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.

Topic		Replies	Views
Issue configuring PETSc during FF installation on Mac FreeFEM installation	20	1405	April 26, 2021
Error running make on SCALAPACK FreeFEM installation	4	757	October 10, 2020
PETSc-Slepc not compiling FreeFEM installation	3	526	January 31, 2022
Trouble installing FreeFEM on CentOS 7 FreeFEM installation	4	427	February 14, 2023
Install FreeFem on cluster General Discussion	2	283	April 5, 2022

FreeFem Installation PETSc config Error

Related Topics