[petsc-users] --download-fblaslapack libraries cannot be used
Fande Kong
fdkong.jd at gmail.com
Wed Mar 18 16:35:57 CDT 2020
Thanks, Satish,
I keep investigating into this issue. Now, I have more insights. The
fundamental reason is that: Conda-compilers (installed by: conda install -c
conda-forge compilers) have a bunch of system libs in */sysroot/lib and
*/sysroot/usr/lib. Most of them are related to glibc. These libs may or may
not be compatible to the OS system you are using.
PETSc will find these libs, and think they are just regular user libs, and
then hard code with "-rpath".
If I make some changes to ignore sysroot/lib*, and then everything
runs smoothly ( do not need to install glibc because OS will have a right
one).
git diff
diff --git a/config/BuildSystem/config/compilers.py
b/config/BuildSystem/config/compilers.py
index 5367383141..6b26594b4e 100644
--- a/config/BuildSystem/config/compilers.py
+++ b/config/BuildSystem/config/compilers.py
@@ -1132,6 +1132,7 @@ Otherwise you need a different combination of C, C++,
and Fortran compilers")
if m:
arg = '-L'+os.path.abspath(arg[2:])
if arg in ['-L/usr/lib','-L/lib','-L/usr/lib64','-L/lib64']:
continue
+ if 'sysroot/usr/lib' in arg or 'sysroot/lib' in arg: continue
if not arg in lflags:
lflags.append(arg)
self.logPrint('Found library directory: '+arg, 4, 'compilers')
PETSc should treat these libs as system-level libs???
Have a branch here: Fande-Kong/skip_sysroot_libs_maint
Any suggestion are appreciated,
Thanks,
Fande,
On Tue, Mar 17, 2020 at 2:17 PM Satish Balay <balay at mcs.anl.gov> wrote:
> Thanks for the update.
>
> Hopefully Matt can check on the issue with missing stuff in configure.log.
>
> The MR is at https://gitlab.com/petsc/petsc/-/merge_requests/2606
>
> Satish
>
>
> On Tue, 17 Mar 2020, Fande Kong wrote:
>
> > 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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