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 <[email protected]> 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