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Re: [H5part] H5Hut fortran compiling


Chronological Thread  
  • From: "Gsell Achim (PSI)" <achim.gsell AT psi.ch>
  • To: "Koch, Benjamin" <benjamin.koch2 AT rwth-aachen.de>
  • Cc: "h5part AT lists.psi.ch" <h5part AT lists.psi.ch>
  • Subject: Re: [H5part] H5Hut fortran compiling
  • Date: Mon, 8 Mar 2021 15:40:36 +0000
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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>




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