Interesting question: why the heck does Slurm package an “mpi.h”??? That just seems like a formula for problems. Is that just a mistake?
> On Sep 14, 2015, at 9:43 AM, Michael Gutteridge > <[email protected]> wrote: > > I see your point there- they might be trying to compensate for broken MPI > distributions that don't define the necessary IO routines in mpi.h. > > Removing that include *might* fix it, but I think that the core issue is that > Slurm has an 'mpi.h' that does very different things and appears to be > getting loaded by the compiler in favor of the OpenMPI 'mpi.h' requested by > the HDF5 headers. > > FWIW, I patched Makefile.am, removed 'src/common' from the includes, and it > builds just fine: > > --- a/src/plugins/acct_gather_profile/hdf5/sh5util/libsh5util_old/Makefile.am > +++ b/src/plugins/acct_gather_profile/hdf5/sh5util/libsh5util_old/Makefile.am > @@ -4,7 +4,7 @@ > > AUTOMAKE_OPTIONS = foreign > > -AM_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/src/common -I. > +AM_CPPFLAGS = -I$(top_srcdir) -I. > > noinst_LTLIBRARIES = libsh5util_old.la <http://libsh5util_old.la/> > > Just installing it now, will see how it runs. > > M > > On Sat, Sep 12, 2015 at 8:50 PM, Ralph Castain <[email protected] > <mailto:[email protected]>> wrote: > > I think what we are saying is that HDF5 appears to be violating the MPI > standard - they are not supposed to be directly including the mpio.h header. > Someone might want to discuss that with them :-) > > > > On Sep 12, 2015, at 8:13 PM, Christopher Samuel <[email protected] > > <mailto:[email protected]>> wrote: > > > > > > On 12/09/15 18:56, dani wrote: > > > >> You shouldn't need openmpi preinstalled with recent slurm. > >> Slurm build pmi2, and then when building openmpi you supply --with-pmi > >> and point it to the pmi dir created by slurm > > > > But Michael appears to want HDF5 support in Slurm and it is that HDF5 > > code that seems to need these MPI headers. > > > > All the best, > > Chris (finally in DC for the Slurm User Group) > > -- > > Christopher Samuel Senior Systems Administrator > > VLSCI - Victorian Life Sciences Computation Initiative > > Email: [email protected] <mailto:[email protected]> Phone: +61 (0)3 > > 903 55545 <tel:%2B61%20%280%293%20903%2055545> > > http://www.vlsci.org.au/ <http://www.vlsci.org.au/> > > http://twitter.com/vlsci <http://twitter.com/vlsci> >
