Opened 11 years ago
Closed 11 years ago
#39529 closed defect (fixed)
netcdf: cannot locate HDF5
Reported by: | richard.katz@… | Owned by: | tenomoto (Takeshi Enomoto) |
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Priority: | Normal | Milestone: | |
Component: | ports | Version: | 2.1.3 |
Keywords: | Cc: | ||
Port: | netcdf |
Description
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
Attachments (2)
Change History (11)
comment:1 Changed 11 years ago by larryv (Lawrence Velázquez)
Owner: | changed from macports-tickets@… to takeshi@… |
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Summary: | netcdf configure error → netcdf: cannot locate HDF5 |
comment:2 follow-up: 3 Changed 11 years ago by 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.
comment:3 Changed 11 years ago by richard.katz@…
Thank you for your reply. I have attached the logs. Best wishes.
comment:4 Changed 11 years ago by tenomoto (Takeshi Enomoto)
Looking at configure.log, configure failed because of missing mpi.h.
comment:5 Changed 11 years ago by 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
comment:6 Changed 11 years ago by 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.
comment:8 Changed 11 years ago by richard.katz@…
Thanks. I installed with +openmpi and it worked smoothly.
comment:9 Changed 11 years ago by tenomoto (Takeshi Enomoto)
Resolution: | → fixed |
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Status: | new → closed |
In the future, please Cc relevant port maintainers.