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 > > > > > > > > > > > > > >
