Summary: | sci-libs/netcdf-4.0.1 fails to configure with sys-cluster/openmpi and mpi USE flag | ||
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Product: | Gentoo Linux | Reporter: | Juergen Rose <rose> |
Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
Status: | RESOLVED FIXED | ||
Severity: | normal | CC: | xarthisius |
Priority: | High | ||
Version: | 2008.0 | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Bug Depends on: | |||
Bug Blocks: | 302621 | ||
Attachments: |
/var/tmp/portage/sci-libs/netcdf-4.0.1/work/netcdf-4.0.1/config.log
adding cxx flag, mpi as a dependency, hdf5 must use [mpi=] fixing fortran tests when using mpi wrappers and gfortran >4.1.x adding cxx flag, mpi as a dependency, hdf5 must use [mpi=], + epatch |
Description
Juergen Rose
2010-01-24 12:42:46 UTC
Created attachment 217318 [details]
/var/tmp/portage/sci-libs/netcdf-4.0.1/work/netcdf-4.0.1/config.log
Deinstalling openmpi and doing: for p in `equery -qC hasuse mpi` ; do emerge -v1 =$p ; done installs also netcdf-4.0.1 with the mpi USE flag. (In reply to comment #2) > Deinstalling openmpi and doing: > > for p in `equery -qC hasuse mpi` ; do emerge -v1 =$p ; done > > installs also netcdf-4.0.1 with the mpi USE flag. > It's not netcdf, but rather hdf5 issue. Did you compile hdf5[mpi] with openmpi? There is no mpio.h installed because ROM-IO is defined elsewhere in openmpi. I tested once more: 1st step: erasing mpich2: 'emerge -C mpich2" 2nd step: emerging all mpi depending packages: for p in `equery -qC hasuse mpi` ; do emerge -v1 =$p ; done This emerge first openmpi, then hdf5 and then fails netcdf-4.0.1 with the same error: checking for H5Fflush in -lhdf5... yes configure: error: Can't find the hdf5 header and/or library, or can't link a program to it. HDF5 must be built with zlib; the location of zlib must be specified for netCDF-4 with the --with-zlib option. If HDF5 was also built with szlib, then the location of szlib must also be specified with the --with-slib option. !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-libs/netcdf-4.0.1/work/netcdf-4.0.1/config.log (In reply to comment #0) > In config.log you can find. that mpi.h and mpio.h are not found. > openmpi installs the first file under /usr/include/openmpi and there is no > mpio.h in openmpi. My mistake of not not reading your post thoroughly. Why do you have mpi.h in /usr/include/openmpi in the first place?? [ebuild R ] sys-cluster/openmpi-1.4.1 USE="cxx fortran ipv6 pbs romio -debug -heterogeneous -mpi-threads -threads -vt" 6,418 kB Total: 1 package (1 reinstall), Size of downloads: 6,418 kB xarth@hum:~$ equery f openmpi | grep "mpi\.h" /usr/include/mpi.h If you have openmpi in non standard place you'll have to use mpif90 wrapper... Created attachment 217714 [details, diff] adding cxx flag, mpi as a dependency, hdf5 must use [mpi=] (In reply to comment #5) > My mistake of not not reading your post thoroughly. Why do you have mpi.h in > /usr/include/openmpi in the first place?? Again it was me that was outdated, mpi.h was moved to /usr/include/openmpi due to mpif90 include order issues. Try the following patch. Created attachment 217755 [details, diff]
fixing fortran tests when using mpi wrappers and gfortran >4.1.x
gfortran no longer add second underscore to external functions
Created attachment 217756 [details, diff]
adding cxx flag, mpi as a dependency, hdf5 must use [mpi=], + epatch
Now applied in cvs, with some other fixes as well. Thanks. |