[petsc-users] 3.16.4 amd blis libflame linking problem

[Anton Popov]

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.
>
>>> /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.

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/>
>>