h5part AT lists.psi.ch
Subject: H5Part development and discussion
- 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: Wed, 3 Mar 2021 17:07:05 +0000
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> On 2 Mar 2021, at 20:03, Koch, Benjamin <benjamin.koch2 AT rwth-aachen.de>
> 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.
> 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>
>> I'm working on a linux cluster.
> Anything special on this cluster? Or just some standard Linux cluster
>> 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?)
> If you want to build the example, you can run configure with
>> • 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
> h5pcc -showconfig
>> • make install
>> After that, I call al little script in the examples folder:
>> 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 ...
>> 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:
>> 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
> 5232 Villigen PSI
- Re: [H5part] H5Hut fortran compiling, Gsell Achim (PSI), 03/01/2021
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