[CIG-SHORT] How to use cluster installation of HDF5 with Pylith

[Matthew Knepley]

On Wed, Jun 1, 2016 at 5:31 PM, Cesar Sul <csul at usc.edu> wrote:

> Hi,
>
>
> I would like to do a local install of Pylith on a cluster. The sysadmins
> have installed some of the Pylith dependencies in a non standard location
> so I’m running into problems when I try to configure.
>
>
> The commands I’m using are
>
>
> export CPPFLAGS=-I/path/to/hdf5/include
>
> ./configure --disable-hdf5 --prefix=$PYLITH_HOME/pylith
>
>
> The relevant portion of the error message is:
>
>
> ...
>
> checking hdf5.h usability... no
>
> checking hdf5.h presence... no
>
> checking for hdf5.h... no
>
> configure: error: HDF5 header not found; try CPPFLAGS="-I<hdf5 include
> dir>"
>
>
> The file hdf5.h does exist in the location pointed to by $CPPFLAGS and I
> receive similar error messages when I try this with the other dependent
> software. Please see the attached config.log for more information.
>
> Your HDF5 depends on MPI, but you did not give the dependencies in your
options:

configure:22750: checking hdf5.h usability
configure:22750: g++ -c -g -O2 -I/auto/usc/hdf5/1.8.14-parallel/include
conftest.cpp >&5
In file included from /auto/usc/hdf5/1.8.14-parallel/include/hdf5.h:24,
                 from conftest.cpp:57:
/auto/usc/hdf5/1.8.14-parallel/include/H5public.h:61:20: error: mpi.h: No
such file or directory
/auto/usc/hdf5/1.8.14-parallel/include/H5public.h:63:21: error: mpio.h: No
such file or directory
In file included from /auto/usc/hdf5/1.8.14-parallel/include/H5FDmpi.h:59,
                 from /auto/usc/hdf5/1.8.14-parallel/include/hdf5.h:46,
                 from conftest.cpp:57:
/auto/usc/hdf5/1.8.14-parallel/include/H5FDmpio.h:51: error: 'MPI_Comm' has
not been declared
/auto/usc/hdf5/1.8.14-parallel/include/H5FDmpio.h:51: error: 'MPI_Info' has
not been declared
/auto/usc/hdf5/1.8.14-parallel/include/H5FDmpio.h:52: error: 'MPI_Comm' has
not been declared
/auto/usc/hdf5/1.8.14-parallel/include/H5FDmpio.h:53: error: 'MPI_Info' has
not been declared
configure:22750: $? = 1

This is where autoconf is kind of a drag. You can either give the
dependencies in the options, or
let the pylith-installer do it. Using the libraries installed by the
sysdamin is overrated for the most
part (other than MPI).

  Matt

> Any advice would be appreciated.
>
>
> Thanks,
>
> Cesar Sul
>
>
>
>
>
> Research Facilitator
>
> Center for High-Performance Computing
>
> University of Southern California
>
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.geodynamics.org/pipermail/cig-short/attachments/20160601/57e070f1/attachment.html>