Thanks for all the advice- I followed Jared's suggestion- a basic .c that
includes the hdf5 headers. That and the HDF examples all compiled and ran
fine.
Until, that is, I had 'src/common' in the include path. Building my
examples in the Slurm build tree using an include path with src/common and
the slurm source top level fails with the same error.
What I see as possibly problematic is 'src/common/mpi.h'. The HDF include
file ('/usr/include/H5public.h') has a check that handles the MPICH vs.
OpenMPI differences:
60 #ifdef H5_HAVE_PARALLEL
61 # define MPICH_SKIP_MPICXX 1
62 # define OMPI_SKIP_MPICXX 1
63 # include <mpi.h>
64 #ifndef MPI_FILE_NULL /*MPIO may be defined in mpi.h already
*/
65 # include <mpio.h>
66 #endif
67 #endif
It appears that OpenMPI has MPIO defined in mpi.h, whereas MPICH defines
that stuff in mpio.h. As I've got a parallel build, I suspect that the
make includes src/common/mpi.h, doesn't find "MPI_FILE_NULL" defined and
attempts to include mpio.h.
I'm not the strongest C user, so I could be wrong on that, though when I
remove "src/common" from the include path for libsh5util_old it does
compile successfully.
I think worst case I'll end up with bootstrapping as Paul has indicated
(thanks for the procedure, BTW).
Thanks for all your time
M
On Fri, Sep 11, 2015 at 7:30 AM, Van Der Mark, Paul <[email protected]>
wrote:
> I'm glad we were not the only one with that problem. I basically did a
> bootstrap compilation
> 1. compile openmpi without slurm
> 2. compile hdf5 with that openmpi version
> 3. compile slurm with that hpdf5 version
> 4. recompile openmpi with slurm
> 5. for safety recompile hdf5 & slurm
>
> One of the reasons for that slightly confusing setup is because our
> semi-automated building system compiles 3 different versions of openmpi
> and compiles hdf5 for serial and all those openmpi versions at once.
>
> Beet,
> Paul
>
> On Thu, 2015-09-10 at 14:13 -0700, Jared David Baker wrote:
> > Hello Michael,
> >
> >
> >
> > I had this problem the other day when I was building Slurm on Arch. I
> > had hdf-mpi package installed with OpenMPI and there was an
> > inconsistency there as well. Basically the HDF5 implementation was
> > built with mpio in mind, but the compiler invocation does not find an
> > mpio.h as part of the OpenMPI installation. I guess my base point is I
> > have a different HDF5 implementation on our HPC clusters to satisfy
> > the Slurm requirements separate from the MPI enabled versions. Anyway,
> > I’d be suspicious of the OpenMPI/HDF5 packages you’ve installed in
> > Ubuntu and possibly open a bug if the HDF5 uses OpenMPI as the MPI
> > implementation and doesn’t contain the mpio.h file. Can you compile a
> > simple code with your MPI compiler wrapper that includes mpio.h?
> >
> >
> >
> > Best,
> >
> >
> >
> > Jared
> >
> >
> >
> > From: Michael Gutteridge [mailto:[email protected]]
> > Sent: Thursday, September 10, 2015 12:41 PM
> > To: slurm-dev
> > Subject: [slurm-dev] Compile of 15.08.0 fails on trusty missing mpio.h
> >
> >
> >
> >
> > Hi
> >
> >
> >
> >
> >
> > This really feels like an obvious one, but I'm having a devil of a
> > time sorting out how to address this. I'm building Slurm 15.08.0 on
> > Ubuntu 14.04 LTS with a minimal set of configure options:
> >
> >
> >
> >
> >
> > --sysconfdir=/etc/slurm-llnl --localstatedir=/var/run/slurm-llnl
> > --with-munge --without-blcr --enable-pam --without-rpath
> > --disable-debug
> >
> >
> >
> >
> >
> > Configure succeeds OK, but make fails a little while in during the
> > build of the HDF5 components:
> >
> >
> >
> >
> >
> > Making all in libsh5util_old
> >
> >
> > make[8]: Entering directory
> >
> `/home/build/trusty/slurm-llnl/15.08.0/build/slurm-15.08.0/obj-x86_64-linux-gnu/src/plugins/acct_gather_profile/hdf5/sh5util/libsh5util_old'
> >
> >
> > /bin/bash ../../../../../../libtool --tag=CC --mode=compile gcc
> > -DHAVE_CONFIG_H -I.
> >
> -I../../../../../../../src/plugins/acct_gather_profile/hdf5/sh5util/libsh5util_old
> -I../../../../../.. -I../../../../../../slurm -I../../../../../../..
> -I../../../../../../../src/common -I. -I/usr/lib/openmpi/include -I
> /usr/include -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat
> -Werror=format-security -pthread -fno-gcse -c -o sh5util.lo
> ../../../../../../../src/plugins/acct_gather_profile/hdf5/sh5util/libsh5util_old/sh5util.c
> >
> >
> > libtool: compile: gcc -DHAVE_CONFIG_H -I.
> >
> -I../../../../../../../src/plugins/acct_gather_profile/hdf5/sh5util/libsh5util_old
> -I../../../../../.. -I../../../../../../slurm -I../../../../../../..
> -I../../../../../../../src/common -I. -I/usr/lib/openmpi/include -I
> /usr/include -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat
> -Werror=format-security -pthread -fno-gcse -c
> ../../../../../../../src/plugins/acct_gather_profile/hdf5/sh5util/libsh5util_old/sh5util.c
> -fPIC -DPIC -o .libs/sh5util.o
> >
> >
> > In file included from /usr/include/hdf5.h:24:0,
> >
> >
> >
> > from
> ../../../../../../../src/plugins/acct_gather_profile/hdf5/sh5util/libsh5util_old/hdf5_api.h:61,
> >
> >
> >
> > from
> ../../../../../../../src/plugins/acct_gather_profile/hdf5/sh5util/libsh5util_old/sh5util.c:72:
> >
> >
> > /usr/include/H5public.h:65:21: fatal error: mpio.h: No such file or
> > directory
> >
> >
> > # include <mpio.h>
> >
> >
> > ^
> >
> >
> > compilation terminated.
> >
> >
> > make[8]: *** [sh5util.lo] Error 1
> >
> >
> >
> >
> >
> >
> >
> >
> > I have both OpenMPI (1.6.5) and MPICH (3.0.4) development packages
> > installed- mpio.h is present in /usr/include/mpich/mpio.h. If I add
> > "CFLAGS=-I/usr/include/mpich" then the build succeeds. That sort of
> > feels kludgy- I'm of the opinion that the configure should have picked
> > that up or that I don't, in fact, have the correct development headers
> > installed. We'd never needed/used MPICH in past... I thought OpenMPI
> > would have supplied mpio.h.
> >
> >
> >
> >
> >
> > Does anyone have any insights into this? Should configure pick it up?
> > Is it a quirk of Ubuntu?
> >
> >
> >
> >
> >
> > Thanks much
> >
> >
> >
> >
> >
> > Michael
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
>
>
