H5Part development and discussion

["Gsell Achim (PSI)" <achim.gsell AT psi.ch>]

Hi Benjamin

> On 8 Mar 2021, at 14:34, Koch, Benjamin <benjamin.koch2 AT rwth-aachen.de> 
> wrote:
> 
> 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?

The term "(time-)steps" is misleading but is still used mainly out of 
historical reasons. The term "iteration number" would fit better. You can use 
attributes to store additional information per step/iteration. Hence you can 
store the date/time as string or integer in a step/iteration attribute. See 
'examples/H5/write_step_attribsf.f90'.

Best

Achim


> 
> 
> 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>