[FLASH-USERS] HDF5 compilation failed

[Ryan Farber]

Hi Alessandro,

You might be better off contacting the HDF5 group, but since I'm also
having an issue doing a local install of HDF5 (for enhanced debugging of
FLASH) and I was thinking of posting here since my issue is almost
certainly a silly PATH problem, here are some thoughts:

1. environment variables should have no spaces between the equal sign and
the value:
NOT :
  CC = mpicc
GOOD:
  CC=mpicc

2. You'll be better off supplying absolute paths when possible. That is,
what does "which mpicc" return? Use that full path. Additionally, make sure
just executing "mpicc" returns something, otherwise you have a PATH issue.

Similarly, specify the full path of configure rather than "./configure"
Use $HOME rather than ~/ for the full path (or typing the full path is also
fine).

3. I'd be surprised if you have write access to /usr. You more likely will
need to set your prefix to a directory you have full control over (such as
a subdirectory of your home space).

4. For further, perhaps more useful help, it would be nice if you supplied
the result of "echo $PATH" as well as "ls ~/software/flash/hdf5-1.8.10-patch1"
(or whatever the path to your hdf5 is).

Best wishes,
--------
Ryan


On Tue, Jul 9, 2024 at 6:33 AM Alessandro Ruocco <
alessandro.ruocco at fsdynamics.fi> wrote:

> Dear all,
>
> We are trying to install FLASH on our cluster, but we are having issues
> when compiling HDF5 parallel. Below the loaded modules and the error
> message while trying to configure HDF5:
>
>
> [~/software/flash/hdf5-1.8.10-patch1] (33 files, 1.1M) > module list
> Currently Loaded Modulefiles:
>   1) null                 3) toolbox/1.0          5) mpi/openmpi/1.10.7
>   2) uppdrag/base         4) local-soft/1.0       6) mpi/intel-mpi
>
> [~/software/flash/hdf5-1.8.10-patch1] (33 files, 1.1M) > CC = mpicc
> ./configure --prefix=/usr/local/lib/HDF5-parallel --enable-parallel
> -bash: CC: command not found
>
> [~/software/flash/hdf5-1.8.10-patch1] (33 files, 1.1M) > mpicc ./configure
> --prefix=/usr/local/lib/HDF5-parallel --enable-parallel
> ./configure: file not recognized: File format not recognized
> collect2: error: ld returned 1 exit status
>
> [~/software/flash/hdf5-1.8.10-patch1] (33 files, 1.1M) > cc = mpicc
> ./configure --prefix=/usr/local/lib/HDF5-parallel --enable-parallel
> cc: error: =: No such file or directory
> cc: error: mpicc: No such file or directory
>
> Do you have any suggestions on how to fix this?
>
> Best regards
> Alessandro
> ------------------------------
> *Alessandro Ruocco*, PhD [image: FS Dynamics Finland Oy AB]
> <http://fsdynamics.fi/>
> Engineer CFD
>
> FS Dynamics Finland Oy Ab
> c/o Polaris Business Park, Capella
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