netcdf: cannot locate HDF5

[richard.katz@…]

Hello, I've got a configure error with netcdf that I don't know how to fix.

with

sudo port install netcdf

I have the error

:info:configure checking hdf5.h usability... no
:info:configure checking hdf5.h presence... no
:info:configure checking for hdf5.h... no
:info:configure configure: error: NetCDF-4 requires HDF5, but hdf5.h cannot be found.
:info:configure Command failed:  cd "/opt/local/var/macports/build/_opt_scienceports_science_netcdf/netcdf/work/netcdf-4.2.1.1" && ./configure --prefix=/opt/local --disable-doxygen --enable-netcdf-4
:info:configure Exit code: 1

and yet

sudo port installed hdf5-18 

returns

The following ports are currently installed:
  hdf5-18 @1.8.10_0+clang
  hdf5-18 @1.8.10_0+clang+openmpi (active)

and

ls /opt/local/include/hdf5*

gives

/opt/local/include/hdf5.h	/opt/local/include/hdf5.mod	/opt/local/include/hdf5_hl.h 

Thanks, Richard

[larryv (Lawrence Velázquez)]

In the future, please Cc relevant port maintainers.

[tenomoto (Takeshi Enomoto)]

Sorry for slow response. I cannot reproduce the problem. I have little to say from what you wrote. I need to look at main.log and config.log. Can you upload ${prefix}/var/macports/logs/*/netcdf/main.log and ${prefix}/var/macports/build/*/netcdf/work/netcdf-4.2.1.1/config.log, where ${prefix} is usually /opt/local and * changes depending on where you have the port tree.

[richard.katz@…]

Configure log

[richard.katz@…]

Main log

[richard.katz@…]

Thank you for your reply. I have attached the logs. Best wishes.

[tenomoto (Takeshi Enomoto)]

Looking at configure.log, configure failed because of missing mpi.h.

[richard.katz@…]

Interesting. Checking installed mpi ports:

$ port installed openmpi

Warning: port definitions are more than two weeks old, consider using selfupdate
The following ports are currently installed:
  openmpi @1.6.3_0+clang
  openmpi @1.6.3_0+gcc47 (active)

and looking for mpi.h manually:

$ ls /opt/local/include/openmpi/

mpi-ext.h			mpif-common.h			mpif.h
mpi.h				mpif-config.h			openmpi/
mpi_portable_platform.h		mpif-mpi-io.h			vampirtrace/

$ ls /opt/local/include/mpi*

ls: /opt/local/include/mpi*: No such file or directory

so I wonder if these ports expect to find mpi.h in /opt/local/include/ but not in /opt/local/include/openmpi

[tenomoto (Takeshi Enomoto)]

I was able to reproduce the problem. You probably have hdf5-18 +openmpi -cxx. I was able to configure netcdf successfully with +openmpi. I will modify Portfile to force +openmpi when hdf5-18 is installed with +openmpi.

[tenomoto (Takeshi Enomoto)]

Committed the changes in r108224.

[richard.katz@…]

Thanks. I installed with +openmpi and it worked smoothly.