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

[Satish Balay]

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

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?

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]

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,
> >>> > > > > > > > > >
> >>> > > > > > > > >
> >>> > > > > > > > >
> >>> > > > > > > >
> >>> > > > > > >
> >>> > > > > >
> >>> > > > >
> >>> > > > >
> >>> > > >
> >>> > >
> >>> >
> >>>
> >>
>