picongpu-users@hzdr.de Mailing List Archive

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>:

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>>:

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>> 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>>:
>
>> 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>>>:
>> >
>> > 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>>> 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>>>:
>> > >
>> > >> 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
>> > >>
>> > >> $PICSRC/configure ~/paramSets/case001
>> > >>
>> > >> make -j install
>> > >> (please only do the make command inside the build directory
>> > >> - if the configure command writes to any other directory
>than
>> build
>> > >> that is a sign that something went wrong)
>> > >>
>> > >> --> Please send us all the output until there again
>> > >>
>> > >> Best,
>> > >>
>> > >> Marco
>> > >>
>> > >> Am Tue, 9 Aug 2016 16:50:05 -0500 schrieb Alex Francisco <
>> > >> djlexes@gmail.com <mailto:djlexes@gmail.com>
<mailto:djlexes@gmail.com <mailto:djlexes@gmail.com>>>:
>> > >>
>> > >>> alex@alex-Satellite-L635:~/src/picongpu$ ./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 project...
>> > >>> -- 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>>>:
>> > >>>
>> > >>> 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>>>:
>> > >>>>
>> > >>>> 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>>>:
>> > >>>>>
>> > >>>>> 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>>>>:
>> > >>>>>> >
>> > >>>>>> > 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>>>>>:
>> > >>>>>> > >
>> > >>>>>> > > 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>>>>>>:
>> > >>>>>> > >
>> > >>>>>> > >
>> > >>>>>> > > 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:
>> > >>>>>> > > >
>> > >>>>>> > > >
>> > >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>>>
>> > >>>>>> > > <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 <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>>>>>>>:
>> > >>>>>> > > >
>> > >>>>>> > > > I also fixed that compile
>problem in
>> > >>>>>> splash2txt
>> > >>>>>> > by now.
>> > >>>>>> > > >
>> > >>>>>> > > >
>> > >>>>>> > >
>> > >>>>>> > >
>> > >>>>>> >
>> >
>>https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
>> >
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>>
>> > >>>>>> ull/1545
>> >
><https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
>> >
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>>
>> > >>>>>> ull/1545>
>> > >>>>>> > >
>> > >>>>>> >
>> >
><https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
>> >
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>>
>> > >>>>>> ull/1545
>> >
><https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
>> >
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>>
>> > >>>>>> ull/1545>>
>> > >>>>>> > >
>> > >>>>>> > >
>> > >>>>>> >
>> >
><https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
>> >
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>>
>> > >>>>>> ull/1545
>> >
><https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
>> >
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>>
>> > >>>>>> ull/1545>
>> > >>>>>> > >
>> > >>>>>> >
>> >
><https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
>> >
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>>
>> > >>>>>> ull/1545
>> >
><https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
>> >
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>>
>> > >>>>>> ull/1545>>>
>> > >>>>>> > > >
>> > >>>>>> > >
>> > >>>>>> >
>> >
<https://github.com/ComputationalRadiationPhysics/picongpu/
<https://github.com/ComputationalRadiationPhysics/picongpu/>
>> > <https://github.com/ComputationalRadiationPhysics/picongpu/
<https://github.com/ComputationalRadiationPhysics/picongpu/>>
>> > >>>>>> pull/1545
>> > >>>>>> >
>> >
<https://github.com/ComputationalRadiationPhysics/picongpu/
<https://github.com/ComputationalRadiationPhysics/picongpu/>
>> > <https://github.com/ComputationalRadiationPhysics/picongpu/
<https://github.com/ComputationalRadiationPhysics/picongpu/>>
>> > >>>>>> pull/1545>
>> > >>>>>> > >
>> > >>>>>> >
>> >
><https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
>> >
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>>
>> > >>>>>> ull/1545
>> >
><https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
>> >
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>>