[MacPorts] #39529: netcdf configure error
#39529: netcdf configure error ----------------------------+-------------------------------- Reporter: richard.katz@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Keywords: | Port: netcdf ----------------------------+-------------------------------- 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 -- Ticket URL: <https://trac.macports.org/ticket/39529> MacPorts <http://www.macports.org/> Ports system for OS X
#39529: netcdf: cannot locate HDF5 -----------------------------+----------------------- Reporter: richard.katz@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: netcdf | -----------------------------+----------------------- Changes (by larryv@…): * owner: macports-tickets@… => takeshi@… Comment: In the future, please Cc relevant port maintainers. -- Ticket URL: <https://trac.macports.org/ticket/39529#comment:1> MacPorts <http://www.macports.org/> Ports system for OS X
#39529: netcdf: cannot locate HDF5 -----------------------------+----------------------- Reporter: richard.katz@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: netcdf | -----------------------------+----------------------- Comment (by takeshi@…): 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. -- Ticket URL: <https://trac.macports.org/ticket/39529#comment:2> MacPorts <http://www.macports.org/> Ports system for OS X
#39529: netcdf: cannot locate HDF5 -----------------------------+----------------------- Reporter: richard.katz@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: netcdf | -----------------------------+----------------------- Comment (by richard.katz@…): Thank you for your reply. I have attached the logs. Best wishes. -- Ticket URL: <https://trac.macports.org/ticket/39529#comment:3> MacPorts <http://www.macports.org/> Ports system for OS X
#39529: netcdf: cannot locate HDF5 -----------------------------+----------------------- Reporter: richard.katz@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: netcdf | -----------------------------+----------------------- Comment (by takeshi@…): Looking at configure.log, configure failed because of missing mpi.h. -- Ticket URL: <https://trac.macports.org/ticket/39529#comment:4> MacPorts <http://www.macports.org/> Ports system for OS X
#39529: netcdf: cannot locate HDF5 -----------------------------+----------------------- Reporter: richard.katz@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: netcdf | -----------------------------+----------------------- Comment (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 -- Ticket URL: <https://trac.macports.org/ticket/39529#comment:5> MacPorts <http://www.macports.org/> Ports system for OS X
#39529: netcdf: cannot locate HDF5 -----------------------------+----------------------- Reporter: richard.katz@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: netcdf | -----------------------------+----------------------- Comment (by takeshi@…): 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. -- Ticket URL: <https://trac.macports.org/ticket/39529#comment:6> MacPorts <http://www.macports.org/> Ports system for OS X
#39529: netcdf: cannot locate HDF5 -----------------------------+----------------------- Reporter: richard.katz@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: netcdf | -----------------------------+----------------------- Comment (by takeshi@…): Committed the changes in r108224. -- Ticket URL: <https://trac.macports.org/ticket/39529#comment:7> MacPorts <http://www.macports.org/> Ports system for OS X
#39529: netcdf: cannot locate HDF5 -----------------------------+----------------------- Reporter: richard.katz@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: netcdf | -----------------------------+----------------------- Comment (by richard.katz@…): Thanks. I installed with +openmpi and it worked smoothly. -- Ticket URL: <https://trac.macports.org/ticket/39529#comment:8> MacPorts <http://www.macports.org/> Ports system for OS X
#39529: netcdf: cannot locate HDF5 -----------------------------+----------------------- Reporter: richard.katz@… | Owner: takeshi@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: fixed | Keywords: Port: netcdf | -----------------------------+----------------------- Changes (by takeshi@…): * status: new => closed * resolution: => fixed -- Ticket URL: <https://trac.macports.org/ticket/39529#comment:9> MacPorts <http://www.macports.org/> Ports system for OS X
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