Return-Path: Received: from [149.220.60.34] (account widera@hzdr.de [149.220.60.34] verified) by hzdr.de (CommuniGate Pro SMTP 6.1.11) with ESMTPSA id 14560509 for picongpu-users@hzdr.de; Fri, 30 Sep 2016 17:21:26 +0200 Subject: Re: [PIConGPU-Users] [PIConGPU-Users] Running PIConGPU via tbg To: picongpu-users@hzdr.de References: From: =?UTF-8?Q?Ren=c3=a9_Widera?= Message-ID: <71a556ed-3dc4-c263-12b8-88b1a0eb07cf@hzdr.de> Date: Fri, 30 Sep 2016 17:21:26 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:45.0) Gecko/20100101 Thunderbird/45.3.0 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Dear Alex, if possible please deinstall your mpich MPI and install openMPI. This would help if you not know how to use mpirun with mpich. best, René On 09/30/2016 05:12 PM, 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 mca > [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 > picongpu: proceso no encontrado > > =================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = PID 19829 RUNNING AT alex-Satellite-L635 > = EXIT CODE: 1 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > =================================================================================== > > I hope you can help me. > > Thank you very much for your help. > > Alex. > > > 2016-09-29 5:54 GMT-05:00 Huebl, Axel >: > > 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. Joehnk > VR 1693 beim Amtsgericht Dresden > > ############################################################# > This message is sent to you because you are subscribed to > the mailing list >. > To unsubscribe, E-mail to: > > To switch to the DIGEST mode, E-mail to > > > To switch to the INDEX mode, E-mail to > > Send administrative queries to > > > > -- René Widera Abteilung Laser-Teilchenbeschleunigung (FWKT) Helmholtz-Zentrum Dresden-Rossendorf Tel: +49 (0351) 260 3543 r.widera@hzdr.de http://www.hzdr.de Vorstand: Prof. Dr. Dr. h. c. Roland Sauerbrey, Prof. Dr. Dr. h. c. Peter Joehnk Vereinsregister: VR 1693 beim Amtsgericht Dresden