picongpu-users@hzdr.de Mailing List Archive

When I execute this line:
tbg -s qsub -c ~/paramSets/case001/submit/0016gpus.cfg -t ~/paramSets/case001/submit/hypnos/k20_profile.tpl ~/runs/testBatch01

Show me this in my terminal:

alex@alex-Satellite-L635:~/paramSets/case001$ tbg -s qsub -c ~/paramSets/case001/submit/0016gpus.cfg -t ~/paramSets/case001/submit/hypnos/k20_profile.tpl ~/runs/testBatch01

cp: no se puede efectuar `stat' sobre «/home/alex/paramSets/case001/bin»: No existe el archivo o el directorio
/home/alex/src/picongpu/src/tools/bin/tbg: línea 354: qsub: orden no encontrada

thank you very much,
I hope you can help me,

Alex.

2016-08-09 13:36 GMT-05:00 Huebl, Axel <a.huebl@hzdr.de>:

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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> #############################################################
> > >>> This message is sent to you because you are
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> <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