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

Mon Apr 6 22:14:31 CDT 2020

Great! Will have this change in the next petsc update.

Satish

On Mon, 6 Apr 2020, Alfredo Jaramillo wrote:

> it worked fine!
> 
> the previous output:
> 
> [alfredo.jaramillo at sdumont14 petsc]$ ldd
> arch-linux2-c-debug-actual/lib/libhwloc.so
> linux-vdso.so.1 =>  (0x00007ffde6f49000)
> libm.so.6 => /usr/lib64/libm.so.6 (0x00007fb8be4ed000)
> libXNVCtrl.so.0 => /usr/lib64/libXNVCtrl.so.0 (0x00007fb8be2e8000)
> libXext.so.6 => /usr/lib64/libXext.so.6 (0x00007fb8be0d6000)
> libX11.so.6 => /usr/lib64/libX11.so.6 (0x00007fb8bdd98000)
> libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb8bd9cb000)
> /lib64/ld-linux-x86-64.so.2 (0x00007fb8bea4f000)
> libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00007fb8bd7a3000)
> libdl.so.2 => /usr/lib64/libdl.so.2 (0x00007fb8bd59f000)
> libXau.so.6 => /usr/lib64/libXau.so.6 (0x00007fb8bd39b000)
> 
> the updated output:
> 
> [alfredo.jaramillo at sdumont14 petsc]$ ldd
> arch-linux2-c-debug-previous/lib/libhwloc.so
> linux-vdso.so.1 =>  (0x00007fff135c7000)
> libm.so.6 => /usr/lib64/libm.so.6 (0x00007f5ecd5f3000)
> libc.so.6 => /usr/lib64/libc.so.6 (0x00007f5ecd226000)
> /lib64/ld-linux-x86-64.so.2 (0x00007f5ecdb54000
> 
> I added the option --download-hwloc-configure-arguments="--disable-opencl
> --disable-cuda --disable-nvml --disable-gl" to my installation and pastix
> is working fine,
> 
> thank you very much
> regards
> 
> On Mon, Apr 6, 2020 at 6:39 PM Satish Balay <balay at mcs.anl.gov> wrote:
> 
> > I pushed another change to branch balay/fix-hwloc-x-dependency/maint
> >
> > Can you check again?
> >
> > BTW: The following options don't make sense when using --with-mpi=0
> >
> > CPPFLAGS=-I/scratch/app/openmpi/4.0_gnu/include
> > -I/scratch/app/mpc/1.0.3/include -I/scratch/app/isl/0.18/include
> > -I/scratch/app/gcc/6.5/include LDFLAGS=-L/scratch/app/openmpi/4.0_gnu/lib
> > -L/scratch/app/mpc/1.0.3/lib -L/scratch/app/isl/0.18/lib
> > -L/scratch/app/gcc/6.5/lib64 -L/scratch/app/gcc/6.5/lib
> >
> > [And likely these options are missing appropriate quotes..]
> >
> > Satish
> >
> > On Mon, 6 Apr 2020, Alfredo Jaramillo wrote:
> >
> > > 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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