FreeFem Installation PETSc config Error

byb · October 16, 2022, 9:08pm

Hello all,

I am trying to install the new FreeFem version 4.11 on MacOs Monterey.
I am getting this error message when I follow the steps of the installation.

I tried previous versions and get the same error message.

Do you have an idea from where this can come ?

Thank you

=============================================================================================
                         Configuring PETSc to compile on your system
=============================================================================================
=============================================================================================                                                                                                                     WARNING! Found environment variable: MAKEFLAGS=SUDO=sudo                                                                                                                                                    Ignoring it, since its also set on command line                                                                                                                                                       =============================================================================================                                                                                                               TESTING: checkFortranCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:1748)                                                                                                      *******************************************************************************
         UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
-------------------------------------------------------------------------------
Fortran compiler you provided with --with-fc=gfortran cannot be found or does not work.
Cannot compile/link FC with gfortran.
*******************************************************************************

make: *** [petsc-3.17.0/tag-conf-real] Error 1

and

config.log :

## ---------------------- ##
## Running config.status. ##
## ---------------------- ##

This file was extended by FreeFEM config.status 4.11, which was
generated by GNU Autoconf 2.71.  Invocation command line was

  CONFIG_FILES    =
  CONFIG_HEADERS  =
  CONFIG_LINKS    =
  CONFIG_COMMANDS =
  $ ../../config.status --file=Makefile.inc:Makefile-PETSc.inc

on PortYacine.local

config.status:1220: creating Makefile.inc

prj · October 17, 2022, 5:25am

Could you please:

try the develop branch instead of master,
send 3rdparty/ff-petsc/petsc-3.18.0/configure.log if the error persists.

byb · October 17, 2022, 10:13pm

Thank you for your reply.
I have tried with develop branch and observe the same error.

Unfortunatly, as I am a new user I cannot share the configure.log file.

Here the last part of the file.

===== Checking compiler
Executing: gfortran -c -o /var/folders/5z/jkmtl4fj6_qb47sgxkbnjn7h0000gn/T/petsc-zm5iwfo1/config.setCompilers/conftest.o -I/var/folders/5z/jkmtl4fj6_qb47sgxkbnjn7h0000gn/T/petsc-zm5iwfo1/config.setCompilers   /var/folders/5z/jkmtl4fj6_qb47sgxkbnjn7h0000gn/T/petsc-zm5iwfo1/config.setCompilers/conftest.F90 
Successful compile:
Source:
      program main

      end

===== Checking linker
Executing: gfortran -c -o /var/folders/5z/jkmtl4fj6_qb47sgxkbnjn7h0000gn/T/petsc-zm5iwfo1/config.setCompilers/conftest.o -I/var/folders/5z/jkmtl4fj6_qb47sgxkbnjn7h0000gn/T/petsc-zm5iwfo1/config.setCompilers   /var/folders/5z/jkmtl4fj6_qb47sgxkbnjn7h0000gn/T/petsc-zm5iwfo1/config.setCompilers/conftest.F90 
Successful compile:
Source:
      program main

      end

Executing: gfortran  -o /var/folders/5z/jkmtl4fj6_qb47sgxkbnjn7h0000gn/T/petsc-zm5iwfo1/config.setCompilers/conftest    /var/folders/5z/jkmtl4fj6_qb47sgxkbnjn7h0000gn/T/petsc-zm5iwfo1/config.setCompilers/conftest.o 
Possible ERROR while running linker: exit code 1
stderr:
ld: library not found for -lSystem
collect2: error: ld returned 1 exit status
Linker output before filtering:

ld: library not found for -lSystem
collect2: error: ld returned 1 exit status
:
Linker output after filtering:

ld: library not found for -lSystem
collect2: error: ld returned 1 exit status:
          Error testing Fortran compiler: Cannot compile/link FC with gfortran.
            Deleting "FC"
*******************************************************************************
         UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
-------------------------------------------------------------------------------
Fortran compiler you provided with --with-fc=gfortran cannot be found or does not work.
Cannot compile/link FC with gfortran.
*******************************************************************************
  File "/Users/yacine/Desktop/FreeFem-sources-4.11/3rdparty/ff-petsc/petsc-3.17.0/config/configure.py", line 469, in petsc_configure
    framework.configure(out = sys.stdout)
  File "/Users/yacine/Desktop/FreeFem-sources-4.11/3rdparty/ff-petsc/petsc-3.17.0/config/BuildSystem/config/framework.py", line 1404, in configure
    self.processChildren()
  File "/Users/yacine/Desktop/FreeFem-sources-4.11/3rdparty/ff-petsc/petsc-3.17.0/config/BuildSystem/config/framework.py", line 1392, in processChildren
    self.serialEvaluation(self.childGraph)
  File "/Users/yacine/Desktop/FreeFem-sources-4.11/3rdparty/ff-petsc/petsc-3.17.0/config/BuildSystem/config/framework.py", line 1367, in serialEvaluation
    child.configure()
  File "/Users/yacine/Desktop/FreeFem-sources-4.11/3rdparty/ff-petsc/petsc-3.17.0/config/BuildSystem/config/setCompilers.py", line 2651, in configure
    self.executeTest(self.checkFortranCompiler)
  File "/Users/yacine/Desktop/FreeFem-sources-4.11/3rdparty/ff-petsc/petsc-3.17.0/config/BuildSystem/config/base.py", line 138, in executeTest
    ret = test(*args,**kargs)
  File "/Users/yacine/Desktop/FreeFem-sources-4.11/3rdparty/ff-petsc/petsc-3.17.0/config/BuildSystem/config/setCompilers.py", line 1755, in checkFortranCompiler
    for compiler in self.generateFortranCompilerGuesses():
  File "/Users/yacine/Desktop/FreeFem-sources-4.11/3rdparty/ff-petsc/petsc-3.17.0/config/BuildSystem/config/setCompilers.py", line 1680, in generateFortranCompilerGuesses
    raise RuntimeError('Fortran compiler you provided with --with-fc='+self.argDB['with-fc']+' cannot be found or does not work.'+'\n'+self.mesg)
================================================================================
Finishing configure run at Tue, 18 Oct 2022 00:01:31 +0200
================================================================================

prj · October 18, 2022, 6:07am

You are still trying to build PETSc 3.17.0, which means you are not tracking an up-to-date FreeFEM develop branch. Please restart from scratch.

byb · October 19, 2022, 1:28pm

Hi prj,

I downloded the develop branch from this link: https://github.com/FreeFem/FreeFem-sources/tree/develop

I am still getting the same error message :

=============================================================================================
                         Configuring PETSc to compile on your system
=============================================================================================
TESTING: checkFortranCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:1824)*******************************************************************************
         UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
-------------------------------------------------------------------------------
Fortran compiler you provided with --with-fc=gfortran cannot be found or does not work.
Cannot compile/link FC with gfortran.
*******************************************************************************

make: *** [petsc-3.18.0/tag-conf-real] Error 1

Here is a section of : 3rdparty/ff-petsc/petsc-3.18.0/configure.log

618 Executing: gfortran -c -o /tmp/petsc-8jrxzd2j/config.setCompilers/conftest.o -I/tmp/petsc-8jrxzd2j/config.setCompilers   /tmp/petsc-8jrxzd2j/config.setCompilers/conftest.F90
619 Successful compile:
620 Source:
621       program main
622
623       end
624
625 Executing: gfortran  -o /tmp/petsc-8jrxzd2j/config.setCompilers/conftest    /tmp/petsc-8jrxzd2j/config.setCompilers/conftest.o
626 Possible ERROR while running linker: exit code 1
627 stderr:
628 ld: library not found for -lSystem
629 collect2: error: ld returned 1 exit status
630 Linker output before filtering:
631
632 ld: library not found for -lSystem
633 collect2: error: ld returned 1 exit status
634 :
635 Linker output after filtering:
636 ld: library not found for -lSystem
637 collect2: error: ld returned 1 exit status:
638           Error testing Fortran compiler: Cannot compile/link FC with gfortran.
639              MPI compiler wrapper gfortran is likely incorrect.
640   Use --with-mpi-dir to indicate an alternate MPI.
641             Deleting "FC"
642 *******************************************************************************
643          UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
644 -------------------------------------------------------------------------------
645 Fortran compiler you provided with --with-fc=gfortran cannot be found or does not work.
646 Cannot compile/link FC with gfortran.
647 *******************************************************************************
648   File "/Users/yacine/Desktop/FreeFem-sources-develop/3rdparty/ff-petsc/petsc-3.18.0/config/configure.py", line 461, in petsc_configure
649     framework.configure(out = sys.stdout)
650   File "/Users/yacine/Desktop/FreeFem-sources-develop/3rdparty/ff-petsc/petsc-3.18.0/config/BuildSystem/config/framework.py", line 1409, in configure
651     self.processChildren()
652   File "/Users/yacine/Desktop/FreeFem-sources-develop/3rdparty/ff-petsc/petsc-3.18.0/config/BuildSystem/config/framework.py", line 1397, in processChildren
653     self.serialEvaluation(self.childGraph)
654   File "/Users/yacine/Desktop/FreeFem-sources-develop/3rdparty/ff-petsc/petsc-3.18.0/config/BuildSystem/config/framework.py", line 1372, in serialEvaluation
655     child.configure()
656   File "/Users/yacine/Desktop/FreeFem-sources-develop/3rdparty/ff-petsc/petsc-3.18.0/config/BuildSystem/config/setCompilers.py", line 2741, in configure
657     self.executeTest(self.checkFortranCompiler)
658   File "/Users/yacine/Desktop/FreeFem-sources-develop/3rdparty/ff-petsc/petsc-3.18.0/config/BuildSystem/config/base.py", line 138, in executeTest
659     ret = test(*args,**kargs)
660   File "/Users/yacine/Desktop/FreeFem-sources-develop/3rdparty/ff-petsc/petsc-3.18.0/config/BuildSystem/config/setCompilers.py", line 1831, in checkFortranCompiler
661     for compiler in self.generateFortranCompilerGuesses():
662   File "/Users/yacine/Desktop/FreeFem-sources-develop/3rdparty/ff-petsc/petsc-3.18.0/config/BuildSystem/config/setCompilers.py", line 1756, in generateFortranCompilerGuesses
663     raise RuntimeError('Fortran compiler you provided with --with-fc='+self.argDB['with-fc']+' cannot be found or does not work.'+'\n'+self.mesg)
664 ================================================================================
665 Finishing configure run at Wed, 19 Oct 2022 15:22:20 +0200
666 ================================================================================```

Thank you in advance for your time.

prj · October 19, 2022, 1:33pm

Is gfortran installed on your machine? I would really need that file in full Can’t you upload it somewhere, e.g., WeTransfer? Or send it directly to my email address?

prj · October 19, 2022, 1:35pm

I’ve given you enough privilege on the forum so that you can now upload configure.log. Please do so.

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