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

Alfredo Jaramillo ajaramillopalma at gmail.com
Mon Apr 6 16:05:58 CDT 2020 

ops... you can find the attachments here
https://www.dropbox.com/sh/n8scz7wioe01t6p/AAC3P3iU1jLYsW6m3vs6S5DHa?dl=0

I got

$ ldd minimal/lib/libhwloc.so
linux-vdso.so.1 =>  (0x00007fffcc3ae000)
libm.so.6 => /usr/lib64/libm.so.6 (0x00007ff0b90a2000)
libXNVCtrl.so.0 => /usr/lib64/libXNVCtrl.so.0 (0x00007ff0b8e9d000)
libXext.so.6 => /usr/lib64/libXext.so.6 (0x00007ff0b8c8b000)
libX11.so.6 => /usr/lib64/libX11.so.6 (0x00007ff0b894d000)
libc.so.6 => /usr/lib64/libc.so.6 (0x00007ff0b8580000)
/lib64/ld-linux-x86-64.so.2 (0x00007ff0b9604000)
libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00007ff0b8358000)
libdl.so.2 => /usr/lib64/libdl.so.2 (0x00007ff0b8154000)
libXau.so.6 => /usr/lib64/libXau.so.6 (0x00007ff0b7f50000)

On Mon, Apr 6, 2020 at 6:02 PM Satish Balay <balay at mcs.anl.gov> wrote:

> The attachments didn't come through..
>
> >>>>
> DENIAL OF SERVICE ALERT
>
> A denial of service protection limit was exceeded. The file has been
> removed.
> Context: 'hwloc-x11=no.tar.gz\hwloc-x11=no.tar'
> Reason: The data size limit was exceeded
> Limit: 10 MB
> Ticket Number : 0c20-5e8b-97c0-000f
> <<<<<<
>
> Can you retry the test below - i.e './configure --with-mpi=0
> --download-hwloc --with-x=0' - and see if this works?
>
> What do you get for ldd [as shown below]?
>
> Satish
>
> On Mon, 6 Apr 2020, Alfredo Jaramillo wrote:
>
> > 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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