[petsc-users] --download-fblaslapack libraries cannot be used

Tue Mar 17 14:59:22 CDT 2020

On Tue, Mar 17, 2020 at 9:24 AM Satish Balay <balay at mcs.anl.gov> wrote:

> So what was the initial problem? Did conda install gcc without glibc? Or
> was it using the wrong glibc?
>

Looks like GCC installed by conda uses an old version of glibc (2.12).

> Because the compiler appeared partly functional [well the build worked
> with just LIBS="-lmpifort -lgfortran"]
>
> And after the correct glibc was installed - did current maint still fail
> to build?
>

Still failed because PETSc claimed that: there were no needed fortran
libraries when using mpicc as the linker. But in fact, we need these
fortran stuffs when linking blaslapack and mumps.

>
> Can you send configure.log for this?
>
> And its not clear to me why balay/fix-checkFortranLibraries/maint broke
> before this fix. [for one configure.log was incomplete]
>

I am not 100% sure, but I think the complied and linked executable can not
run because  of "glibc_2.14' not found". The version of glibc was too low.

So current solution for me is that: your branch + a new version of glibc
(2.18).

Thanks,

Fande,

>
> Satish
>
> On Tue, 17 Mar 2020, Fande Kong wrote:
>
> > Hi Satish,
> >
> > Could you merge your branch, balay/fix-checkFortranLibraries/maint, into
> > maint?
> >
> > I added glibc to my conda environment (conda install -c dan_blanchard
> > glibc), and your branch ran well.
> >
> > If you are interested, I attached the successful log file here.
> >
> > Thanks,
> >
> > Fande
> >
> > On Sat, Mar 14, 2020 at 5:01 PM Fande Kong <fdkong.jd at gmail.com> wrote:
> >
> > > Without touching the configuration file, the
> > > option: --download-hypre-configure-arguments='LIBS="-lmpifort
> -lgfortran"',
> > > also works.
> > >
> > >
> > > Thanks, Satish,
> > >
> > >
> > > Fande,
> > >
> > > On Sat, Mar 14, 2020 at 4:37 PM Fande Kong <fdkong.jd at gmail.com>
> wrote:
> > >
> > >> OK. I finally got PETSc complied.
> > >>
> > >> "-lgfortran" was required by fblaslapack
> > >> "-lmpifort" was required by mumps.
> > >>
> > >> However, I had to manually add the same thing for hypre as well:
> > >>
> > >> git diff
> > >> diff --git a/config/BuildSystem/config/packages/hypre.py
> > >> b/config/BuildSystem/config/packages/hypre.py
> > >> index 4d915c312f..f4300230a6 100644
> > >> --- a/config/BuildSystem/config/packages/hypre.py
> > >> +++ b/config/BuildSystem/config/packages/hypre.py
> > >> @@ -66,6 +66,7 @@ class Configure(config.package.GNUPackage):
> > >>      args.append('--with-lapack-lib=" "')
> > >>      args.append('--with-blas=no')
> > >>      args.append('--with-lapack=no')
> > >> +    args.append('LIBS="-lmpifort -lgfortran"')
> > >>      if self.openmp.found:
> > >>        args.append('--with-openmp')
> > >>        self.usesopenmp = 'yes'
> > >>
> > >>
> > >> Why hypre could not pick up LIBS options automatically?
> > >>
> > >>
> > >> Thanks,
> > >>
> > >> Fande,
> > >>
> > >>
> > >>
> > >>
> > >> On Sat, Mar 14, 2020 at 2:49 PM Satish Balay via petsc-users <
> > >> petsc-users at mcs.anl.gov> wrote:
> > >>
> > >>> Configure Options: --configModules=PETSc.Configure
> > >>> --optionsModule=config.compilerOptions --download-hypre=1
> > >>> --with-debugging=no --with-shared-libraries=1
> --download-fblaslapack=1
> > >>> --download-metis=1 --download-ptscotch=1 --download-parmetis=1
> > >>> --download-superlu_dist=1 --download-mumps=1 --download-scalapack=1
> > >>> --download-slepc=git://https://gitlab.com/slepc/slepc.git
> > >>> --download-slepc-commit= 59ff81b --with-mpi=1
> --with-cxx-dialect=C++11
> > >>> --with-fortran-bindings=0 --with-sowing=0 CFLAGS=-march=nocona
> > >>> -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong
> -fno-plt -O2
> > >>> -ffunction-sections -pipe -isystem
> > >>> /home/kongf/workhome/rod/miniconda3/include CXXFLAGS= LDFLAGS=-Wl,-O2
> > >>> -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now
> > >>> -Wl,--with-new-dtags=0 -Wl,--gc-sections
> > >>> -Wl,-rpath,/home/kongf/workhome/rod/miniconda3/lib
> > >>> -Wl,-rpath-link,/home/kongf/workhome/rod/miniconda3/lib
> > >>> -L/home/kongf/workhome/rod/miniconda3/lib
> > >>>
> AR=/home/kongf/workhome/rod/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ar
> > >>> --with-mpi-dir=/home/kongf/workhome/rod/mpich LIBS=-lgfortran
> -lmpifort
> > >>>
> > >>> You are missing quotes with LIBS option - and likely the libraries in
> > >>> the wrong order.
> > >>>
> > >>> Suggest using:
> > >>>
> > >>> LIBS="-lmpifort -lgfortran"
> > >>> or
> > >>> 'LIBS=-lmpifort -lgfortran'
> > >>>
> > >>> Assuming you are invoking configure from shell.
> > >>>
> > >>> Satish
> > >>>
> > >>> On Sat, 14 Mar 2020, Satish Balay via petsc-users wrote:
> > >>>
> > >>> > to work around - you can try:
> > >>> >
> > >>> > LIBS="-lmpifort -lgfortran"
> > >>> >
> > >>> > Satish
> > >>> >
> > >>> > On Sat, 14 Mar 2020, Satish Balay via petsc-users wrote:
> > >>> >
> > >>> > > Its the same location as before. For some reason configure is not
> > >>> saving the relevant logs.
> > >>> > >
> > >>> > > I don't understand saveLog() restoreLog() stuff. Matt, can you
> check
> > >>> on this?
> > >>> > >
> > >>> > > Satish
> > >>> > >
> > >>> > > On Sat, 14 Mar 2020, Fande Kong wrote:
> > >>> > >
> > >>> > > > The configuration crashed earlier than before with your
> changes.
> > >>> > > >
> > >>> > > > Please see the attached log file when using your branch. The
> > >>> trouble lines
> > >>> > > > should be:
> > >>> > > >
> > >>> > > >  "    asub=self.mangleFortranFunction("asub")
> > >>> > > >     cbody = "extern void "+asub+"(void);\nint main(int
> argc,char
> > >>> > > > **args)\n{\n  "+asub+"();\n  return 0;\n}\n";
> > >>> > > > "
> > >>> > > >
> > >>> > > > Thanks,
> > >>> > > >
> > >>> > > > Fande,
> > >>> > > >
> > >>> > > > On Thu, Mar 12, 2020 at 7:06 PM Satish Balay <
> balay at mcs.anl.gov>
> > >>> wrote:
> > >>> > > >
> > >>> > > > > I can't figure out what the stack in the attached
> configure.log.
> > >>> [likely
> > >>> > > > > some stuff isn't getting logged in it]
> > >>> > > > >
> > >>> > > > > Can you retry with branch
> > >>> 'balay/fix-checkFortranLibraries/maint'?
> > >>> > > > >
> > >>> > > > > Satish
> > >>> > > > >
> > >>> > > > > On Thu, 12 Mar 2020, Fande Kong wrote:
> > >>> > > > >
> > >>> > > > > > Thanks, Satish,
> > >>> > > > > >
> > >>> > > > > > But still have the problem. Please see the attached log
> file.
> > >>> > > > > >
> > >>> > > > > > Thanks,
> > >>> > > > > >
> > >>> > > > > > Fande.
> > >>> > > > > >
> > >>> > > > > > On Thu, Mar 12, 2020 at 3:42 PM Satish Balay <
> > >>> balay at mcs.anl.gov> wrote:
> > >>> > > > > >
> > >>> > > > > > > Can you retry with the attached patch?
> > >>> > > > > > >
> > >>> > > > > > > BTW: Its best to use the latest patched version - i.e
> > >>> > > > > petsc-3.12.4.tar.gz
> > >>> > > > > > >
> > >>> > > > > > > Satish
> > >>> > > > > > >
> > >>> > > > > > > On Thu, 12 Mar 2020, Fande Kong wrote:
> > >>> > > > > > >
> > >>> > > > > > > > This fixed the fblaslapack issue. Now have another
> issue
> > >>> about mumps.
> > >>> > > > > > > >
> > >>> > > > > > > > Please see the log file attached.
> > >>> > > > > > > >
> > >>> > > > > > > > Thanks,
> > >>> > > > > > > >
> > >>> > > > > > > > Fande,
> > >>> > > > > > > >
> > >>> > > > > > > > On Thu, Mar 12, 2020 at 1:38 PM Satish Balay <
> > >>> balay at mcs.anl.gov>
> > >>> > > > > wrote:
> > >>> > > > > > > >
> > >>> > > > > > > > > For some reason - the fortran compiler libraries
> check
> > >>> worked fine
> > >>> > > > > > > without
> > >>> > > > > > > > > -lgfortran.
> > >>> > > > > > > > >
> > >>> > > > > > > > > But now - flbaslapack check is failing without it.
> > >>> > > > > > > > >
> > >>> > > > > > > > > To work arround - you can use option LIBS=-lgfortran
> > >>> > > > > > > > >
> > >>> > > > > > > > > Satish
> > >>> > > > > > > > >
> > >>> > > > > > > > > On Thu, 12 Mar 2020, Fande Kong wrote:
> > >>> > > > > > > > >
> > >>> > > > > > > > > > Hi All,
> > >>> > > > > > > > > >
> > >>> > > > > > > > > > I had an issue when configuring petsc on a linux
> > >>> machine. I have
> > >>> > > > > the
> > >>> > > > > > > > > > following error message:
> > >>> > > > > > > > > >
> > >>> > > > > > > > > >      Compiling FBLASLAPACK; this may take several
> > >>> minutes
> > >>> > > > > > > > > >
> > >>> > > > > > > > > >
> > >>> > > > > > > > >
> > >>> > > > > > >
> > >>> > > > >
> > >>>
> ===============================================================================
> > >>> > > > > > > > > >
> > >>> > > > > > > > > >    TESTING: checkLib from
> > >>> > > > > > > > > >
> > >>> > > > > > > > >
> > >>> > > > > > >
> > >>> > > > >
> > >>>
> config.packages.BlasLapack(config/BuildSystem/config/packages/BlasLapack.py:120)
> > >>> > > > > > > > > >
> > >>> > > > > > > > > >
> > >>> > > > > > > > >
> > >>> > > > > > >
> > >>> > > > >
> > >>>
> *******************************************************************************
> > >>> > > > > > > > > >          UNABLE to CONFIGURE with GIVEN OPTIONS
> (see
> > >>> > > > > > > configure.log for
> > >>> > > > > > > > > > details):
> > >>> > > > > > > > > >
> > >>> > > > > > > > >
> > >>> > > > > > >
> > >>> > > > >
> > >>>
> -------------------------------------------------------------------------------
> > >>> > > > > > > > > > --download-fblaslapack libraries cannot be used
> > >>> > > > > > > > > >
> > >>> > > > > > > > >
> > >>> > > > > > >
> > >>> > > > >
> > >>>
> *******************************************************************************
> > >>> > > > > > > > > >
> > >>> > > > > > > > > >
> > >>> > > > > > > > > > The configuration log was attached.
> > >>> > > > > > > > > >
> > >>> > > > > > > > > > Thanks,
> > >>> > > > > > > > > >
> > >>> > > > > > > > > > Fande,
> > >>> > > > > > > > > >
> > >>> > > > > > > > >
> > >>> > > > > > > > >
> > >>> > > > > > > >
> > >>> > > > > > >
> > >>> > > > > >
> > >>> > > > >
> > >>> > > > >
> > >>> > > >
> > >>> > >
> > >>> >
> > >>>
> > >>
> >
>
>
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