[petsc-dev] To add a PETSc dependent package to PETSc as an external package.
Matthew Knepley
knepley at gmail.com
Thu Aug 18 04:16:06 CDT 2011
On Thu, Aug 18, 2011 at 3:31 AM, Xuefei (Rebecca) Yuan <xyuan at lbl.gov>wrote:
> Dear all,
>
> I have a problem for compile PDSLin with PETSc, the configure.log says
>
> ------------------------------------------------------
> ====== Compiling PDSLin; this may take several minutes
>
> ===============================================================================
> sh: cd
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0
> &&
> PDSLIN_INSTALL_DIR=/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/arch-cray-xt6-pkgs-opt-doubleprecision-pdslin/lib
> && export PDSLIN_INSTALL_DIR && make clean && make lib LAAUX="" && mv -f *.a
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/arch-cray-xt6-pkgs-opt-doubleprecision-pdslin/lib
> && cp -f include/*.h
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/arch-cray-xt6-pkgs-opt-doubleprecision-pdslin/include/.Executing:
> cd
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0
> &&
> PDSLIN_INSTALL_DIR=/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/arch-cray-
> xt6-pkgs-opt-doubleprecision-pdslin/lib && export PDSLIN_INSTALL_DIR &&
> make clean && make lib LAAUX="" && mv -f *.a
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/arch-cray-xt6-pkgs-opt-doubleprecision-pdslin/lib
> && cp -f include/*.h
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/arch-cray-xt6-pkgs-opt-doubleprecision-pdslin/include/.
> sh: (cd src/; make clean; cd
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/fortran;
> make clean; cd /scratch2/scratchdirs/xyuan/Software_Hopper/pet
> sc-dev/externalpackages/pdslin_0.0/fortran/examples; make clean; cd
> /scratch2/scratchdirs/x
> yuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/examples; make
> clean; rm -f ; )
>
> make[1]: Entering directory
> `/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/src'
> ( rm -f *.o; rm -f ./slu/*.o;)
> make[1]: Leaving directory
> `/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/src'
> make[1]: Entering directory
> `/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/fortran'
> (rm -f *.o; rm -f *.mod;)
> make[1]: Leaving directory
> `/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/fortran'
> make[1]: Entering directory
> `/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/fortran/examples'
> (rm -f *.o; rm -f *.mod; rm -f dtest_pdslinf; rm -f ztest_pdslinf;)
> make[1]: Leaving directory
> `/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/fortran/examples'
> make[1]: Entering directory
> `/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/examples'
> (rm -f *.o; rm -f *.dat; rm -f dtest_pdslin; rm -f ztest_pdslin; rm -f
> dtest; rm -f ztest;)
> make[1]: Leaving directory
> `/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/examples'
> make: Nothing to be done for `lib'.
>
>
> *******************************************************************************
> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for
> details):
>
> -------------------------------------------------------------------------------
> Error running make on PDSLIN: Could not execute "cd
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0
> &&
> PDSLIN_INSTALL_DIR=/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/arch-cray-xt6-pkgs-opt-doubleprecision-pdslin/lib
> && export PDSLIN_INSTALL_DIR && make clean && make lib LAAUX="" && mv -f *.a
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/arch-cray-xt6-pkgs-opt-doubleprecision-pdslin/lib
> && cp -f include/*.h
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/arch-cray-xt6-pkgs-opt-doubleprecision-pdslin/include/.":
> (cd src/; make clean; cd
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/fortran;
> make clean; cd
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/fortran/examples;
> make clean; cd
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/examples;
> make clean; rm -f ; )
> make[1]: Entering directory
> `/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/src'
> ( rm -f *.o; rm -f ./slu/*.o;)
> make[1]: Leaving directory
> `/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/src'
> make[1]: Entering directory
> `/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/fortran'
> (rm -f *.o; rm -f *.mod; rm -f dtest_pdslinf; rm -f ztest_pdslinf;)
> make[1]: Leaving directory
> `/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/fortran/examples'
> make[1]: Entering directory
> `/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/external
> packages/pdslin_0.0/examples'
> (rm -f *.o; rm -f *.dat; rm -f dtest_pdslin; rm -f ztest_pdslin; rm -f
> dtest; rm -f ztest;)
> make[1]: Leaving directory
> `/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0/examples'
> make: Nothing to be done for `lib'.
> mv: cannot stat `*.a': No such file or
> directory*******************************************************************************
>
^^^^^^^^^^^^^^^^^^^^^
Your install is failing.
Matt
> File
> "/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/config/configure.py",
> line 27
> 2, in petsc_configure framework.configure(out = sys.stdout)
> File
> "/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/config/BuildSystem/config/fra
> mework.py", line 925, in configure child.configure()
> File
> "/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/config/BuildSystem/config/package.py",
> line 500, in configure
> self.executeTest(self.configureLibrary)
> File
> "/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/config/BuildSystem/config/base.py",
> line 115, in executeTest
> ret = apply(test, args,kargs)
> File
> "/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/config/BuildSystem/config/package.py",
> line 427, in configureLibrary
> for location, directory, lib, incl in self.generateGuesses():
> File
> "/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/config/BuildSystem/config/package.py",
> line 223, in generateGuesses
> d = self.checkDownload(1)
> File
> "/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/config/BuildSystem/config/package.py",
> line 308, in checkDownload
> return self.getInstallDir()
> File
> "/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/config/BuildSystem/config/package.py",
> line 181, in getInstallDir
> return os.path.abspath(self.Install())
> File
> "/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/config/PETSc/packages/PDSLin.py",
> line 74, in Install
> raise RuntimeError('Error running make on PDSLIN: '+str(e))
>
>
>
> -----------------------------------------------------
> I started to copy and paste the error message including commands:
>
>
> Error running make on PDSLIN: Could not execute "cd
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0
> &&
> PDSLIN_INSTALL_DIR=/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/arch-cray-xt6-pkgs-opt-doubleprecision-pdslin/lib
> && export PDSLIN_INSTALL_DIR && make clean && make lib LAAUX="" && mv -f *.a
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/arch-cray-xt6-pkgs-opt-doubleprecision-pdslin/lib
> && cp -f include/*.h
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/arch-cray-xt6-pkgs-opt-doubleprecision-pdslin/include/.":
>
>
> And found that
>
> Software_Hopper/petsc-dev> cd
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0
> Directory:
> /scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/externalpackages/pdslin_0.0
> externalpackages/pdslin_0.0>
> PDSLIN_INSTALL_DIR=/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/arch-cray-xt6-pkgs-opt-doubleprecision-pdslin/lib
> PDSLIN_INSTALL_DIR=/scratch2/scratchdirs/xyuan/Software_Hopper/petsc-dev/arch-cray-xt6-pkgs-opt-doubleprecision-pdslin/lib:
> Command not found.
> externalpackages/pdslin_0.0>
>
> Then I realized that it is a csh not a bash. However, there is no error
> message for other packages, such as SuperLU_DIST. My PDSLin.py looks like
> (modified from SuperLU_DIST.py):
>
>
> -------------------------------------
> import PETSc.package
>
> class Configure(PETSc.package.NewPackage):
> def __init__(self, framework): PETSc.package.NewPackage.__init__(self,
> framework)
> self.downloadname = self.name.lower()
> self.download = ['
> http://portal.nersc.gov/project/nerscpd/pdslin_0.0.tar.gz']
> self.functions = ['dpdslin_solver']
> self.includes = ['dpdslin_solver.h']
> self.liblist = [['libpdslin.a']]
> #
> # PDSLin supports 64 bit integers but uses ParMetis which does not, see
> the comment in
> ParMetis.py
> # in the method configureLibrary()
> self.requires32bitint = 0
> self.complex = 1
> return
> def setupDependencies(self, framework):
> PETSc.package.NewPackage.setupDependencies(self, framework)
> self.blasLapack = framework.require('config.packages.BlasLapack',self)
> self.parmetis = framework.require('PETSc.packages.ParMetis',self)
> self.scotch = framework.require('PETSc.packages.Scotch',self)
> self.superlu_dist =
> framework.require('PETSc.packages.SuperLU_DIST',self)
> self.deps =
> [self.mpi,self.blasLapack,self.parmetis,self.scotch,self.superlu_dist]
> return
>
> def Install(self):
> import os
> import sys
>
> g = open(os.path.join(self.packageDir,'make.inc'),'w')
> g.write('SHELL = '+self.programs.SHELL+'\n')
> g.write('DPDSLINroot = '+self.packageDir+'\n')
> g.write('HOME = $(DPDSLINroot)\n')
> g.write('DPDSLINLIB = $(DPDSLINroot)/lib/libpdslin.a\n')
> g.write('BLASDEF = -DUSE_VENDOR_BLAS\n')
> g.write('BLASLIB =
> '+self.libraries.toString(self.blasLapack.dlib)+'\n')
> g.write('IMPI = '+self.headers.toString(self.mpi.include)+'\n')
> g.write('MPILIB = '+self.libraries.toString(self.mpi.lib)+'\n')
> g.write('PMETISLIB =
> '+self.libraries.toString(self.parmetis.lib)+'\n')
> g.write('PSCOTCHLIB =
> '+self.libraries.toString(self.scotch.lib)+'\n')
> g.write('SUPERLUDISTLIB =
> '+self.libraries.toString(self.superlu_dist.lib)+'\n')
> g.write('LIBS = $(DPDSLINLIB) $(BLASLIB) $(PMETISLIB) $(MPILIB)
> $(PSCOTCHLIB) $(SUPERLUDISTLIB)\n')
> g.write('ARCH = '+self.setCompilers.AR+'\n')
> g.write('ARCHFLAGS = '+self.setCompilers.AR_FLAGS+'\n')
> g.write('RANLIB = '+self.setCompilers.RANLIB+'\n')
> self.setCompilers.pushLanguage('C')
> g.write('CC = '+self.setCompilers.getCompiler()+' $(IMPI)\n')
> #build fails without $(IMPI)
> g.write('CFLAGS = '+self.setCompilers.getCompilerFlags()+'\n')
> g.write('LOADER = '+self.setCompilers.getLinker()+'\n')
> g.write('LOADOPTS = \n')
> self.setCompilers.popLanguage()
> # set blas/lapack name mangling
> if self.blasLapack.mangling == 'underscore':
> g.write('CDEFS = -DAdd_')
> elif self.blasLapack.mangling == 'caps':
> g.write('CDEFS = -DUpCase')
> else:
> g.write('CDEFS = -DNoChange')
> if self.framework.argDB['with-64-bit-indices']:
> g.write(' -D_LONGINT')
> g.write('\n')
> # not sure what this is for
> g.write('NOOPTS =
> '+self.blasLapack.getSharedFlag(self.setCompilers.getCompilerFlags())+'
> '+self.blasLapack.getPrecisionFlag(self.setCompilers.getCompilerFlags())+'
> '+self.blasLapack.getWindowsNonOptFlags(self.setCompilers.getCompilerFlags())+'\n')
> g.close()
>
> if self.installNeeded('make.inc'):
> try:
> self.logPrintBox('Compiling PDSLin; this may take several minutes')
> if not os.path.exists(os.path.join(self.packageDir,'lib')):
> os.makedirs(os.path.join(self.packageDir,'lib'))
> output,err,ret = PETSc.package.NewPackage.executeShellCommand('cd
> '+self.packageDir+' && PDSLIN_INSTALL_DIR='+self.installDir+'/lib && export
> PDSLIN_INSTALL_DIR && make clean && make lib LAAUX="" && mv -f *.a
> '+os.path.join(self.installDir,'lib')+' && cp -f include/*.h
> '+os.path.join(self.installDir,'include')+'/.', timeout=2500, log =
> self.framework.log)
> except RuntimeError, e:
> raise RuntimeError('Error running make on PDSLIN: '+str(e))
> self.postInstall(output+err,'make.inc')
> return self.installDir
>
> def consistencyChecks(self):
> PETSc.package.NewPackage.consistencyChecks(self)
> if self.framework.argDB['with-'+self.package]:
> if not self.blasLapack.checkForRoutine('slamch'):
> raise RuntimeError('PDSLin requires the BLAS routine slamch()')
> self.framework.log.write('Found slamch() in BLAS library as needed by
> PDSLin\n')
> if not self.blasLapack.checkForRoutine('dlamch'):
> raise RuntimeError('PDSLin requires the BLAS routine dlamch()')
> self.framework.log.write('Found dlamch() in BLAS library as needed by
> PDSLin\n')
> if not self.blasLapack.checkForRoutine('xerbla'):
> raise RuntimeError('PDSLin requires the BLAS routine xerbla()')
> self.framework.log.write('Found xerbla() in BLAS library as needed by
> PDSLin\n')
> return
>
>
> ------------------------------------
>
> What could be wrong here?
>
> Thanks very much!
>
> Cheers,
>
> Rebecca
>
>
> On Aug 17, 2011, at 1:46 PM, Barry Smith wrote:
>
> >
> > Rebecca,
> >
> > It would probably be best if you email to petsc-maint the PDSLin
> tarball so we can look at the PDSlin structure and come up with the best way
> to proceed. The way to handle the packaging will depend on how PDSLin
> interacts with PETSc.
> >
> > Thanks
> >
> > Barry
> >
> > On Aug 17, 2011, at 3:19 PM, Xuefei (Rebecca) Yuan wrote:
> >
> >> Dear all,
> >>
> >> We are trying to add a PETSc dependent package called PDSLin to PETSc as
> an external package. PDSLin is a hybrid linear solver and we would like to
> have it been imported to PETSc as SuperLU_DIST used to be, and it provides
> an alternative way to solving a linear system in parallel.
> >>
> >> Even though the package has not been released yet (should be released
> soon) and it is under testing for some problems, we are still interesting in
> putting it as an external package to PETSc for now.
> >>
> >> I did some search of the old threads to the petsc-dev team and there is
> a request from Lious for the PaStiX a few years ago.
> >>
> >> My understanding to add a package is the following steps:
> >>
> >> 1) create a python code called "PDSLin.py" under
> /petsc-dev/config/PETSc/packages
> >>
> >> 2) write an interface file between PETSc and PDSLin.
> >>
> >> As PDSLin is very similar to SuperLU_DIST, and it also depending on
> PETSc (similar to Prometheus), the PDSLin.py is created based on
> SuperLU_DIST.py and Prometheus.py.
> >>
> >> Before putting the interface file in some places under petsc-dev
> directory, would you please help me understand how those option calls go to
> this interface file?
> >>
> >> a) am I missing another file to create/modify to have those options
> connected to PDSLin in a very similar way to SuperLU_DIST?
> >>
> >> b) do I have some flexibility to add more options called from PETSc to
> this package?
> >>
> >> Moreover, I am not sure how to put the interface file in the dev
> package.
> >>
> >> c) where shall it go? The SuperLU_DIST is located at
> >>
> >> ./src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c
> >>
> >> shall I put it as
> >>
> >> ./src/mat/impls/aij/mpi/pdslin/pdslin.c ?
> >>
> >> d) what is the rule of writing this interface file?
> >>
> >> In superlu_dist.c, the extern functions are
> >>
> >> extern PetscErrorCode MatFactorInfo_SuperLU_DIST(Mat,PetscViewer);
> >> extern PetscErrorCode MatLUFactorNumeric_SuperLU_DIST(Mat,Mat,const
> MatFactorInfo *);
> >> extern PetscErrorCode MatDestroy_SuperLU_DIST(Mat);
> >> extern PetscErrorCode MatView_SuperLU_DIST(Mat,PetscViewer);
> >> extern PetscErrorCode MatSolve_SuperLU_DIST(Mat,Vec,Vec);
> >> extern PetscErrorCode
> MatLUFactorSymbolic_SuperLU_DIST(Mat,Mat,IS,IS,const MatFactorInfo *);
> >> extern PetscErrorCode MatDestroy_MPIAIJ(Mat);
> >>
> >> What kind of functions should I have in the interface file for PDSLin?
> >>
> >> I am not sure if I have stated the problem clearly, in short is that we
> would like to add some package to PETSc but not sure the right way and steps
> to approach the goal.
> >>
> >> Thanks very much!
> >>
> >> Best regards,
> >>
> >> Rebecca
> >>
> >> Xuefei (Rebecca) Yuan
> >> Postdoctoral Fellow
> >> Lawrence Berkeley National Laboratory
> >> Tel: 1-510-486-7031
> >>
> >>
> >
>
>
--
What most experimenters take for granted before they begin their experiments
is infinitely more interesting than any results to which their experiments
lead.
-- Norbert Wiener
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