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 <[email protected]> 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 <[email protected]> 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 < > >> [email protected]> 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 <[email protected]> > >>> 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 < > >>> [email protected]> 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 < > >>> [email protected]> > >>> > > > > 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, > >>> > > > > > > > > > > >>> > > > > > > > > > >>> > > > > > > > > > >>> > > > > > > > > >>> > > > > > > > >>> > > > > > > >>> > > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > >>> > >> >
