[petsc-users] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: deactivating x11 in PETSc 3.13.0 with pastix/hwloc

Mon Apr 6 15:55:41 CDT 2020

I've tried two installations in that branch, a "full installation" with
every package I need, and a minimal one. I attach the results here, these
libraries are still being linked

On Mon, Apr 6, 2020 at 4:41 PM Satish Balay <balay at mcs.anl.gov> wrote:

> Hm - its working for me on CentOS7 [I see you are using RHEL7/CentOS7]
>
>
> Can you try the branch balay/fix-hwloc-x-dependency/maint - and see what
> you get?
>
> [balay at petsc-c7 petsc:d409bfc]$ ./configure --with-mpi=0 --download-hwloc
> --with-x=0
> <snip>
> [balay at petsc-c7 petsc:d409bfc]$ ldd arch-linux2-c-debug/lib/libhwloc.so
>
>
>         linux-vdso.so.1 =>  (0x00007ffe88bae000)
>         libm.so.6 => /lib64/libm.so.6 (0x00007ff75c7b9000)
>         libc.so.6 => /lib64/libc.so.6 (0x00007ff75c3eb000)
>         /lib64/ld-linux-x86-64.so.2 (0x00007ff75cd1a000)
> [balay at petsc-c7 petsc:d409bfc]$ ./configure --with-mpi=0 --download-hwloc
> --with-x=1
>                           <snip>
> [balay at petsc-c7 petsc:d409bfc]$ ldd arch-linux2-c-debug/lib/libhwloc.so
>
>
>         linux-vdso.so.1 =>  (0x00007ffe129cc000)
>         libm.so.6 => /lib64/libm.so.6 (0x00007f89920fa000)
>         libX11.so.6 => /lib64/libX11.so.6 (0x00007f8991dbc000)
>         libc.so.6 => /lib64/libc.so.6 (0x00007f89919ee000)
>         /lib64/ld-linux-x86-64.so.2 (0x00007f899265b000)
>         libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f89917c6000)
>         libdl.so.2 => /lib64/libdl.so.2 (0x00007f89915c2000)
>         libXau.so.6 => /lib64/libXau.so.6 (0x00007f89913be000)
> [balay at petsc-c7 petsc:d409bfc]$
>
> Satish
>
> On Mon, 6 Apr 2020, Alfredo Jaramillo wrote:
>
> > No, it doesn't work... I also tried --with-x=disabled. I gave a look to
> > ./configure --help in the hwloc directory and to the configure file
> itself,
> > but Im not finding the right option.
> >
> > On Mon, Apr 6, 2020 at 3:53 PM Satish Balay <balay at mcs.anl.gov> wrote:
> >
> > > Looks like the option is --with-x=no
> > >
> > > Can you give this a try? Branch balay/fix-hwloc-x-dependency/maint has
> > > this update now
> > >
> > > Satish
> > >
> > > On Mon, 6 Apr 2020, Alfredo Jaramillo wrote:
> > >
> > > > Hello Satish, Im sorry but I think I tested this workaround with the
> > > wrong
> > > > installation, my bad.
> > > > In fact the libXNVC, X11 libraries are still being linked even with
> the
> > > > --download-hwloc-configure-arguments=--without-x option
> > > >
> > > > Im attaching the config.log file located in
> > > > $PETSC_DIR/$PETSC_ARCH/externalpackages/hwloc-2.1.0
> > > > you can see that the option --without-x is there (line 7) but by
> means of
> > > > $ ldd foo
> > > > I see that the links are still there
> > > >
> > > > On Mon, Apr 6, 2020 at 2:57 PM Satish Balay <balay at mcs.anl.gov>
> wrote:
> > > >
> > > > > Great!
> > > > >
> > > > > Wrt pastix dependency on hwloc -
> > > > > config/BuildSystem/config/packages/PaStiX.py has the following
> comment:
> > > > >
> > > > >     # PaStiX.py does not absolutely require hwloc, but it performs
> > > better
> > > > > with it and can fail (in ways not easily tested) without it
> > > > >     #
> > > > >
> > >
> https://gforge.inria.fr/forum/forum.php?thread_id=32824&forum_id=599&group_id=186
> > > > >     #
> https://solverstack.gitlabpages.inria.fr/pastix/Bindings.html
> > > > >
> > > > > I have a fix in branch balay/fix-hwloc-x-dependency/maint [that
> does
> > > not
> > > > > need the extra --download-hwloc-configure-arguments=--without-x
> > > option].
> > > > > Can you give this a try?
> > > > >
> > > > > Satish
> > > > >
> > > > > On Mon, 6 Apr 2020, Alfredo Jaramillo wrote:
> > > > >
> > > > > > hello Satish,
> > > > > > adding
> > > > > > --download-hwloc-configure-arguments=--without-x
> > > > > > worked perfectly
> > > > > >
> > > > > > thank you!
> > > > > >
> > > > > > On Mon, Apr 6, 2020 at 2:12 PM Satish Balay <balay at mcs.anl.gov>
> > > wrote:
> > > > > >
> > > > > > > you can try:
> > > > > > >
> > > > > > > --download-pastix --download-hwloc
> > > > > > > --download-hwloc-configure-arguments=--without-x
> > > > > > >
> > > > > > > We should fix this to automatically use --with-x=0/1
> > > > > > >
> > > > > > > Satish
> > > > > > >
> > > > > > > On Mon, 6 Apr 2020, Alfredo Jaramillo wrote:
> > > > > > >
> > > > > > > > hello everyone,
> > > > > > > >
> > > > > > > > I have a fresh installation of the 3.13.0 version with
> pastix.
> > > Like
> > > > > with
> > > > > > > > previous versions, I'm using the options
> > > > > > > >
> > > > > > > > --with-x11=0 --with-x=0 --with-windows-graphics=0
> > > > > > > >
> > > > > > > > to disable X11
> > > > > > > >
> > > > > > > > however, when compiling my program foo and doing
> > > > > > > >
> > > > > > > > $ ldd foo
> > > > > > > >
> > > > > > > > between the linked libraries there appear:
> > > > > > > > libXNVCtrl.so.0 and libX11.so.6
> > > > > > > >
> > > > > > > > the first one related to NVIDIA. I observed that this does
> not
> > > happen
> > > > > > > when
> > > > > > > > installing PETSc without hwloc. In this new version, PETSc
> > > requires
> > > > > to
> > > > > > > > install hwloc when trying to install pastix. In previous
> > > versions of
> > > > > > > PETSc
> > > > > > > > (eg 3.11.2) that wasn't necessary.
> > > > > > > >
> > > > > > > > I'm working in a cluster where I have no access to these
> > > X11-related
> > > > > > > > libraries and that's why I need them not be linked. Is it
> there
> > > some
> > > > > way
> > > > > > > to
> > > > > > > > disable X11 when installing hwloc? maybe enforcing some
> > > configuration
> > > > > > > > variables when installing it through petsc or installing it
> > > > > > > independently?
> > > > > > > >
> > > > > > > > thanks a lot!
> > > > > > > >
> > > > > > > > Below the configuration command of the two installations I've
> > > tried
> > > > > with
> > > > > > > > the 3.13.0 version.
> > > > > > > >
> > > > > > > > =================== WITH PASTIX ===================
> > > > > > > >
> > > > > > > > ./configure --with-make-np=20
> > > > > > > > --with-petsc-arch=x64go-3.13-openmpi-4.0.1-pastix-64
> > > > > --with-debugging=0
> > > > > > > > --doCleanup=0 \
> > > > > > > > --with-mpi=1 \
> > > > > > > > --with-valgrind=1
> > > > > --with-valgrind-dir=$PATH_TO_VALGRIND/valgrind-3.15.0 \
> > > > > > > > --download-scalapack \
> > > > > > > > --download-openblas \
> > > > > > > > --download-mumps \
> > > > > > > > --download-superlu_dist \
> > > > > > > > --download-metis \
> > > > > > > > --download-parmetis \
> > > > > > > > --download-ptscotch \
> > > > > > > > --download-hypre \
> > > > > > > >
> > > > > > > > *--download-pastix \--download-hwloc \*
> > > > > > > > --with-64-bit-indices=1 \
> > > > > > > > LDFLAGS=$LDFLAGS CPPFLAGS=$CPPFLAGS \
> > > > > > > > --with-cxx-dialect=C++11 \
> > > > > > > > --with-x11=0 --with-x=0 --with-windows-graphics=0 \
> > > > > > > > COPTFLAGS="-O3 -march=native -mtune=native" \
> > > > > > > > CXXOPTFLAGS="-O3 -march=native -mtune=native" \
> > > > > > > > FOPTFLAGS="-O3 -march=native -mtune=native"
> > > > > > > >
> > > > > > > > =================== WITHOUT PASTIX ===================
> > > > > > > >
> > > > > > > > the same as above but the options "--download-pastix
> > > > > --download-hwloc"
> > > > > > > >
> > > > > > > > ======================================================
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> >
>
>
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