Hi Gilles,
> a simple workaround is you always run configure in an empty directory
> in this example, please recreate
>
> rm -rf /export2/src/openmpi-1.8.6/openmpi-1.8.6-Linux.x86_64.64_gcc
> mkdir /export2/src/openmpi-1.8.6/openmpi-1.8.6-Linux.x86_64.64_gcc
>
> before invoking configure and make
I always start with an empty directory and I always remove an old
package before installing a new one.
mkdir openmpi-1.8.6-${SYSTEM_ENV}.${MACHINE_ENV}.64_gcc
cd openmpi-1.8.6-${SYSTEM_ENV}.${MACHINE_ENV}.64_gcc
../openmpi-v1.8.5-46-g9f5f498/configure \
--prefix=/usr/local/openmpi-1.8.6_64_gcc \
...
make |& tee log.make.$SYSTEM_ENV.$MACHINE_ENV.64_gcc
rm -r /usr/local/openmpi-1.8.6_64_gcc.old
mv /usr/local/openmpi-1.8.6_64_gcc /usr/local/openmpi-1.8.6_64_gcc.old
make install |& tee log.make-install.$SYSTEM_ENV.$MACHINE_ENV.64_gcc
make check |& tee log.make-check.$SYSTEM_ENV.$MACHINE_ENV.64_gcc
Thank you very much for your answer and kind regards
Siegmar
> Jeff,
>
> that can happen indeed, in a complex but legitimate environment :
>
> mkdir ~/src
> cd ~/src
> tar xvfj openmpi-1.8.tar.bz2
> mkdir ~/build/openmpi-v1.8
> cd ~/build/openmpi-v1.8
> ~/src/openmpi-1.8/configure
> make
>
> then a few days later
>
> cd ~/src
> tar xvfj openmpi-v1.8.5-46-g9f5f498.tar.bz2
> # use the *same* build directory
> cd ~/build/openmpi-v1.8
> #
> (~/src/openmpi-v1.8.5-46-g95f5f498/opal/include/opal/opal_portable_platform.h
> # must be more recent than
> ~/src/openmpi-1.8/ompi/include/mpi_portable_platform.h
> # just touch
> ~/src/openmpi-v1.8.5-46-g95f5f498/opal/include/opal/opal_portable_platform.h
> # to force the issue
> ~/src/openmpi-v1.8.5-46-g9f5f498/configure
> make => BOUM
>
> i just found an other issue with this scenario :
> symlinks in the profile directories (ompi/mpi/c/profile,
> ompi/mpi/fortran/mpif-h/profile, oshmem/shmem/c/profile) are not
> recreated and points to the previous source tree.
> (that caused one crash at least, and likely silently compiles old
> sources most of the time)
>
> Cheers,
>
> Gilles
>
> On 6/10/2015 10:01 AM, Jeff Squyres (jsquyres) wrote:
> > Siegmar --
> >
> > I don't see any reason why this should be happening to you only sometimes;
this code has been unchanged in *forever*. :-(
> >
> > Did your NFS server drift out of time sync with your build machine,
perchance?
> >
> > Regardless, I just pushed what should be a workaround to master and I'll PR
it over to v1.8 and v1.10 (it'll take a day or so for these to show up in the
nightly tarballs) -- it should avoid the issue altogether.
> >
> >
> >
> >> On Jun 9, 2015, at 6:44 AM, Siegmar Gross
<siegmar.gr...@informatik.hs-fulda.de> wrote:
> >>
> >> Hi,
> >>
> >> today I tried to build openmpi-v1.8.5-46-g9f5f498 on my machines
> >> (Solaris 10 Sparc, Solaris 10 x86_64, and openSUSE Linux 12.1
> >> x86_64) with gcc-4.9.2 and Sun C 5.13 and I got the same error
> >> on all three platforms with both compilers. I have already
> >> reported the problem a few days ago. I used the following command
> >> to configure the package.
> >>
> >> ../openmpi-v1.8.5-46-g9f5f498/configure \
> >> --prefix=/usr/local/openmpi-1.8.6_64_gcc \
> >> --libdir=/usr/local/openmpi-1.8.6_64_gcc/lib64 \
> >> --with-jdk-bindir=/usr/local/jdk1.8.0/bin \
> >> --with-jdk-headers=/usr/local/jdk1.8.0/include \
> >> JAVA_HOME=/usr/local/jdk1.8.0 \
> >> LDFLAGS="-m64" CC="gcc" CXX="g++" FC="gfortran" \
> >> CFLAGS="-m64" CXXFLAGS="-m64" FCFLAGS="-m64" \
> >> CPP="cpp" CXXCPP="cpp" \
> >> CPPFLAGS="" CXXCPPFLAGS="" \
> >> --enable-mpi-cxx \
> >> --enable-cxx-exceptions \
> >> --enable-mpi-java \
> >> --enable-heterogeneous \
> >> --enable-mpi-thread-multiple \
> >> --with-threads=posix \
> >> --with-hwloc=internal \
> >> --without-verbs \
> >> --with-wrapper-cflags="-std=c11 -m64" \
> >> --with-wrapper-cxxflags="-m64" \
> >> --with-wrapper-fcflags="-m64" \
> >> --enable-debug \
> >> |& tee log.configure.$SYSTEM_ENV.$MACHINE_ENV.64_gcc
> >>
> >>
> >> ...
> >> make[3]: Entering directory
`/export2/src/openmpi-1.8.6/openmpi-1.8.6-Linux.x86_64.64_gcc/ompi/include'
> >> ../../../openmpi-v1.8.5-46-g9f5f498/ompi/mpi/fortran/base/gen-mpi-sizeof.pl
> >>
\
> >> --header=mpif-sizeof.h --ierror=mandatory \
> >> --maxrank=7 \
> >> --generate=1 \
> >> --real16=1 \
> >> --complex32=1
> >> ln -s
../../../openmpi-v1.8.5-46-g9f5f498/opal/include/opal/opal_portable_platform.h
mpi_portable_platform.h
> >> ln: failed to create symbolic link `mpi_portable_platform.h': File exists
> >> make[3]: *** [mpi_portable_platform.h] Error 1
> >> make[3]: Leaving directory
`/export2/src/openmpi-1.8.6/openmpi-1.8.6-Linux.x86_64.64_gcc/ompi/include'
> >> make[2]: *** [all] Error 2
> >> make[2]: Leaving directory
`/export2/src/openmpi-1.8.6/openmpi-1.8.6-Linux.x86_64.64_gcc/ompi/include'
> >> make[1]: *** [all-recursive] Error 1
> >> make[1]: Leaving directory
`/export2/src/openmpi-1.8.6/openmpi-1.8.6-Linux.x86_64.64_gcc/ompi'
> >> make: *** [all-recursive] Error 1
> >> linpc1 openmpi-1.8.6-Linux.x86_64.64_gcc 261
> >>
> >>
> >> I would be grateful, if somebody could fix the problem. Thank
> >> you very much for any help in advance.
> >>
> >>
> >> Kind regards
> >>
> >> Siegmar
> >>
> >> _______________________________________________
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> >
>
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