|
|
Use the attached template file instead.
(Just replace the one you use right now with it.)
Cheers,
Axel
On 28.09.2016 15:58, Alex Francisco wrote:
> Dear developers PiconGpu:
>
> alex@alex-Satellite-L635:~/paramSets/case001$ tbg -s bash -c
> /home/alex/paramSets/case001/submit/0001gpus.cfg -t
> submit/bash/bash_mpirun.tpl ~/runs/testBatch01
> Running program...
> [mpiexec@alex-Satellite-L635] match_arg (utils/args/args.c:159):
> unrecognized argument display-map
> [mpiexec@alex-Satellite-L635] HYDU_parse_array (utils/args/args.c:174):
> argument matching returned error
> [mpiexec@alex-Satellite-L635] parse_args (ui/mpich/utils.c:1596): error
> parsing input array
> [mpiexec@alex-Satellite-L635] HYD_uii_mpx_get_parameters
> (ui/mpich/utils.c:1648): unable to parse user arguments
> [mpiexec@alex-Satellite-L635] main (ui/mpich/mpiexec.c:153): error
> parsing parameters
> [mpiexec@alex-Satellite-L635] match_arg (utils/args/args.c:159):
> unrecognized argument npernode
> [mpiexec@alex-Satellite-L635] HYDU_parse_array (utils/args/args.c:174):
> argument matching returned error
> [mpiexec@alex-Satellite-L635] parse_args (ui/mpich/utils.c:1596): error
> parsing input array
> [mpiexec@alex-Satellite-L635] HYD_uii_mpx_get_parameters
> (ui/mpich/utils.c:1648): unable to parse user arguments
> [mpiexec@alex-Satellite-L635] main (ui/mpich/mpiexec.c:153): error
> parsing parameters
>
> I hope you can help me.
>
> thank you very much for your help.
>
> Alex.
>
>
>
>
>
> 2016-09-28 8:47 GMT-05:00 René Widera <r.widera@hzdr.de
> <mailto:r.widera@hzdr.de>>:
>
> HI Alex,
>
> please install mpi with mpirun on your system.
> After that please run
> touch /home/alex/picongpu.profile
>
> Call tbg again.
>
> best,
> René
>
> On 09/28/2016 03:44 PM, Alex Francisco wrote:
>
> Dear PiconGPU developers:
>
> alex@alex-Satellite-L635:~/paramSets/case001$ tbg -s bash -c
> /home/alex/paramSets/case001/submit/0001gpus.cfg -t
> submit/bash/bash_mpirun.tpl ~/runs/testBatch01
>
> Running program ...
> tbg/submit.start: line 37: /home/alex/picongpu.profile: No such
> file or
> directory
> tbg/submit.start: line 46: mpirun: command not found
> tbg/submit.start: line 52: mpirun: command not found
>
> I hope you can help me.
>
> thank you very much for your help.
>
> Alex.
>
> 2016-09-28 8:35 GMT-05:00 René Widera <r.widera@hzdr.de
> <mailto:r.widera@hzdr.de>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>>:
>
> Hi Alex,
>
> please execute exactly the following command:
>
> tbg -s bash -c
> /home/alex/paramSets/case001/submit/0001gpus.cfg -t
> submit/bash/bash_mpirun.tpl ~/runs/testBatch01
>
> best,
>
> René
>
>
>
> On 09/28/2016 03:23 PM, Alex Francisco wrote:
>
> Dear PiconGPU developers:
>
> When I execute the next line of comands use tbg, the
> terminal of
> ubuntu
> show me this:
>
> alex@alex-Satellite-L635:~/paramSets/case001$ tbg bash
> -c -s -t
> /home/alex/paramSets/case001/submit/0001gpus.cfg
> submit/bash/bash_mpirun.tpl ~/runs/testBatch01
> Running program ...
> tbg/submit.start: line 37: /home/alex/picongpu.profile:
> No such
> file or
> directory
> tbg/submit.start: line 46: mpirun: command not found
> tbg/submit.start: line 52: mpirun: command not found
>
> I hope you can help me.
>
> thank you very much for your help.
>
> Alex.
>
> 2016-09-21 10:14 GMT-05:00 Axel Huebl <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>>>>:
>
> Alex,
>
> The first parameter is simply
> -s bash
>
> as I wrote you in the previous mail.
>
> Or for sake of simplicity:
> tbg -s bash -c submit/0016gpus.cfg -t
> submit/bash/bash_mpirun.tpl
> ~/runs/testBatch06
>
> Did you read the output of
> tbg --help
> yet?
>
> Cheers,
> Axel
>
> On September 21, 2016 4:14:55 PM CEST, Alex Francisco
> <djlexes@gmail.com <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>>> wrote:
> >Dear developers PicOnGpu:
> >
> >
> >I'm running my simulation on my machine locally. when I
> execute the
> >line
> >how you say to me, the next form:
> >
> >tbg -s /home/alex/paramSets/case001/submit/bash/ -c
> submit/0016gpus.cfg
> >-t
>
> >/home/alex/paramSets/case001/submit/bash/bash_mpirun.tpl
> >~/runs/testBatch05
> >
> >/home/alex/paramSets/case001/submit/bash/:
> >
> >is a directory
> >
> >Also, I try this comman.
> >
> >tbg -s
> /home/alex/paramSets/case001/submit/bash/bash_mpirun.tpl -c
> >submit/0016gpus.cfg -t
>
> >/home/alex/paramSets/case001/submit/bash/bash_mpirun.tpl
> >~/runs/testBatch05
> >
> >/home/alex/src/picongpu/src/tools/bin/tbg: línea 354:
>
> >/home/alex/paramSets/case001/submit/bash/bash_mpirun.tpl:
> permission
> >denied
> >
> >
> >
> >I hope you can help me.
> >
> >Thank you very much.
> >
> >Alex.
> >
> >
> >
> >
> >2016-09-14 8:36 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>>>>:
> >
> >> Dear Alex,
> >>
> >> please read the output of
> >> tbg --help
> >>
> >> first. As any command in the unix/linux/mac
> world, the
> order of
> >> parameters you specify behind it have a meaning
> that you
> need to
> >> understand first.
> >>
> >> a)
> >> -s is the submit command
> >> if you are not on a cluster, run locally with -s
> bash
> >>
> >> b) -t is a template to execute PIConGPU
> >> if you are not on the cluster hypnos (which
> would be in
> our lab)
> >> then use the other templates in submit/ such as
> bash/bash_mpirun.tpl
> >or
> >> write your own.
> >>
> >>
> >> Also before sending us error messages, please set
> your
> locale to
> >english
> >> so we can understand them.
> >>
> >> You can do so by running
> >> export LC_ALL=en_US.UTF-8
> >>
> >> before doing anything else. This will temporarily
> set the
> language to
> >> english until you close your terminal (or SSH
> session) again.
> >>
> >>
> >> Best regards,
> >> Axel
> >>
> >> On 11.09.2016 20:54, Alex Francisco wrote:
> >> > Dear developers PicOnGpu:
> >> >
> >> > when i execute the line how you say to me, the
> next form:
> >> >
> >> > tbg -s /home/alex/build/ -c submit/0016gpus.cfg -t
> >> > submit/hypnos/k20_profile.tpl ~/runs/testBatch01
> >> >
> >> > This create this files in this directory
> >> >
> >> > /home/alex/build/
> >> >
> >> > alex@alex-Satellite-L635:~/build$ ls
> >> > CMake CMakeCache.txt CMakeFiles Show
> >> >
> >> > and also create this folder: testBatch01
> >> >
> >> > alex@alex-Satellite-L635:~/runs/testBatch02$ ls
> >> > picongpu tbg
> >> >
> >> > All is alright, is it this the output of the
> simulation
> of example?
> >> >
> >> >
> >> > Thanks for your great help they have given me,
> and I
> hope your
> >answer
> >> > about my question.
> >> >
> >> > Thank you very much.
> >> >
> >> > Alex.
> >> >
> >> >
> >> > 2016-08-28 6:47 GMT-05:00 Axel Huebl
> <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>>>
> >> > <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 <mailto:a.huebl@hzdr.de>>>>>:
> >> >
> >> > Hi Alex,
> >> >
> >> > Are you even on a cluster with a batch system?
> >> > If yes, which one? PBS, Slurm, ...?
> >> >
> >> > Otherwise, use -s bash and the -t
> submit/bash/...
> >"mpiexec"/"mpirun"
> >> > bash .tpl file for locsl runs.
> >> >
> >> > Axel
> >> >
> >> > On August 28, 2016 12:38:37 AM CEST, Alex
> Francisco
> >> > <djlexes@gmail.com
> <mailto:djlexes@gmail.com> <mailto:djlexes@gmail.com
> <mailto:djlexes@gmail.com>>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>>>> wrote:
> >> > >Dear developers PicOnGpu:
> >> > >
> >> > >I install the program again and I already are
> creating the
> >"bin"
> >> folder
> >> > >in
> >> > >the directory ~ / ParamSet / case001
> >> > >
> >> >
> >alex@alex-Satellite-L635:~/paramSets/case001$ ls
> >> > >bin cmakeFlags include lib share submit
> >> > >
> >> > >
> >> > >When I execute the netx instructions, show
> me this:
> >> > >
> >> >
> >alex@alex-Satellite-L635:~/paramSets/case001$ tbg
> -s qsub -c
> >> > >submit/0016gpus.cfg -t
> submit/hypnos/k20_profile.tpl
> >> ~/runs/testBatch01
> >> > >
> >> > >/home/alex/src/picongpu/src/tools/bin/tbg:
> línea
> 354: qsub:
> >orden
> >> no
> >> > >encontrada
> >> > >
> >> > >alex@alex-Satellite-L635:~/runs/testBatch01$
> >> > >$PICSRC/configure
> >> > >-i ~/paramSets/case002 ~/runs/testBatch01
> >> > >cmake command: cmake
> >> >
> >-DCMAKE_INSTALL_PREFIX=/home/alex/paramSets/case002
> >> >
> >-DPIC_EXTENSION_PATH=/home/alex/runs/testBatch01
> >> > >/home/alex/src/picongpu
> >> > >-- Building libSplash version 1.4.0
> >> > >-- Building RELEASE version
> >> > >-- Parallel HDF5 found. Building parallel
> version
> >> > >-- Building splashtools
> >> > >-- Building splashtools parallel version
> >> > >-- Configuring done
> >> > >-- Generating done
> >> > >-- Build files have been written to:
> /home/alex/src/picongpu
> >> > >
> >> > >
> >> > >it is an error or that the order does not
> exist
> for the
> >> instructions of
> >> > >tbg
> >> > >or qsub "wrong Fingered".
> >> > >
> >> > >I hope can you help me,
> >> > >
> >> > >Thank you very much.
> >> > >
> >> > >Alex
> >> > >
> >> > >2016-08-10 3:35 GMT-05:00 Garten, Marco
> <m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>
> >> > <mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de> <mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>>>:
> >> > >
> >> > >> Did you perhaps execute the
> $PICSRC/configure
> command inside
> >your
> >> > >> home/alex/src/picongpu before? That will
> create
> some files
> >there
> >> and
> >> > >will
> >> > >> stop you
> >> > >> from compiling correctly.
> >> > >>
> >> > >> First check if you have any changes in your
> source code:
> >> > >>
> >> > >> cd ~/src/picongpu
> >> > >>
> >> > >> git status
> >> > >>
> >> > >> --> Please show us the output of this
> >> > >>
> >> > >> If you have any modified or new files in
> there
> and NO
> >intentional
> >> > >changes
> >> > >> you can do:
> >> > >>
> >> > >> git reset --hard HEAD
> >> > >>
> >> > >> That resets your local index and working
> tree to
> the state
> >of the
> >> > >branch
> >> > >> as it was when you downloaded it.
> (Careful: it
> will also
> >delete
> >> your
> >> > >> changes
> >> > >> if you made some)
> >> > >>
> >> > >> Now you can retry building PIConGPU again:
> >> > >>
> >> > >> rm -r ~/build/*
> >> > >>
> >> > >> cd ~/build
> >> > >>
> >> > >> $PICSRC/configure ~/paramSets/case001
> >> > >>
> >> > >> make -j install
> >> > >> (please only do the make command inside the
> build directory
> >> > >> - if the configure command writes to any
> other
> directory
> >than
> >> build
> >> > >> that is a sign that something went wrong)
> >> > >>
> >> > >> --> Please send us all the output until
> there again
> >> > >>
> >> > >> Best,
> >> > >>
> >> > >> Marco
> >> > >>
> >> > >> Am Tue, 9 Aug 2016 16:50:05 -0500
> schrieb Alex
> Francisco <
> >> > >> djlexes@gmail.com
> <mailto:djlexes@gmail.com> <mailto:djlexes@gmail.com
> <mailto:djlexes@gmail.com>>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>>>>:
> >> > >>
> >> > >>> alex@alex-Satellite-L635:~/src/picongpu$
> ./configure
> >> > >~/paramSets/case001
> >> > >>> cmake command: cmake -DCUDA_ARCH=sm_20
> >> > >>>
> -DCMAKE_INSTALL_PREFIX=/home/alex/paramSets/case001
> >> > >>>
> -DPIC_EXTENSION_PATH=/home/alex/paramSets/case001 .
> >> > >>> -- Building Debug
> >> > >>> -- libSplash supports PARALLEL output
> >> > >>> -- libSplash compiler definitions:
> >> > >>>
> >> >
> >-D_LARGEFILE_SOURCE;-D_LARGEFILE64_SOURCE;-D_BSD_
> >> SOURCE;-DENABLE_HDF5=1
> >> > >>> -- Found 'adios_config':
> /usr/bin/adios_config
> >> > >>> /usr/bin/adios_config: línea 121:
> pkgconfig:
> orden no
> >encontrada
> >> > >>> -- The directory provided by
> 'adios_config -d'
> does not
> >exist:
> >> > >>> -- Could NOT find ADIOS (missing:
> ADIOS_LIBRARIES
> >> > >ADIOS_INCLUDE_DIRS)
> >> > >>> (Required is at least version "1.6.0")
> >> > >>> -- Boost version: 1.55.0
> >> > >>> -- Found the following Boost libraries:
> >> > >>> -- program_options
> >> > >>> -- regex
> >> > >>> -- Configuring done
> >> > >>> -- Generating done
> >> > >>> -- Build files have been written to:
> >/home/alex/src/picongpu
> >> > >>>
> >> > >>>
> alex@alex-Satellite-L635:~/src/picongpu$ make -j
> >> > >>> [100%] Built target splash2txt
> >> > >>>
> >> > >>>
> alex@alex-Satellite-L635:~/src/picongpu$ make
> install
> >> > >>> [100%] Built target splash2txt
> >> > >>> Install the pro ject...
> >> > >>> -- Install configuration: "Debug"
> >> > >>> -- Up-to-date:
> /home/alex/paramSets/case001/./splash2txt
> >> > >>>
> >> > >>> alex@alex-Satellite-L635:~/src/picongpu$ cd
> >~/paramSets/case001/
> >> > >>>
> >> > >>>
> alex@alex-Satellite-L635:~/paramSets/case001$ ls
> >> > >>> cmakeFlags include splash2txt submit
> >> > >>>
> >> > >>>
> >> > >>>
> >> > >>>
> >> > >>> 2016-08-09 16:37 GMT-05:00 Alex Francisco
> ><djlexes@gmail.com <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>>
> >> > <mailto:djlexes@gmail.com
> <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>>>>:
> >> > >>>
> >> > >>> alex@alex-Satellite-L635:~/build$ make
> -j install
> >> > >>>> make: *** No rule to make target
> 'install'. Alto.
> >> > >>>> alex@alex-Satellite-L635:~/build$ make -j
> >> > >>>> make: *** No se especificó ningún
> objetivo y no se
> >encontró
> >> ningún
> >> > >>>> makefile. Alto.
> >> > >>>>
> >> > >>>>
> >> > >>>> 2016-08-09 16:35 GMT-05:00 Alex Francisco
> ><djlexes@gmail.com <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>>
> >> > <mailto:djlexes@gmail.com
> <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>
> <mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>>>>:
> >> > >>>>
> >> > >>>> alex@alex-Satellite-L635:~/build$
> >~/src/picongpu/./configure
> >> > >>>>> ~/paramSets/case001/
> >> > >>>>> cmake command: cmake -DCUDA_ARCH=sm_20
> >> > >-DCMAKE_INSTALL_PREFIX=/home/a
> >> > >>>>> lex/paramSets/case001/
> >> > >>>>>
> -DPIC_EXTENSION_PATH=/home/alex/paramSets/case001/
> >> > >>>>> /home/alex/src/picongpu/.
> >> > >>>>> -- Building Debug
> >> > >>>>> -- libSplash supports PARALLEL output
> >> > >>>>> -- libSplash compiler definitions:
> >> -D_LARGEFILE_SOURCE;-D_LARGEFI
> >> > >>>>> LE64_SOURCE;-D_BSD_SOURCE;-DENABLE_HDF5=1
> >> > >>>>> -- Found 'adios_config':
> /usr/bin/adios_config
> >> > >>>>> /usr/bin/adios_config: línea 121:
> pkgconfig:
> orden no
> >> encontrada
> >> > >>>>> -- The directory provided by
> 'adios_config
> -d' does not
> >exist:
> >> > >>>>> -- Could NOT find ADIOS (missing:
> ADIOS_LIBRARIES
> >> > >ADIOS_INCLUDE_DIRS)
> >> > >>>>> (Required is at least version "1.6.0")
> >> > >>>>> -- Boost version: 1.55.0
> >> > >>>>> -- Found the following Boost libraries:
> >> > >>>>> -- program_options
> >> > >>>>> -- regex
> >> > >>>>> -- Configuring done
> >> > >>>>> -- Generating done
> >> > >>>>> CMake Warning:
> >> > >>>>> Manually-specified variables were
> not used
> by the
> >project:
> >> > >>>>>
> >> > >>>>> PIC_EXTENSION_PATH
> >> > >>>>>
> >> > >>>>>
> >> > >>>>> -- Build files have been written to:
> >/home/alex/src/picongpu
> >> > >>>>> alex@alex-Satellite-L635:~/build$
> make -j intall
> >> > >>>>> make: *** No rule to make target
> 'intall'. Alto.
> >> > >>>>> alex@alex-Satellite-L635:~/build$
> >> > >>>>>
> >> > >>>>>
> >> > >>>>>
> >> > >>>>> 2016-08-09 16:17 GMT-05:00 Marco Garten
> <m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>
> >> > <mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de> <mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>>>:
> >> > >>>>>
> >> > >>>>> This still looks like as if your compile
> process has not
> >been
> >> > >successful
> >> > >>>>>> and the executable has not been
> built (nor
> has the bin
> >folder
> >> > >been
> >> > >>>>>> created).
> >> > >>>>>>
> >> > >>>>>> Could you please remove all the contents
> inside the
> >~/build
> >> > >directory,
> >> > >>>>>> repeat the following steps and show
> us all
> the output
> >from
> >> your
> >> > >>>>>> terminal?
> >> > >>>>>>
> >> > >>>>>> 1. Configure the example (cd ~/build &&
> >$PICSRC/configure
> >> > >>>>>> ~/paramSets/case001)
> >> > >>>>>>
> >> > >>>>>> 2. Compile the code (make -j install)
> >> > >>>>>>
> >> > >>>>>> Hope we can get your code running soon!
> >> > >>>>>>
> >> > >>>>>> Best,
> >> > >>>>>>
> >> > >>>>>> Marco
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>> Am 09.08.2016 um 22:34 schrieb Alex
> Francisco:
> >> > >>>>>> > When I execute this line|: |
> >> > >>>>>> > tbg -s qsub -c
> ~/paramSets/case001/submit/0016gpus.cfg
> >-t
> >> > >>>>>> >
> ~/paramSets/case001/submit/hypnos/k20_profile.tpl
> >> > >~/runs/testBatch01
> >> > >>>>>> >
> >> > >>>>>> > Show me this in my terminal:
> >> > >>>>>> >
> >> > >>>>>> >
> alex@alex-Satellite-L635:~/paramSets/case001$ 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 <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>>>
> >> > <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 <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>
> <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 <mailto:a.huebl@hzdr.de>
> <mailto:a.huebl@hzdr.de <mailto: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>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>>>
> >> > >>>>>> > <mailto:r.widera@hzdr.de
> <mailto:r.widera@hzdr.de>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>>
> ><mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>>>>
> >> > >>>>>> > > <mailto:r.widera@hzdr.de
> <mailto:r.widera@hzdr.de>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>>
> ><mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>>>
> >> > <mailto:r.widera@hzdr.de
> <mailto:r.widera@hzdr.de> <mailto:r.widera@hzdr.de
> <mailto:r.widera@hzdr.de>>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>
> <mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>
> <mailto: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>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>>
> >> > >>>>>> > <mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>
> ><mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>>>
> >> > >>>>>> > >
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>
> >> > <mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de> <mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>>
> >> > ><mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de> <mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>>>>
> >> > >>>>>> > >
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>
> >> > <mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de> <mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>>
> >> > ><mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de> <mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>>>
> >> > >>>>>> > <mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>>
> >> > <mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de> <mailto:m.garten@hzdr.de
> <mailto:m.garten@hzdr.de>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
> <mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>
> <mailto: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/hyp
> >> > >>>>>> nos/.
> >> > >>>>>> > > 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:
>
>
--
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
|
|