[petsc-dev] Configure --with-X-dir= Using Relative Path

[Barry Smith]

  Jacob,

    Since the reconfigure scripts are python you'll need to use python variables to access environmental variables like os.environ['PETSC_DIR'] 

  Barry


> On Aug 2, 2020, at 1:57 PM, Jacob Faibussowitsch <jacob.fai at gmail.com> wrote:
> 
> Hello All,
> 
> I am reconfiguring an arch within a docker using the attached reconfigure script. My petsc dir is mounted via the following commands to docker -v ${PETSC_DIR}:/petsc:delegated. I am trying to use the existing arches on my native machine as the install directories for packages compiled within the docker images because SSH keys aren’t persistent in the images and hence git pull’s won’t work. I encountered this odd bug when trying —with-zlib-dir where it prepends the existing $PETSC_DIR to the directory name automatically, but this problem persists for any package. 
> 
> There is no configure.log generated since this I guess is early enough in the configure process, so unfortunately the only error output is the wall of error text from terminal. The error indicates that configure is passing ./[COMMAND LINE DIRECTORY] instead of [COMMAND LINE DIRECTORY] to configure.
> 
> $ ls ${PETSC_DIR}/master-arch-darwin-c-debug/externalpackages/
> Permissions Size User Date Modified Name
> drwxrwxr-x    - root  8 Jul 16:07    petsc-pkg-mumps-d1a5c931b762
> drwxr-xr-x     - root  3 Jul 21:39    hdf5-1.12.0
> drwxrwxr-x    - root  1 Aug 21:34  netcdf-c-4.5.0
> drwxr-xr-x     - root  3 Jul 21:38    zlib-1.2.11
> drwxr-xr-x     - root 29 Jul 17:43   mpich-3.3.2
> drwxr-xr-x     - root  6 Jul 17:06    Chaco-2.2-p2
> drwxr-xr-x     - root  1 Aug 21:36  git.ctetgen
> drwxr-xr-x     - root  1 Aug 21:34  git.exodusii
> drwxr-xr-x     - root  1 Aug 21:31  git.med
> drwxr-xr-x     - root  1 Aug 21:31  git.metis
> drwxr-xr-x     - root  1 Aug 21:31  git.parmetis
> drwxr-xr-x     - root  1 Aug 21:32  git.pnetcdf
> drwxr-xr-x     - root  1 Aug 21:35  git.scalapack
> drwxr-xr-x     - root  1 Aug 21:31  git.sowing
> drwxr-xr-x     - root  1 Aug 21:34  git.triangle
> 
> $ echo $PETSC_DIR
> /petsc
> 
> $./reconfigure-arch-linux-c-debug
> ===============================================================================
>              Configuring PETSc to compile on your system                       
> ===============================================================================
> *******************************************************************************
>     TypeError or ValueError possibly related to ERROR in COMMAND LINE ARGUMENT while running ./configure 
> -------------------------------------------------------------------------------
> Nonexistent directory: /petsc/${PETSC_DIR}/master-arch-darwin-c-debug/externalpackages/zlib-1.2.11 for key with-zlib-dir
> *******************************************************************************
> 
> 
>   File "/petsc/config/configure.py", line 449, in petsc_configure
>     framework = config.framework.Framework(['--configModules=PETSc.Configure','--optionsModule=config.compilerOptions']+sys.argv[1:], loadArgDB = 0)
>   File "/petsc/config/BuildSystem/config/framework.py", line 107, in __init__
>     self.createChildren()
>   File "/petsc/config/BuildSystem/config/framework.py", line 324, in createChildren
>     self.getChild(moduleName)
>   File "/petsc/config/BuildSystem/config/framework.py", line 309, in getChild
>     config.setupDependencies(self)
>   File "/petsc/config/PETSc/Configure.py", line 91, in setupDependencies
>     obj = self.registerPythonFile(package,'config.packages')
>   File "/petsc/config/PETSc/Configure.py", line 49, in registerPythonFile
>     utilityObj                             = self.framework.require(directory+utilityName, self)
>   File "/petsc/config/BuildSystem/config/framework.py", line 329, in require
>     config = self.getChild(moduleName, keywordArgs)
>   File "/petsc/config/BuildSystem/config/framework.py", line 309, in getChild
>     config.setupDependencies(self)
>   File "/petsc/config/BuildSystem/config/packages/ADIOS.py", line 17, in setupDependencies
>     self.zlib           = framework.require('config.packages.zlib',self)
>   File "/petsc/config/BuildSystem/config/framework.py", line 329, in require
>     config = self.getChild(moduleName, keywordArgs)
>   File "/petsc/config/BuildSystem/config/framework.py", line 307, in getChild
>     config.setup()
>   File "/petsc/config/BuildSystem/config/base.py", line 94, in setup
>     script.Script.setup(self)
>   File "/petsc/config/BuildSystem/script.py", line 108, in setup
>     logger.Logger.setup(self)
>   File "/petsc/config/BuildSystem/logger.py", line 75, in setup
>     args.ArgumentProcessor.setup(self)
>   File "/petsc/config/BuildSystem/args.py", line 76, in setup
>     self.setupArguments(self.argDB)
>   File "/petsc/config/BuildSystem/script.py", line 92, in setupArguments
>     self.setupHelp(self.help)
>   File "/petsc/config/BuildSystem/config/packages/zlib.py", line 16, in setupHelp
>     config.package.Package.setupHelp(self, help)
>   File "/petsc/config/BuildSystem/config/package.py", line 156, in setupHelp
>     help.addArgument(self.PACKAGE,'-with-'+self.package+'-dir=<dir>',nargs.ArgDir(None,None,'Indicate the root directory of the '+self.name+' installation',mustExist = 1))
>   File "/petsc/config/BuildSystem/help.py", line 108, in addArgument
>     self.argDB.setType(self.getArgName(name), argType, forceLocal = 1)
>   File "/petsc/config/BuildSystem/RDict.py", line 222, in setType
>     value.setValue(v.getValue())
>   File "/petsc/config/BuildSystem/nargs.py", line 325, in setValue
>     raise ValueError('Nonexistent directory: '+str(value)+' for key '+str(self.key))
> 
> 
> <reconfigure-arch-linux-c-debug.py>
> 
> Best regards,
> 
> Jacob Faibussowitsch
> (Jacob Fai - booss - oh - vitch)
> Cell: (312) 694-3391
> 

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