/1545>
>            
>         <https://github.com/ComputationalRadiationPhysics/picongpu/pull/1545
>         <https://github.com/ComputationalRadiationPhysics/picongpu/pull/1545>>>
>             >
>             >     You can just remove or comment out via "//" the line
>         that is causing the
>             >     error.
>             >
>             >
>             >     Axel
>             >
>             >     On 06.08.2016 11:07, Axel Huebl wrote:
>             >     > Dear Alex,
>             >     >
>             >     > You don't need to build the helper tool in
>         post-processing,
>             >     splash2txt for now. Just skip step 6.
>             >     >
>             >     > Otherwise: please make sure the source code is
>         unmodified. For
>             >     compile errors, please report compiler version, cmake
>         version, cmake
>             >     -L . output and ubuntu version.
>             >     >
>             >     > Compile issues are also best tracked in our github
>         since we can
>             >     assign, track, link and archive it there.
>             >     >
>             >     > Axel
>             >     >
>             >     > On August 6, 2016 10:56:09 AM EDT, "Bussmann, Dr.
>         Michael (FWKT) -
>              >     4167" <m.bussmann@hzdr.de <mailto:m.bussmann@hzdr.de>
>         <mailto:m.bussmann@hzdr.de <mailto:m.bussmann@hzdr.de>>
>             <mailto:m.bussmann@hzdr.de <mailto:m.bussmann@hzdr.de>
>         <mailto:m.bussmann@hzdr.de <mailto:m.bussmann@hzdr.de>>>> wrote:
>              >     >> Dear Alex,
>              >     >>
>              >     >> Could you please tell us which version of PIConGPU
>         you are
>             using,
>              >     >> provide CMake log files and CMakeLists.txt so we
>         can have
>             a look at
>              >     >> what
>              >     >> is going on.
>              >     >>
>              >     >> Best, Michael
>              >     >>
>              >     >> Am 05.08.2016 um 18:13 schrieb Alex Francisco:
>              >     >>> Dear Michael Bussmann and picongpu users:
>              >     >>>
>              >     >>> I appreciate your help, I already understood that
>         ADIOS
>             is optional,
>              >     >> but
>              >     >>> when i continue, my ubuntu terminal show me, the
>             following error,
>              >     >> when I
>              >     >>> execute the step 6 "make -j":
>              >     >>>
>              >     >>> [ 50%] Building CXX object
>              >     CMakeFiles/splash2txt.dir/splash2txt.cpp.o
>              >     >>>
>             /home/alex/src/picongpu/src/tools/splash2txt/splash2txt.cpp: In
>              >     >> function
>              >     >>> ‘bool parseOptions(int, char**, ProgramOptions&)’:
>              >     >>>
>            
>         /home/alex/src/picongpu/src/tools/splash2txt/splash2txt.cpp:164:24:
>              >     >>> error: ‘desc’ was not declared in this scope
>              >     >>>          errorStream << desc << "\n";
>              >     >>>                         ^
>              >     >>> CMakeFiles/splash2txt.dir/build.make:54: recipe
>         for target
>              >     >>> 'CMakeFiles/splash2txt.dir/splash2txt.cpp.o' failed
>              >     >>> make[2]: ***
>         [CMakeFiles/splash2txt.dir/splash2txt.cpp.o]
>             Error 1
>              >     >>> CMakeFiles/Makefile2:60: recipe for target
>              >     >>> 'CMakeFiles/splash2txt.dir/all' failed
>              >     >>> make[1]: *** [CMakeFiles/splash2txt.dir/all] Error 2
>              >     >>> Makefile:117: recipe for target 'all' failed
>              >     >>> make: *** [all] Error 2
>              >     >>>
>              >     >>> Imágenes integradas 1
>              >     >>>
>              >     >>>
>              >     >>> I hope you can help me.
>              >     >>>
>              >     >>> Thank you very much.
>              >     >>>
>              >     >>> Alex Estupiñán.
>              >     >>>
>              >     >>>
>              >     >>> 2016-08-02 6:34 GMT-05:00 Bussmann, Dr. Michael
>         (FWKT) - 4167
>              >     >>> <m.bussmann@hzdr.de <mailto:m.bussmann@hzdr.de>
>         <mailto:m.bussmann@hzdr.de <mailto:m.bussmann@hzdr.de>>
>             <mailto:m.bussmann@hzdr.de <mailto:m.bussmann@hzdr.de>
>         <mailto:m.bussmann@hzdr.de <mailto:m.bussmann@hzdr.de>>>
>              >     <mailto:m.bussmann@hzdr.de
>         <mailto:m.bussmann@hzdr.de> <mailto:m.bussmann@hzdr.de
>         <mailto:m.bussmann@hzdr.de>>
>             <mailto:m.bussmann@hzdr.de <mailto:m.bussmann@hzdr.de>
>         <mailto:m.bussmann@hzdr.de <mailto:m.bussmann@hzdr.de>>>>>:
>              >     >>>
>              >     >>>     Oops, sorry, you completed step 5 and can go
>         to step
>             6. My bad!
>              >     >>>
>              >     >>>     Am 02.08.2016 um 13:25 schrieb Bussmann, Dr.
>         Michael
>             (FWKT) -
>              >     >> 4167:
>              >     >>>     > Dear Alex,
>              >     >>>     >
>              >     >>>     > As Axel pointed out in his E-mail, this is no
>             error. It simply
>              >     >>>     tells you
>              >     >>>     > that a software component is missing that is
>             optional, but not
>              >     >>>     required
>              >     >>>     > to build PIConGPU. This means PIConGPU can use
>             ADIOS, but does
>              >     >> not
>              >     >>>     need
>              >     >>>     > it to run properly.
>              >     >>>     >
>              >     >>>     > Yes, this is a bit confusing, but as you
>         see the
>             output tells
>              >     >> you that
>              >     >>>     > your build files have been written to
>             /home/alex/src/picongpu.
>              >     >> So
>              >     >>>     > everything is fine!
>              >     >>>     >
>              >     >>>     > You have now completed step 6 in the install
>             process, see
>              >     here:
>              >     >>>     >
>              >     >>>
>              >     >>
>              >
>            
>         https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md
>         <https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md>
>            
>         <https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md
>         <https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md>>
>              >
>              
>         <https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md
>         <https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md>
>         <https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md
>         <https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md>>>
>              >     >>>
>              >     >>
>              >
>              
>         <https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md
>         <https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md>
>         <https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md
>         <https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md>>
>              >
>              
>         <https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md
>         <https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md>
>         <https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md
>         <https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md>>>>
>              >     >>>     >
>              >     >>>     > As Axel also wrote, you can now simply go
>         to step
>             7, typing
>              >     >> 'make'.
>              >     >>>     >
>              >     >>>     > If you run into problems, please provide
>         error log
>             files with
>              >     >> your
>              >     >>>     > E-mails and keep posting to the Users
>         mailing list.
>              >     >>>     >
>              >     >>>     > Hope this helps, Michael
>              >     >>>     >
>              >     >>>     > Am 02.08.2016 um 03:38 schrieb Alex Francisco:
>              >     >>>     >> Dear Michael Bussmann:
>              >     >>>     >>
>              >     >>>     >> I hope you are well. I am a doctoral
>         student at the
>              >     University
>              >     >> of
>              >     >>>     >> Colombia UIS. I am installing the PiconGpu
>         program
>             on my
>              >     >> laptop, my
>              >     >>>     >> laptop has a software ubuntu 16.04 LTS 64-bit.
>              >     >>>     >>
>              >     >>>     >> My ubuntu terminal shows me the following
>         error:
>              >     >>>     >>
>              >     >>>     >> -- Could NOT find ADIOS (missing:
>         ADIOS_LIBRARIES
>              >     >>>     ADIOS_INCLUDE_DIRS)
>              >     >>>     >> (Required is at least version "1.6.0")
>              >     >>>     >>
>              >     >>>     >>
>              >     >>>     >> Imágenes integradas 1
>              >     >>>     >>
>              >     >>>     >>
>              >     >>>     >> the problem still, I am very interested in
>         I can
>             solve this
>              >     >>>     problem. I
>              >     >>>     >> need install this program for work in my
>         doctoral job.
>              >     >>>     >>
>              >     >>>     >> I hope you can help me.
>              >     >>>     >>
>              >     >>>     >> Thank you very much.
>              >     >>>     >>
>              >     >>>     >> Alex Estupiñán.
>              >     >>>     >>
>              >     >>>     >
>              >     >>>     >
>             #############################################################
>              >     >>>     > This message is sent to you because you are
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>             <mailto:picongpu-users@hzdr.de <mailto:picongpu-users@hzdr.de>>
>              >     <mailto:picongpu-users@hzdr.de
>         <mailto:picongpu-users@hzdr.de> <mailto:picongpu-users@hzdr.de
>         <mailto:picongpu-users@hzdr.de>>>
>              >     >>>     <mailto:picongpu-users@hzdr.de
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>              >     >
>              >
>              >     --
>              >
>              >     Axel Huebl
>              >     Phone +49 351 260 3582 <tel:%2B49%20351%20260%203582>
>         <tel:%2B49%20351%20260%203582>
>             <tel:%2B49%20351%20260%203582>
>             >https://www.hzdr.de/crp
>             >     Computational Radiation Physics
>             >     Laser Particle Acceleration Division
>             >     Helmholtz-Zentrum Dresden - Rossendorf e.V.
>             >
>             >     Bautzner Landstrasse 400, 01328 Dresden
>             >     POB 510119, D-01314 Dresden
>             >     Vorstand: Prof. Dr.Dr.h.c. R. Sauerbrey
>             >               Prof. Dr.Dr.h.c. P. Joehnk
>             >     VR 1693 beim Amtsgericht Dresden
>             >
>             >
>
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>
>
>
>     --
>     René Widera
>     Abteilung Laser-Teilchenbeschleunigung (FWKT)
>     Helmholtz-Zentrum Dresden-Rossendorf
>     Tel: +49 (0351) 260 3543 <tel:%2B49%20%280351%29%20260%203543>
>     r.widera@hzdr.de <mailto:r.widera@hzdr.de>
>     http://www.hzdr.de
>
>     Vorstand: Prof. Dr. Dr. h. c. Roland Sauerbrey,
>               Prof. Dr. Dr. h. c. Peter Joehnk
>     Vereinsregister: VR 1693 beim Amtsgericht Dresden
>
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>
>

--

Axel Huebl
Phone +49 351 260 3582
https://www.hzdr.de/crp
Computational Radiation Physics
Laser Particle Acceleration Division
Helmholtz-Zentrum Dresden - Rossendorf e.V.

Bautzner Landstrasse 400, 01328 Dresden
POB 510119, D-01314 Dresden
Vorstand: Prof. Dr.Dr.h.c. R. Sauerbrey
          Prof. Dr.Dr.h.c. P. Joehnk
VR 1693 beim Amtsgericht Dresden

Përmbajtja e pandryshuar, sipas verifikimit të:
presented certificate is issued by an unknown authority:Huebl, Axel <a.huebl@hzdr.de>
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