[FLASH-USERS] hdf5_flash.h:34:10: fatal error: hdf5.h: No such file or directory

[Ernesto Zurbriggen]

Hi!

Honestly, I don't know exactly what could be the problem, but I give you
below some ideas to fix it.

Maybe you installed a very new hdf5 library release. I tried flash4.7 (I
haven't got flash4.7.1) with the releases 1.10.7 and 1.12.1 and it worked
well, but the newest release 1.14.3 may be incompatible.

I'm assuming you are in a linux system. How did you install the library? I
installed it like this.

*Installation*:
$ tar xzf hdf5-1.10.7.tar.gz
$ cd hdf5-1.10.7/
$ ./configure --enable-parallel --enable-static --enable-shared
--enable-fortran --prefix=/opt/hdf5/1.10.7/
$ make -j4
$ sudo make -j4 install

*Add path in your bash*:
export PATH=$PATH:/opt/hdf5/1.10.7/bin
export INCLUDE=$INCLUDE:/opt/hdf5/1.10.7/include
export CPATH=$CPATH:/opt/hdf5/1.10.7/include
export LIBRARY_PATH=$LIBRARY_PATH:/opt/hdf5/1.10.7/lib
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/hdf5/1.10.7/lib

*Add path in your Makefile*:
HDF5_PATH=/opt/hdf5/1.10.7

Good luck!
Ernesto.


On Fri, 2 Feb 2024 at 01:47, 郑佳乐 <zhengjl1103 at shu.edu.cn> wrote:

> Hi!
>
>
> Thank you for your previous help. That works! But again I encountered a
> problem I couldn't solve.
>
>
>
>
>
>
>
>
>
>
>
>
> *layoneu at layoneu:~/Desktop/FLASH4.7.1/simulation/Sedov$ make rm -f
> reorder.sh /usr/bin/mpif90 -ggdb -c -O2 -fdefault-real-8 -fdefault-double-8
> -fallow-argument-mismatch -Wuninitialized  -DMAXBLOCKS=1000 -DNXB=8 -DNYB=8
> -DNZB=1 -DN_DIM=2 Hydro_recalibrateEints.F90 /usr/bin/mpif90 -ggdb -c -O2
> -fdefault-real-8 -fdefault-double-8 -fallow-argument-mismatch
> -Wuninitialized  -DMAXBLOCKS=1000 -DNXB=8 -DNYB=8 -DNZB=1 -DN_DIM=2
> gr_xyzToBlock.F90 /usr/bin/mpicc -I/usr/include -DH5_USE_16_API -ggdb -c
> -O2 -Wuninitialized -D_FORTIFY_SOURCE=2 -DMAXBLOCKS=1000 -DNXB=8 -DNYB=8
> -DNZB=1 -DN_DIM=2 io_attribute.c In file included from io_h5_attribute.h:6,
>                  from io_attribute.h:13,                  from
> io_attribute.c:2: hdf5_flash.h:34:10: fatal error: hdf5.h: No such file or
> directory    34 | #include <hdf5.h>       |          ^~~~~~~~ compilation
> terminated. make: *** [Makefile:124: io_attribute.o] Error 1*
> I've changed the hdf5 path in Makefile.h and export the hdf5 installation
> path to PATH, but that doesn't seem to work.
>
> Any help would be highly appreciated！
> Best!
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>
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