Fail to find hdf5.h file

[frank-stonybrook]

I edit HDF5LDFLAGS and HDF5CPPFLAGS to the path which I installed hdf5 and run the make. However, I get error message: gcc h5mdtest.c -o h5mdtest h5mdplugin.c -I/usr/local/lib/vmd/plugins/include -std=c99 -L /home/frank/HDF5/lib -L -Wl,-rpath,/home/frank/Documents/VMD-h5mdplugin-master -lhdf5_hl -lhdf5 -lh5md h5mdplugin.c:21:18: fatal error: hdf5.h: No such file or directory

Actually the hdf5.h is in the path specified by HDF5CPPFLAGS, why gcc complaints that hdf5.h couldn't be find?

Thanks

[jonaslandsgesell]

Actually the plugin supports two build systems: 1) the autotools (make) 2) cmake If you run make you need to adapt (only) the makefile and refer to the correct paths. The corresponding part where you need to adapt the makefile is the following: VMDDIR, HDF5LDFLAGS, HDF5CPPFLAGS

[frank-stonybrook]

Hi Jonaslandsgesell,

Is there any reason which causes the make fails? Because I already changed the three variables to the correct paths. This is part of my Makefile script, I am not sure whether there is any other problem.

Thanks

[jonaslandsgesell]

Hi Frank, this will not directly solve the problem but I think in the original version of the makefile there is a point behind -L in the following line LDFLAGS=$(HDF5LDFLAGS) -L. (maybe try a make clean after you added the point)

[frank-stonybrook]

Hi Jonaslandsgesell, Unfortunately, I still get error when running make. However if I manually copy the hdf5.h file in the current directory of Makefile, this error is fixed. Any idea why it happens?

Thanks

[jonaslandsgesell]

I think your adapted Makefile does not correctly try to use the header files. Otherwise your gcc command should look like:

gcc h5mdtest.c -o h5mdtest h5mdplugin.c -I/usr/local/lib/vmd/plugins/include -I/home/frank/HDF5/include -std=c99 -L /home/frank/HDF5/lib -L -Wl,-rpath,/home/frank/Documents/VMD-h5mdplugin-master -lhdf5_hl -lhdf5 -lh5md

Maybe the easiest way for a further analysis of the problem would be, if you clone the project from scratch. Adapt the makefile only in these 3 places and then try again to run make.

[frank-stonybrook]

Hi Jonaslandsgesell,

I just download all files and rerun the make. The error still appears.

After carefully checking the standard gcc command you provided and my results, I find out that the only difference is '-I/home/frank/HDF5/include'. I look at the original Makefile script on github. I think that this command is encoded by the this line in Makefile:

It seems that there is something which encoded this part '-I/home/frank/HDF5/include' is missing?? Another thing which confirms my suspension is that the variable 'CPPFLAGS' never used after defining. Thanks Frank

[frank-stonybrook]

Hi Jonaslandsgesell,

I figure out the problem. There is $(HDF5CPPFLAGS) missing in the command. When I fix it, the make doesn't complain this problem.

[jonaslandsgesell]

Thanks for the hint. I will fix this.