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

Tue Mar 17 10:08:42 CDT 2020

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,
>>> > > > > > > > > >
>>> > > > > > > > >
>>> > > > > > > > >
>>> > > > > > > >
>>> > > > > > >
>>> > > > > >
>>> > > > >
>>> > > > >
>>> > > >
>>> > >
>>> >
>>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20200317/5e40714f/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: configure.log
Type: text/x-log
Size: 3626620 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20200317/5e40714f/attachment-0001.bin>