H5Part development and discussion

["Koch, Benjamin" <benjamin.koch2 AT rwth-aachen.de>]

Hey Achim,

thanks again for the help.

I have one more question.

Using the example "write_stridedf.f90" I created some particles and displayed them with Paraview. After that I edited the example and added a new time step. This worked fine, but I can only assign integers to the time step. For us it would be nice to be able to display also the real time. So far I could not find anything in the code to do this. Is there already something implemented for this?

Best regards

Benjamin Koch

---

Von: Gsell Achim (PSI) <achim.gsell AT psi.ch>
Gesendet: Mittwoch, 3. März 2021 18:07:05
An: Koch, Benjamin
Cc: h5part AT lists.psi.ch
Betreff: Re: [H5part] H5Hut fortran compiling

 

Hi Benjamin

> On 2 Mar 2021, at 20:03, Koch, Benjamin <benjamin.koch2 AT rwth-aachen.de> wrote:
>
> Hey Achim,
>
> I'm working on the standard linux cluster @RWTH.
>
> With --enable-examples --enable-parallel compiling the examples worked.
> After that I browsed through the Makefiles of the examples and found the error. I did not include the C library -lH5hut.
> Now i have learned how to compile Fortran and C Code together 😅
>
> Because of the test error, I still attached the h5cc output. The h5pcc command could not be found on the cluster.
> Can the test error create problems? Where should I expect errors?

The tests should pass without problems. If you are using the Intel compile make sure you use a hdf5 library compiled with Intel compiler and Intel MPI.

Best

Achim


>
>
> Thank you very much and best regards
> Benjamin Koch
> Von: Gsell Achim (PSI) <achim.gsell AT psi.ch>
> Gesendet: Montag, 1. März 2021 16:39:56
> An: Koch, Benjamin
> Cc: h5part AT lists.psi.ch
> Betreff: Re: [H5part] H5Hut fortran compiling
> 
> Hi Benjamin,
>
> I just tried with GCC without any problems. With Intel I still have to test.
>
>
>> On 1 Mar 2021, at 11:56, Koch, Benjamin <benjamin.koch2 AT rwth-aachen.de> wrote:
>>
>> I'm working on a linux cluster.
>
> Anything special on this cluster? Or just some standard Linux cluster @RWTH?
>>
>> Today, i tried it again, to have a clean environement.
>> Here is a list of how I installed H5hut, did I something wrong?
>>
>>       • git clone https://gitlab.psi.ch/H5Hut/src.git
>>       • ./autogen.sh (in the src folder of course)
>>       • ./configure --enable-fortran (Is this what you mean by how I call the configure script?)
>
> Yes.
>
> If you want to build the example, you can run configure with ‘--enable-examples’.
>
>>       • make
>>       • make test (Ouput: Nothing to do for test)
>>       • Tried the tests in the test folder. The h5u_test gives an error for "read4" that the values are incorrect.
>
> Which hdf5 version are you using? Please send the output of
>
> h5cc -showconfig
>
> and
>
> h5pcc -showconfig
>
>
>>       • make install
>>
>> After that, I call al little script in the examples folder:
>> <Script.png>
>> In a similar way I was able to compile the C code, but maybe I'm missing something for Fortran?
>
> In the script you are using the MPI wrapper of the Intel Fortran compiler but you compiled H5hut without MPI! To compile H5hut with MPI you have to run something like
>
> configure --enable-parallel --enable-fortran ...
>
> On some systems you have to set the environment variables CC and FC:
> CC=mpiicc FC=mpiifort ./configure ...
> make
> ...
>
>
>
>
> Best
>
> Achim
>
>>
>> Best regards
>> Benjamin Koch
>>
>> Of topic:
>> One could say, because the institute for Combustion Technology is known for the thermodynamics lecture. But there is also another Institute for technical thermodynamics.
>>
>>
>> Von: Gsell Achim (PSI) <achim.gsell AT psi.ch>
>> Gesendet: Freitag, 26. Februar 2021 13:29
>> An: Koch, Benjamin
>> Cc: h5part AT lists.psi.ch
>> Betreff: Re: [H5part] H5Hut fortran compiling
>> 
>> Hi Benjamin,
>>
>> I just tried to reproduce on macOS 10.15 with gcc8 from Macports. For me everything compiled and linked fine.
>>
>> On which system (Linux (distribution?), macOS, ...) are you compiling?
>>
>> How do you call the configure script?
>>
>> From where did you downloaded/cloned H5hut? The "official" URL is:
>>
>> https://gitlab.psi.ch/H5hut/src
>>
>>
>> Best
>>
>> Achim
>> --
>> Of topic: is the Institute for Combustion Technology the former Institut für Thermodynamik?
>>
>>
>> > On 25 Feb 2021, at 11:45, Koch, Benjamin <benjamin.koch2 AT rwth-aachen.de> wrote:
>> >
>> > Hello team of H5Hut,
>> >
>> > I'm a master student of the RWTH-Aachen and I work for the Institute for Combustion Technology. My supervisor and I are interested in data management via HDF5.
>> > We are working on the simulation of nano-particle combustion. Because the current method for writing out particle quantities could be faster, we discover your program on github.
>> > Our simulation program uses fortran code, so we try to include the fortran part of H5Hut.
>> >
>> > I tried to run the examples and it worked for the C part of the code, but I can't get the fortran code working.
>> >
>> > I think there is a problem with the linking of the library. The library seems to be linked, but then the error messages follow that some functions are not found. For example "pathto/src/build/lib/libH5hutF.so: undefined reference to `h5_flush_iteration'".
>> >
>> > Before I get too deep into the solving this problem, I like to ask:
>> > The last updates of the fortran code seem to be some time ago, is it still up to date?
>> >
>> > Best regards
>> > Benjamin Koch
>
> Senior Scientist
> Paul Scherrer Institut
> Laboratory for Scientific Computing and Modeling
> OHSA/D04
> 5232 Villigen PSI
>
> <h5cc.txt>