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 14044603 for picongpu-users@hzdr.de; Tue, 09 Aug 2016 18:27:49 +0200 Subject: Re: [PIConGPU-Users] [PIConGPU-Users] [PIConGPU-Users] [PIConGPU-Users] Compiling splash2txt To: picongpu-users@hzdr.de References: From: =?UTF-8?Q?Ren=c3=a9_Widera?= Message-ID: <57AA0485.6090802@hzdr.de> Date: Tue, 9 Aug 2016 18:27:49 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:38.0) Gecko/20100101 Thunderbird/38.8.0 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit 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 >: > > Dear Alex, > > the TBG command as you executed it uses the relative path from inside > your paramSet. The config file is located inside > ~/paramSets/case001/submit - just like the hardware template file > k20_profile.tpl is in ~/paramSets/case001/submit/hypnos/. > So either execute the command from ~/paramSets/case001 or use the > absolute path. > > Don't forget to delete the folder ~/runs/testBatch01/ before because > otherwise TBG will tell you that the job name is already in use. (The > run folders all contain a copy of the executable and the parameter set > regardless if the job is running or not) > > You seem to be using the config files and the architecture template of > our home cluster on your local machine, though. That would require you > to have 16 GPUs if you use the 0016gpus.cfg file. If you want to do a > quick test whether the code is running at all you can just execute: > > cd ~/paramSets/case001/bin > > ./picongpu -d 1 1 1 -g 64 128 64 -s 1000 > > This will run the code with one GPU on a grid of 64 x 128 x 64 cells for > 1000 steps. > Please look at any of the *gpus.cfg files for additional options to the > command that will generate output. I would recommend something like: > > --png_e.period 50 --png_e.axis yz --png_e.slicePoint 0.5 --png_e.folder > pngElectronsYZ --elec_cnt.period 50 > > This will give you the total count of electrons in the simulation at > every 50th time step and also a PNG showing a YZ slice of the electron > charge density. The output will now be created directly in the "bin" > folder where your executable is. > > Hope this works for you! > > Best, > > Marco > > Am 08.08.2016 um 18:14 schrieb Alex Francisco: > > Thank you very much this worked!!! > > > > When I do execute this line of code in my terminal show this: > > > > alex@alex-Satellite-L635:~/src/picongpu$ tbg -s qsub -c > > submit/0016gpus.cfg -t ~/paramSets/case001/submit/hypnos/k20_profile.tpl > > ~/runs/testBatch01/ > > > > The given cfg file "submit/0016gpus.cfg" does not exist (-c|--cfg). > > > > > > However, I turn to the folder case001 and there show me the folder > > testBatch01, I ask to yours, if it can be showing me this because I once > > create and do not need to recreate the subfolder (testBatch01) ?? > > > > alex@alex-Satellite-L635:~/runs$ ls > > testBatch01 > > > > and in the folder testBatch01 show me this files: > > > > alex@alex-Satellite-L635:~/runs/testBatch01$ ls > > picongpu tbg > > > > > > Furthermore, as I view the simulation output? > > > > > > I hope you can help me. > > > > Thank you very much. > > > > Alex Estupiñán. > > > > > > 2016-08-06 11:33 GMT-05:00 Huebl, Axel > > >>: > > > > I also fixed that compile problem in splash2txt by now. > > > > > >https://github.com/ComputationalRadiationPhysics/picongpu/pull/1545 > > > > > > > > You can just remove or comment out via "//" the line that is causing the > > error. > > > > > > Axel > > > > On 06.08.2016 11:07, Axel Huebl wrote: > > > Dear Alex, > > > > > > You don't need to build the helper tool in post-processing, > > splash2txt for now. Just skip step 6. > > > > > > Otherwise: please make sure the source code is unmodified. For > > compile errors, please report compiler version, cmake version, cmake > > -L . output and ubuntu version. > > > > > > Compile issues are also best tracked in our github since we can > > assign, track, link and archive it there. > > > > > > Axel > > > > > > On August 6, 2016 10:56:09 AM EDT, "Bussmann, Dr. Michael (FWKT) - > > 4167" > >> wrote: > > >> Dear Alex, > > >> > > >> Could you please tell us which version of PIConGPU you are > using, > > >> provide CMake log files and CMakeLists.txt so we can have > a look at > > >> what > > >> is going on. > > >> > > >> Best, Michael > > >> > > >> Am 05.08.2016 um 18:13 schrieb Alex Francisco: > > >>> Dear Michael Bussmann and picongpu users: > > >>> > > >>> I appreciate your help, I already understood that ADIOS > is optional, > > >> but > > >>> when i continue, my ubuntu terminal show me, the > following error, > > >> when I > > >>> execute the step 6 "make -j": > > >>> > > >>> [ 50%] Building CXX object > > CMakeFiles/splash2txt.dir/splash2txt.cpp.o > > >>> > /home/alex/src/picongpu/src/tools/splash2txt/splash2txt.cpp: In > > >> function > > >>> ‘bool parseOptions(int, char**, ProgramOptions&)’: > > >>> > /home/alex/src/picongpu/src/tools/splash2txt/splash2txt.cpp:164:24: > > >>> error: ‘desc’ was not declared in this scope > > >>> errorStream << desc << "\n"; > > >>> ^ > > >>> CMakeFiles/splash2txt.dir/build.make:54: recipe for target > > >>> 'CMakeFiles/splash2txt.dir/splash2txt.cpp.o' failed > > >>> make[2]: *** [CMakeFiles/splash2txt.dir/splash2txt.cpp.o] > Error 1 > > >>> CMakeFiles/Makefile2:60: recipe for target > > >>> 'CMakeFiles/splash2txt.dir/all' failed > > >>> make[1]: *** [CMakeFiles/splash2txt.dir/all] Error 2 > > >>> Makefile:117: recipe for target 'all' failed > > >>> make: *** [all] Error 2 > > >>> > > >>> Imágenes integradas 1 > > >>> > > >>> > > >>> I hope you can help me. > > >>> > > >>> Thank you very much. > > >>> > > >>> Alex Estupiñán. > > >>> > > >>> > > >>> 2016-08-02 6:34 GMT-05:00 Bussmann, Dr. Michael (FWKT) - 4167 > > >>> > > > > > >>>: > > >>> > > >>> Oops, sorry, you completed step 5 and can go to step > 6. My bad! > > >>> > > >>> Am 02.08.2016 um 13:25 schrieb Bussmann, Dr. Michael > (FWKT) - > > >> 4167: > > >>> > Dear Alex, > > >>> > > > >>> > As Axel pointed out in his E-mail, this is no > error. It simply > > >>> tells you > > >>> > that a software component is missing that is > optional, but not > > >>> required > > >>> > to build PIConGPU. This means PIConGPU can use > ADIOS, but does > > >> not > > >>> need > > >>> > it to run properly. > > >>> > > > >>> > Yes, this is a bit confusing, but as you see the > output tells > > >> you that > > >>> > your build files have been written to > /home/alex/src/picongpu. > > >> So > > >>> > everything is fine! > > >>> > > > >>> > You have now completed step 6 in the install > process, see > > here: > > >>> > > > >>> > > >> > > > https://github.com/ComputationalRadiationPhysics/picongpu/blob/release-0.1.2/doc/INSTALL.md > > > > > > > >>> > > >> > > > > > > >> > > >>> > > > >>> > As Axel also wrote, you can now simply go to step > 7, typing > > >> 'make'. > > >>> > > > >>> > If you run into problems, please provide error log > files with > > >> your > > >>> > E-mails and keep posting to the Users mailing list. > > >>> > > > >>> > Hope this helps, Michael > > >>> > > > >>> > Am 02.08.2016 um 03:38 schrieb Alex Francisco: > > >>> >> Dear Michael Bussmann: > > >>> >> > > >>> >> I hope you are well. I am a doctoral student at the > > University > > >> of > > >>> >> Colombia UIS. I am installing the PiconGpu program > on my > > >> laptop, my > > >>> >> laptop has a software ubuntu 16.04 LTS 64-bit. > > >>> >> > > >>> >> My ubuntu terminal shows me the following error: > > >>> >> > > >>> >> -- Could NOT find ADIOS (missing: ADIOS_LIBRARIES > > >>> ADIOS_INCLUDE_DIRS) > > >>> >> (Required is at least version "1.6.0") > > >>> >> > > >>> >> > > >>> >> Imágenes integradas 1 > > >>> >> > > >>> >> > > >>> >> the problem still, I am very interested in I can > solve this > > >>> problem. I > > >>> >> need install this program for work in my doctoral job. > > >>> >> > > >>> >> I hope you can help me. > > >>> >> > > >>> >> Thank you very much. > > >>> >> > > >>> >> Alex Estupiñán. > > >>> >> > > >>> > > > >>> > > ############################################################# > > >>> > 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 > > > > > > >>> > > >>> > > >>> > > > >>> > > >>> ############################################################# > > >>> 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 > > > > > > >>> > > >>> > > >>> > > >>> > > >> > > >> ############################################################# > > >> 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 > > > >> > > > > > > > > > ############################################################# > > > 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 > > > >> > > > > > > > -- > > > > 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