picongpu-users@hzdr.de Mailing List Archive

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>:

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>>:
>
> I also fixed that compile problem in splash2txt by now.
>
>
> 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>> 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>>>:

> >>>
> >>> 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>>
> >>> >
> >>> > 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.
> >>> >>
> >>> >
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> --
>
> Axel Huebl
> Phone +49 351 260 3582 <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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