Return-Path: Received: from [93.37.191.122] (account huebl@hzdr.de HELO [192.168.1.100]) by hzdr.de (CommuniGate Pro SMTP 6.1.11) with ESMTPSA id 14544539 for picongpu-users@hzdr.de; Thu, 29 Sep 2016 12:54:30 +0200 Subject: Re: Running PIConGPU via tbg To: picongpu-users@hzdr.de References: From: "Huebl, Axel" Message-ID: <013db498-178e-f9ef-b666-0e4ad28eb832@hzdr.de> Date: Thu, 29 Sep 2016 12:54:29 +0200 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/mixed; boundary="------------752356BF5D8169B012064839" This is a multi-part message in MIME format. --------------752356BF5D8169B012064839 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit 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 >: > > 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 > >>: > > 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 > > > > >>>: > > 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 > > > > > >>> 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 > > > > > >>>: > > > >> 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 > > > > > >> > >> > > > > >>>>: > >> > > >> > 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 > >> > > > > >> > > > > > >>>> 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 > > > > > >> > >> > > > > >>>>: > >> > > > >> > >> 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 > >> > >> > >> > >> $PICSRC/configure ~/paramSets/case001 > >> > >> > >> > >> make -j install > >> > >> (please only do the make command inside the > build directory > >> > >> - if the configure command writes to any > other > directory > >than > >> build > >> > >> that is a sign that something went wrong) > >> > >> > >> > >> --> Please send us all the output until > there again > >> > >> > >> > >> Best, > >> > >> > >> > >> Marco > >> > >> > >> > >> Am Tue, 9 Aug 2016 16:50:05 -0500 > schrieb Alex > Francisco < > >> > >> djlexes@gmail.com > > > > >> > > > > > >>>>: > >> > >> > >> > >>> alex@alex-Satellite-L635:~/src/picongpu$ > ./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 > > > > > > >> > >> > > > > > >>>>: > >> > >>> > >> > >>> 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 > > > > > > >> > >> > > > > > >>>>: > >> > >>>> > >> > >>>> 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 > > > > > >> > >> > > > > >>>>: > >> > >>>>> > >> > >>>>> 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 > > > > > > >> > >> > > > > >>> > >> > >>>>>> > > > > > >> > > > > > >>>>>: > >> > >>>>>> > > >> > >>>>>> > 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 > >> > > > > > >> > > > > > >>> > >> > >>>>>> > > > > > >> > > > > > > >>>> > >> > >>>>>> > > > > > > >> > > > > > > >>> > >> > > > > >> > > > > > >>>>>>: > >> > >>>>>> > > > >> > >>>>>> > > 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 > > > > >> > > > > > >>> > >> > >>>>>> > > > > > >> > > > > > > >>>> > >> > >>>>>> > > > > > > > >> > >> > > > > >>> > >> > > > > > >> > > > > > >>>>> > >> > >>>>>> > > > > > > > >> > >> > > > > >>> > >> > > > > > >> > > > > > >>>> > >> > >>>>>> > > > > > >> > > > > > >>> > >> > > > > >> > > > > > >>>>>>>: > >> > >>>>>> > > > >> > >>>>>> > > > >> > >>>>>> > > 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. 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