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 <ba...@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...@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...@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@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 < > > ba...@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 < > > > >>> ba...@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 < > > > >>> ba...@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, > > > >>> > > > > > > > > > > > > >>> > > > > > > > > > > > >>> > > > > > > > > > > > >>> > > > > > > > > > > >>> > > > > > > > > > >>> > > > > > > > > >>> > > > > > > > >>> > > > > > > > >>> > > > > > > >>> > > > > > >>> > > > > >>> > > > >> > > > > > > > >