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[re-sent from yesterday]
Hi Danila,
let us move this to github, so we can track what this tool needs in
terms of updates.
https://github.com/ComputationalRadiationPhysics/picongpu/issues/1544
> I'm not exactly clear what modules are...
seems not to be the problem. modules are just a way to load libraries on
HPC systems via "module load <someVersionOf GCC MPI or HDF5>"
Thanks,
Axel
On 12.07.2016 05:44, Khikhlukha Danila wrote:
> Dear Axel,
> sorry for such a big delay in response. Now I going back to the problem of splash2txt.
> I'm not exactly clear what modules are... ldd shows no problems, the binary itself starts normally. I'm not using ADIOS module at the moment, however it mentioned as an optional module.
>
> Below you can find the output of the -v option:
> danila@GPU: simOutput$ splash2txt -v
> Usage splash2txt [options] <input-file>
> :
> -h [ --help ] print help message
> -v [ --verbose ] verbose output, print status messages
> -m [ --mode ] arg (=splash) File Mode [splash]
> -l [ --list ] list the available datasets for an input file
> --input-file arg parallel input file
> -o [ --output-file ] arg output file (otherwise stdout)
> -s [ --step ] arg (=0) requested simulation step
> -d [ --data ] arg name of datasets to print
> --slice arg (=xy) dimensions of slice for field data, e.g. xy
> --offset arg (=0) offset of slice in dataset
> --delimiter arg (= ) select a delimiter for data elements. default is
> a single space character
> --no-units no conversion of stored data elements with their
> respective unit
>
> So the command
>
> danila@GPU: simOutput$ splash2txt --slice xy -s 50000 -d fields/FieldE/y --offset 128 --delimiter " " --input-file simData >& output
>
> gives the same error after the long table of numbers...
>
> danila@GPU: simOutput$ tail -n16 output
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> splash2txt: /home/danila/tools/picongpu/src/tools/splash2txt/tools_splash_parallel.cpp:200: void ToolsSplashParallel::printFields(std::vector<ExDataContainer>): Assertion `element != __null' failed.
> [GPU-SERVER-97:07250] *** Process received signal ***
> [GPU-SERVER-97:07250] Signal: Aborted (6)
> [GPU-SERVER-97:07250] Signal code: (-6)
> [GPU-SERVER-97:07250] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xf8d0) [0x7f0fa91e28d0]
> [GPU-SERVER-97:07250] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37) [0x7f0fa7e94067]
> [GPU-SERVER-97:07250] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x148) [0x7f0fa7e95448]
> [GPU-SERVER-97:07250] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x2e266) [0x7f0fa7e8d266]
> [GPU-SERVER-97:07250] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x2e312) [0x7f0fa7e8d312]
> [GPU-SERVER-97:07250] [ 5] splash2txt(_ZN19ToolsSplashParallel11printFieldsESt6vectorI15ExDataContainerSaIS1_EE+0x2b2) [0x46e9fa]
> [GPU-SERVER-97:07250] [ 6] splash2txt(_ZN19ToolsSplashParallel13convertToTextEv+0xa9a) [0x46f638]
> [GPU-SERVER-97:07250] [ 7] splash2txt(main+0x278) [0x454597]
> [GPU-SERVER-97:07250] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f0fa7e80b45]
> [GPU-SERVER-97:07250] [ 9] splash2txt() [0x452c2f]
> [GPU-SERVER-97:07250] *** End of error message ***
>
> Best regards,
> Danila.
> ________________________________________
> From: picongpu-users@hzdr.de [picongpu-users@hzdr.de] on behalf of Huebl, Axel [a.huebl@hzdr.de]
> Sent: Thursday, June 16, 2016 3:05 PM
> To: picongpu-users@hzdr.de
> Subject: Re: [PIConGPU-Users] splash2txt assert fail
>
> Hi,
>
>
> looks odd.
>
> With
> --offset
> better set exactly the box size // 2 to get the middle of your
> simulation (e.g., L_z = 512 -> "--slice xy --offset 256").
>
> Can you check if
> splash2txt --list --input-file h5_file_prefix
>
> works and if -d was selected correctly?
>
> It's likely you have to set the file prefix without the _timestep.h5
> extension.
>
> Also, can you check what -v (verbose) prints with it?
>
> Modules loaded correctly?
>
>
> Axel
>
> On 16.06.2016 13:24, Khikhlukha Danila wrote:
>> Dear all,
>> Recently with 0.1.2 I observe a strange behavior of splash2txt. Likely
>> I'm misusing the tool, however I just want to confirm...
>>
>> So my simulation was launched with an option " --hdf5.period 1000
>> --hdf5.file simData". In the ouput directory I observe a bunch of files
>> simData_*.h5 with numeration starts from 0.
>> I want to plot Ey fieled sliced in xy direction @ step = 10000. I found
>> the example of how to use splash2txt here https://git.io/vo07M. I
>> modified it a bit and invoke the following:
>> splash2txt --slice xy -s 10000 -d fields/FieldE/y --offset 0 --delimiter
>> " " --input-file simData
>>
>> I got an array of data to stdout and in the end:
>> splash2txt:
>> /home/danila/tools/picongpu/src/tools/splash2txt/tools_splash_parallel.cpp:200:
>> void ToolsSplashParallel::printFields(std::vector<ExDataContainer>
>> [GPU:11444] *** Process received signal
>> ***
>>
>> [GPU:11444] Signal: Aborted
>> (6)
>>
>> [GPU:11444] Signal code:
>> (-6)
>>
>> [GPU:11444] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xf8d0
>> [0x7fe3085468d0]
>> [GPU:11444] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37)
>> [0x7fe3071f8067]
>> [GPU:11444] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x148)
>> [0x7fe3071f9448]
>> [GPU:11444] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x2e266)
>> [0x7fe3071f1266]
>> [GPU:11444] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x2e312)
>> [0x7fe3071f1312]
>> [GPU:11444] [ 5]
>> splash2txt(_ZN19ToolsSplashParallel11printFieldsESt6vectorI15ExDataContainerSaIS1_EE+0x2b2)
>> [0x46e9fa]
>> [GPU:11444] [ 6]
>> splash2txt(_ZN19ToolsSplashParallel13convertToTextEv+0xa9a)
>> [0x46f638]
>> [GPU:11444] [ 7] splash2txt(main+0x278)
>> [0x454597]
>>
>> [GPU:11444] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)
>> [0x7fe3071e4b45]
>> [GPU:11444] [ 9] splash2txt()
>> [0x452c2f]
>>
>> [GPU:11444] *** End of error message
>> ***
>>
>> Aborted
>>
>>
>> However I'm not sure that I'm using splash2txt correctly. Could you
>> please take a look?
>>
>> Thank you in advance,
>> Danila.
>
> --
>
> 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
>
--
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
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