[petsc-users] 3.16.4 amd blis libflame linking problem

[Satish Balay]

On Fri, 4 Feb 2022, Anton Popov wrote:

> 
> Am 04.02.2022 um 18:54 schrieb Satish Balay:
> > On Fri, 4 Feb 2022, Anton Popov wrote:
> >
> >> Thanks Matt, Barry and Satish, for  your suggestions.
> >>
> >> The problem was indeed in mismatch between the gfortran library version
> >> (system has libgfortran.so.4 libflame needs libgfortran.so.5)
> >>
> >> 3.9.4 did not detect this during configure, but only gave error later
> >> during
> >> test.
> >>
> >> 3.16.4 detected this immediately.
> >>
> >> After installing libgfortran.so.5, both PETSc versions install just fine,
> >> however I get the warning mentioned by Satish.
> > Hm - you could install libgfortran.so.5 without the corresponding compiler?
> Yes, apparently it is possible on Ubuntu 18.04.

Presumably it also comes with the corresponding gcc/gfortran [gcc-8, gfortran-8?]. Perhaps these compilers would avoid this issue.

> >
> >>> /opt/amd/amd-libflame-3.1.0/lib/lp64/libflame.so
> > Ah - this is a binary download - not something compiled locally?
> Yes it is the latest binary from AMD website.
> >
> > I wonder if the compiler gave both an error [return code] and a warning
> > previously [with the missing libgfortran.so.5] - as Barry was suggesting.
> It was an error at runtime, configure was just fine.
> >
> >
> > As you say - you still get that warning [which is expected - as you are
> > using a different version of gfortran than what libflame.so was built with]
> 
> Now since libgfortran.so.5 coexists with libgfortran.so.4 it links against the
> proper one, but gives a warning that both versions are available.
> 
> I think I will just compile BLIS and LibFLAME from sources on my system to
> avoid these problems altogether.

Yeah - generally building everything with the same version of the compiler avoids these issues.

Satish

> 
> Best,
> 
> Anton
> 
> 
> >
> > Satish
> >
> >> Maybe it is indeed worth upgrading everything to the compatible versions.
> >>
> >> Best,
> >>
> >> Anton
> >>
> >>
> >> On 04.02.22 18:33, Barry Smith wrote:
> >>>> On Feb 4, 2022, at 12:27 PM, Satish Balay <balay at mcs.anl.gov> wrote:
> >>>>
> >>>> Probably best if you can use the same version of gfortran to build both
> >>>> petsc and libflame/blis
> >>>>
> >>>>> /usr/bin/ld: warning: libgfortran.so.5, needed by
> >>>>> /opt/amd/amd-libflame-3.1.0/lib/lp64/libflame.so, not found (try using
> >>>>> -rpath or -rpath-link):
> >>>> This is probably an ignore-able warning - but configure defaults to
> >>>> -Werror
> >>>> mode here.
> >>>     Hmm, if it needs libgfortran.so.5 then it needs it and it cannot be
> >>>     ignored since a link cannot succeed. Flame presumably contains a lot
> >>>     of
> >>>     old Fortran code from Lapack so would normally need the fortran
> >>>     libraries.
> >>>
> >>>> Wrt forcing link with static libraries - you can try:
> >>>>
> >>>> LIBS="/opt/amd/amd-libflame-3.1.0/lib/lp64/libflame.a
> >>>> /opt/amd/amd-blis-3.1.0/lib/lp64/libblis.a"
> >>>>
> >>>> [instead of --with-blas-lib= --with-lapack-lib= options].
> >>>>
> >>>> Satish
> >>>>
> >>>>
> >>>> On Fri, 4 Feb 2022, Barry Smith wrote:
> >>>>
> >>>>> Please do
> >>>>>
> >>>>>    ldd -O /opt/amd/amd-libflame-3.1.0/lib/lp64/libflame.so
> >>>>>
> >>>>> You may need to list the gfortran library directory of libgfortran.so.5
> >>>>> it
> >>>>> needs to use in LDFLAGS passed to PETSc configure
> >>>>>
> >>>>> Barry
> >>>>>
> >>>>> Note: Even though you explicitly listed a static library of libflame to
> >>>>> use our configure is goofy and loses that information and wants to link
> >>>>> with the shared version
> >>>>>
> >>>>>
> >>>>>> On Feb 4, 2022, at 12:00 PM, Anton Popov <popov at uni-mainz.de> wrote:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> On 04.02.22 17:39, Matthew Knepley wrote:
> >>>>>>> On Fri, Feb 4, 2022 at 11:35 AM Anton Popov <popov at uni-mainz.de
> >>>>>>> <mailto:popov at uni-mainz.de>> wrote:
> >>>>>>> Hi Satish,
> >>>>>>>
> >>>>>>> I just discovered that PETSc 3.16.4 fails to link against the latest
> >>>>>>> AMD
> >>>>>>> BLIS and LibFLAME libraries on a Linux box.
> >>>>>>>
> >>>>>>> -------------------------------------------------------------------------------
> >>>>>>> You set a value for --with-blas-lib=<lib> and --with-lapack-lib=<lib>,
> >>>>>>> but ['/opt/amd/amd-blis-3.1.0/lib/lp64/libblis.a'] and
> >>>>>>> ['/opt/amd/amd-libflame-3.1.0/lib/lp64/libflame.a'] cannot be used
> >>>>>>> *******************************************************************************
> >>>>>>>
> >>>>>>> My previous experience with 3.9.4 on the same system was fully
> >>>>>>> successful. Looking in the configure logs (attached) reveals small
> >>>>>>> difference in the linking compared to 3.9.4
> >>>>>>>
> >>>>>>> Could you please make a guess what went wrong?
> >>>>>>>
> >>>>>>> Down in the log I see:
> >>>>>>>
> >>>>>>> /usr/bin/ld: warning: libgfortran.so.5, needed by
> >>>>>>> /opt/amd/amd-libflame-3.1.0/lib/lp64/libflame.so, not found (try using
> >>>>>>> -rpath or -rpath-link):
> >>>>>> Thanks Matt, I'll try.
> >>>>>>
> >>>>>>> Did the gfortran library move or get upgraded?
> >>>>>> Not at all. I have configured 3.9.4 just now to make a test, and it
> >>>>>> perfectly finds all the libraries. So there must be something that
> >>>>>> 3.16.4
> >>>>>> does differently.
> >>>>>>
> >>>>>> Best,
> >>>>>>
> >>>>>> Anton
> >>>>>>
> >>>>>>>    Thanks,
> >>>>>>>
> >>>>>>>       Matt
> >>>>>>>
> >>>>>>> Best regards,
> >>>>>>>
> >>>>>>> Anton
> >>>>>>>
> >>>>>>>
> >>>>>>> -- 
> >>>>>>> What most experimenters take for granted before they begin their
> >>>>>>> experiments is infinitely more interesting than any results to which
> >>>>>>> their experiments lead.
> >>>>>>> -- Norbert Wiener
> >>>>>>>
> >>>>>>> https://www.cse.buffalo.edu/~knepley/
> >>>>>>> <http://www.cse.buffalo.edu/~knepley/>
> >>
>