Re: petsc interface to other packages
On 08/11/17 14:13, Drew Parsons wrote:
On Wed, 2017-11-08 at 12:00 +0100, Matteo Semplice wrote:
On 08/11/17 08:33, Drew Parsons wrote:
Hi Drew,
I cloned the git repo, switched to experimental branch,
branched
off again to "local" to make my changes but it does not compile. So
I
returned to experimental and realized that I cannot even compile the
experimental branch without modifications:
matteo@signalkuppe:~/software/petsc$ git branch -vv
* experimental 4b7653fcb [origin/experimental] upload 3.8.0+dfsg1-
1exp1
to experimental
local 4b7653fcb upload 3.8.0+dfsg1-1exp1 to experimental
master f4811ce9c [origin/master] upload 3.7.7+dfsg1-2 to
unstable
matteo@signalkuppe:~/software/petsc$ git diff
matteo@signalkuppe:~/software/petsc$ dpkg-buildpackage
dpkg-buildpackage: info: source package petsc
dpkg-buildpackage: info: source version 3.8.0+dfsg1-1exp1
dpkg-buildpackage: info: source distribution experimental
dpkg-buildpackage: info: source changed by Drew Parsons
<dparsons@debian.org>
dpkg-buildpackage: info: host architecture amd64
dpkg-source --before-build petsc
Your dpkg-buildpackage did not apply the debian patches for some
reason, which is unusual. That may be why it then complains about
petscvariables. Which version of dpkg-dev do you have? And which
version of debian are you working with?
I am using the stable distribution (stretch) and in particular apt
search says:
dpkg/stable,now 1.18.24 amd64 [installed]
Debian package management system
dpkg-dev/stable,now 1.18.24 all [installed,automatic]
Debian package development tools
dpkg-buildpackage is supposed to just work, and additionally helps
ensure Build-Depends are installed. But you can also build manually
1) apply the patches
$ dh_quilt_patch
2) "manual" build
$ fakeroot debian/rules binary
See if that gets it going.
Drew
Sorry to be a pain, but the only good news I see is that
dpkg-buildpackage and the "manual" way error out in the same way... Here
is the terminal output:
matteo@signalkuppe:~/software/petsc$ git reset --hard
HEAD ora si trova a 4b7653fcb upload 3.8.0+dfsg1-1exp1 to experimental
matteo@signalkuppe:~/software/petsc$ dh_quilt_patch
File series fully applied, ends at patch test_mpi_conditional_bug816101
matteo@signalkuppe:~/software/petsc$ fakeroot debian/rules binary
dh binary --with python2
dh_testdir
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: ingresso nella directory "/home/matteo/software/petsc"
===================== libpetsc-real3.8-dbg =====================
if dh_auto_configure -plibpetsc-real3.8-dbg -ppetsc3.8-doc -- \
--with-debugging=1 \
--shared-library-extension=_real \
--with-clanguage=C++ \
--with-shared-libraries --with-pic=1 --with-cc=mpicc
--with-cxx=mpicxx --with-fc=mpif90 --useThreads=0
--with-fortran-interfaces=1 --with-blas-lib=-lblas
--with-lapack-lib=-llapack --with-scalapack=1
--with-scalapack-lib=-lscalapack-openmpi --with-mumps=1
--with-mumps-include=[] --with-mumps-lib="-ldmumps -lzmumps -lsmumps
-lcmumps -lmumps_common -lpord" --with-suitesparse=1
--with-suitesparse-include=/usr/include/suitesparse
--with-suitesparse-lib="-lumfpack -lamd -lcholmod -lklu"
--with-spooles=1 --with-spooles-include=/usr/include/spooles
--with-spooles-lib=-lspooles --with-ptscotch=1
--with-ptscotch-include=/usr/include/scotch
--with-ptscotch-lib="-lptesmumps -lptscotch -lptscotcherr" --with-fftw=1
--with-fftw-include=[] --with-fftw-lib="-lfftw3 -lfftw3_mpi"
--with-superlu=1 --with-superlu-include=/usr/include/superlu
--with-superlu-lib=-lsuperlu
--with-hdf5-include=/usr/include/hdf5/openmpi
--with-hdf5-lib="-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi
-L/usr/lib/openmpi/lib -lhdf5 -lmpi"
--CXX_LINKER_FLAGS="-Wl,--no-as-needed" \
--with-hypre=1 --with-hypre-include=/usr/include/hypre
--with-hypre-lib="-lHYPRE_IJ_mv -lHYPRE_parcsr_ls -lHYPRE_sstruct_ls
-lHYPRE_sstruct_mv -lHYPRE_struct_ls -lHYPRE_struct_mv -lHYPRE_utilities" \
--prefix=/usr/lib/petscdir/petsc3.8/x86_64-linux-gnu-real-debug \
PETSC_DIR=/home/matteo/software/petsc
--PETSC_ARCH=x86_64-linux-gnu-real-debug \
CFLAGS="-g -O2
-fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -Wformat -Werror=format-security -fPIC"
CXXFLAGS="-g -O2 -fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -Wformat -Werror=format-security -fPIC" \
FCFLAGS="-g -O2
-fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -fPIC" FFLAGS="-g -O2
-fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -fPIC" \
CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2"
LDFLAGS="-Wl,-z,relro -fPIC" MAKEFLAGS="w"; then \
: ; \
else \
cat configure.log; \
false; \
fi
./configure --build=x86_64-linux-gnu --prefix=/usr
--includedir=\${prefix}/include --mandir=\${prefix}/share/man
--infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var
--disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu
--libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode
--disable-dependency-tracking --with-debugging=1
--shared-library-extension=_real --with-clanguage=C\+\+
--with-shared-libraries --with-pic=1 --with-cc=mpicc --with-cxx=mpicxx
--with-fc=mpif90 --useThreads=0 --with-fortran-interfaces=1
--with-blas-lib=-lblas --with-lapack-lib=-llapack --with-scalapack=1
--with-scalapack-lib=-lscalapack-openmpi --with-mumps=1
--with-mumps-include=\[\] "--with-mumps-lib=-ldmumps -lzmumps -lsmumps
-lcmumps -lmumps_common -lpord" --with-suitesparse=1
--with-suitesparse-include=/usr/include/suitesparse
"--with-suitesparse-lib=-lumfpack -lamd -lcholmod -lklu"
--with-spooles=1 --with-spooles-include=/usr/include/spooles
--with-spooles-lib=-lspooles --with-ptscotch=1
--with-ptscotch-include=/usr/include/scotch
"--with-ptscotch-lib=-lptesmumps -lptscotch -lptscotcherr" --with-fftw=1
--with-fftw-include=\[\] "--with-fftw-lib=-lfftw3 -lfftw3_mpi"
--with-superlu=1 --with-superlu-include=/usr/include/superlu
--with-superlu-lib=-lsuperlu
--with-hdf5-include=/usr/include/hdf5/openmpi
"--with-hdf5-lib=-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi
-L/usr/lib/openmpi/lib -lhdf5 -lmpi"
--CXX_LINKER_FLAGS=-Wl,--no-as-needed --with-hypre=1
--with-hypre-include=/usr/include/hypre "--with-hypre-lib=-lHYPRE_IJ_mv
-lHYPRE_parcsr_ls -lHYPRE_sstruct_ls -lHYPRE_sstruct_mv
-lHYPRE_struct_ls -lHYPRE_struct_mv -lHYPRE_utilities"
--prefix=/usr/lib/petscdir/petsc3.8/x86_64-linux-gnu-real-debug
PETSC_DIR=/home/matteo/software/petsc
--PETSC_ARCH=x86_64-linux-gnu-real-debug "CFLAGS=-g -O2
-fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -Wformat -Werror=format-security -fPIC"
"CXXFLAGS=-g -O2 -fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -Wformat -Werror=format-security -fPIC"
"FCFLAGS=-g -O2 -fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -fPIC" "FFLAGS=-g -O2
-fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -fPIC" "CPPFLAGS=-Wdate-time
-D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -fPIC" MAKEFLAGS=w
===============================================================================
Configuring PETSc to compile on your system
===============================================================================
===============================================================================
WARNING -with-clanguage=C++ is a developer feature and is *not* required
for regular usage of PETSc either from C or C++
===============================================================================
TESTING: configureInstallationMethod from
PETSc.options.petscclone(config/PETSc/options/petscclone.py:20)
*******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log
for details):
-------------------------------------------------------------------------------
Your petsc source tree is broken. Use "git status" to check, or remove
the entire directory and start all over again
*******************************************************************************
dh_auto_configure: ./configure --build=x86_64-linux-gnu --prefix=/usr
--includedir=${prefix}/include --mandir=${prefix}/share/man
--infodir=${prefix}/share/info --sysconfdir=/etc --localstatedir=/var
--disable-silent-rules --libdir=${prefix}/lib/x86_64-linux-gnu
--libexecdir=${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode
--disable-dependency-tracking --with-debugging=1
--shared-library-extension=_real --with-clanguage=C++
--with-shared-libraries --with-pic=1 --with-cc=mpicc --with-cxx=mpicxx
--with-fc=mpif90 --useThreads=0 --with-fortran-interfaces=1
--with-blas-lib=-lblas --with-lapack-lib=-llapack --with-scalapack=1
--with-scalapack-lib=-lscalapack-openmpi --with-mumps=1
--with-mumps-include=[] --with-mumps-lib=-ldmumps -lzmumps -lsmumps
-lcmumps -lmumps_common -lpord --with-suitesparse=1
--with-suitesparse-include=/usr/include/suitesparse
--with-suitesparse-lib=-lumfpack -lamd -lcholmod -lklu --with-spooles=1
--with-spooles-include=/usr/include/spooles --with-spooles-lib=-lspooles
--with-ptscotch=1 --with-ptscotch-include=/usr/include/scotch
--with-ptscotch-lib=-lptesmumps -lptscotch -lptscotcherr --with-fftw=1
--with-fftw-include=[] --with-fftw-lib=-lfftw3 -lfftw3_mpi
--with-superlu=1 --with-superlu-include=/usr/include/superlu
--with-superlu-lib=-lsuperlu
--with-hdf5-include=/usr/include/hdf5/openmpi
--with-hdf5-lib=-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi
-L/usr/lib/openmpi/lib -lhdf5 -lmpi
--CXX_LINKER_FLAGS=-Wl,--no-as-needed --with-hypre=1
--with-hypre-include=/usr/include/hypre --with-hypre-lib=-lHYPRE_IJ_mv
-lHYPRE_parcsr_ls -lHYPRE_sstruct_ls -lHYPRE_sstruct_mv
-lHYPRE_struct_ls -lHYPRE_struct_mv -lHYPRE_utilities
--prefix=/usr/lib/petscdir/petsc3.8/x86_64-linux-gnu-real-debug
PETSC_DIR=/home/matteo/software/petsc
--PETSC_ARCH=x86_64-linux-gnu-real-debug CFLAGS=-g -O2
-fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -Wformat -Werror=format-security -fPIC
CXXFLAGS=-g -O2 -fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -Wformat -Werror=format-security -fPIC
FCFLAGS=-g -O2 -fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -fPIC FFLAGS=-g -O2
-fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -fPIC CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2
LDFLAGS=-Wl,-z,relro -fPIC MAKEFLAGS=w returned exit code 1
Pushing language C
Popping language C
Pushing language CUDA
Popping language CUDA
Pushing language Cxx
Popping language Cxx
Pushing language FC
Popping language FC
================================================================================
================================================================================
Starting Configure Run at Wed Nov 8 15:32:58 2017
Configure Options: --configModules=PETSc.Configure
--optionsModule=config.compilerOptions --build=x86_64-linux-gnu
--prefix=/usr --includedir=${prefix}/include
--mandir=${prefix}/share/man --infodir=${prefix}/share/info
--sysconfdir=/etc --localstatedir=/var --with-silent-rules=0
--libdir=${prefix}/lib/x86_64-linux-gnu
--libexecdir=${prefix}/lib/x86_64-linux-gnu --with-maintainer-mode=0
--with-dependency-tracking=0 --with-debugging=1
--shared-library-extension=_real --with-clanguage=C++
--with-shared-libraries --with-pic=1 --with-cc=mpicc --with-cxx=mpicxx
--with-fc=mpif90 --useThreads=0 --with-fortran-interfaces=1
--with-blas-lib=-lblas --with-lapack-lib=-llapack --with-scalapack=1
--with-scalapack-lib=-lscalapack-openmpi --with-mumps=1
--with-mumps-include="[]" --with-mumps-lib="-ldmumps -lzmumps -lsmumps
-lcmumps -lmumps_common -lpord" --with-suitesparse=1
--with-suitesparse-include=/usr/include/suitesparse
--with-suitesparse-lib="-lumfpack -lamd -lcholmod -lklu"
--with-spooles=1 --with-spooles-include=/usr/include/spooles
--with-spooles-lib=-lspooles --with-ptscotch=1
--with-ptscotch-include=/usr/include/scotch
--with-ptscotch-lib="-lptesmumps -lptscotch -lptscotcherr" --with-fftw=1
--with-fftw-include="[]" --with-fftw-lib="-lfftw3 -lfftw3_mpi"
--with-superlu=1 --with-superlu-include=/usr/include/superlu
--with-superlu-lib=-lsuperlu
--with-hdf5-include=/usr/include/hdf5/openmpi
--with-hdf5-lib="-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi
-L/usr/lib/openmpi/lib -lhdf5 -lmpi"
--CXX_LINKER_FLAGS=-Wl,--no-as-needed --with-hypre=1
--with-hypre-include=/usr/include/hypre --with-hypre-lib="-lHYPRE_IJ_mv
-lHYPRE_parcsr_ls -lHYPRE_sstruct_ls -lHYPRE_sstruct_mv
-lHYPRE_struct_ls -lHYPRE_struct_mv -lHYPRE_utilities"
--prefix=/usr/lib/petscdir/petsc3.8/x86_64-linux-gnu-real-debug
PETSC_DIR=/home/matteo/software/petsc
--PETSC_ARCH=x86_64-linux-gnu-real-debug CFLAGS="-g -O2
-fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -Wformat -Werror=format-security -fPIC"
CXXFLAGS="-g -O2 -fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -Wformat -Werror=format-security -fPIC"
FCFLAGS="-g -O2 -fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -fPIC" FFLAGS="-g -O2
-fdebug-prefix-map=/home/matteo/software/petsc=.
-fstack-protector-strong -fPIC" CPPFLAGS="-Wdate-time
-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro -fPIC" MAKEFLAGS=w
Working directory: /home/matteo/software/petsc
Machine platform:
('Linux', 'signalkuppe', '4.9.0-4-amd64', '#1 SMP Debian 4.9.51-1
(2017-09-28)', 'x86_64', '')
Python version:
2.7.13 (default, Jan 19 2017, 14:48:08)
[GCC 6.3.0 20170118]
================================================================================
Pushing language C
Popping language C
Pushing language CUDA
Popping language CUDA
Pushing language Cxx
Popping language Cxx
Pushing language FC
Popping language FC
================================================================================
TEST configureExternalPackagesDir from
config.framework(/home/matteo/software/petsc/config/BuildSystem/config/framework.py:841)
TESTING: configureExternalPackagesDir from
config.framework(config/BuildSystem/config/framework.py:841)
================================================================================
TEST configureDebuggers from
config.utilities.debuggers(/home/matteo/software/petsc/config/BuildSystem/config/utilities/debuggers.py:22)
TESTING: configureDebuggers from
config.utilities.debuggers(config/BuildSystem/config/utilities/debuggers.py:22)
Find a default debugger and determine its arguments
Checking for program /home/matteo/bin/gdb...not found
Checking for program /usr/local/bin/gdb...not found
Checking for program /usr/bin/gdb...found
Defined make macro "GDB" to "/usr/bin/gdb"
Checking for program /home/matteo/bin/dbx...not found
Checking for program /usr/local/bin/dbx...not found
Checking for program /usr/bin/dbx...not found
Checking for program /bin/dbx...not found
Checking for program /usr/local/games/dbx...not found
Checking for program /usr/games/dbx...not found
Checking for program /home/matteo/dbx...not found
Checking for program /home/matteo/bin/xdb...not found
Checking for program /usr/local/bin/xdb...not found
Checking for program /usr/bin/xdb...not found
Checking for program /bin/xdb...not found
Checking for program /usr/local/games/xdb...not found
Checking for program /usr/games/xdb...not found
Checking for program /home/matteo/xdb...not found
Checking for program /home/matteo/bin/dsymutil...not found
Checking for program /usr/local/bin/dsymutil...not found
Checking for program /usr/bin/dsymutil...not found
Checking for program /bin/dsymutil...not found
Checking for program /usr/local/games/dsymutil...not found
Checking for program /usr/games/dsymutil...not found
Checking for program /home/matteo/dsymutil...not found
Defined make macro "DSYMUTIL" to "true"
Defined "USE_GDB_DEBUGGER" to "1"
================================================================================
TEST configureGit from
config.sourceControl(/home/matteo/software/petsc/config/BuildSystem/config/sourceControl.py:24)
TESTING: configureGit from
config.sourceControl(config/BuildSystem/config/sourceControl.py:24)
Find the Git executable
Checking for program /home/matteo/bin/git...not found
Checking for program /usr/local/bin/git...not found
Checking for program /usr/bin/git...found
Defined make macro "GIT" to "git"
Executing: git --version
stdout: git version 2.11.0
================================================================================
TEST configureMercurial from
config.sourceControl(/home/matteo/software/petsc/config/BuildSystem/config/sourceControl.py:35)
TESTING: configureMercurial from
config.sourceControl(config/BuildSystem/config/sourceControl.py:35)
Find the Mercurial executable
Checking for program /home/matteo/bin/hg...not found
Checking for program /usr/local/bin/hg...not found
Checking for program /usr/bin/hg...not found
Checking for program /bin/hg...not found
Checking for program /usr/local/games/hg...not found
Checking for program /usr/games/hg...not found
Checking for program /home/matteo/hg...not found
================================================================================
TEST configureCLanguage from
PETSc.options.languages(/home/matteo/software/petsc/config/PETSc/options/languages.py:27)
TESTING: configureCLanguage from
PETSc.options.languages(config/PETSc/options/languages.py:27)
Choose whether to compile the PETSc library using a C or C++ compiler
===============================================================================
WARNING -with-clanguage=C++ is a developer feature
and is *not* required for regular usage of PETSc either from C or C++
===============================================================================
C language is Cxx
Defined "CLANGUAGE_CXX" to "1"
================================================================================
TEST configureDirectories from
PETSc.options.petscdir(/home/matteo/software/petsc/config/PETSc/options/petscdir.py:23)
TESTING: configureDirectories from
PETSc.options.petscdir(config/PETSc/options/petscdir.py:23)
Checks PETSC_DIR and sets if not set
Version Information:
#define PETSC_VERSION_RELEASE 1
#define PETSC_VERSION_MAJOR 3
#define PETSC_VERSION_MINOR 8
#define PETSC_VERSION_SUBMINOR 0
#define PETSC_VERSION_PATCH 0
#define PETSC_VERSION_DATE "Sep, 26, 2017"
#define PETSC_VERSION_GIT "v3.8"
#define PETSC_VERSION_DATE_GIT "2017-09-26 17:50:05 -0500"
#define PETSC_VERSION_EQ(MAJOR,MINOR,SUBMINOR) \
#define PETSC_VERSION_ PETSC_VERSION_EQ
#define PETSC_VERSION_LT(MAJOR,MINOR,SUBMINOR) \
#define PETSC_VERSION_LE(MAJOR,MINOR,SUBMINOR) \
#define PETSC_VERSION_GT(MAJOR,MINOR,SUBMINOR) \
#define PETSC_VERSION_GE(MAJOR,MINOR,SUBMINOR) \
Defined make macro "DIR" to "/home/matteo/software/petsc"
================================================================================
TEST getDatafilespath from
PETSc.options.dataFilesPath(/home/matteo/software/petsc/config/PETSc/options/dataFilesPath.py:29)
TESTING: getDatafilespath from
PETSc.options.dataFilesPath(config/PETSc/options/dataFilesPath.py:29)
Checks what DATAFILESPATH should be
================================================================================
TEST configureInstallationMethod from
PETSc.options.petscclone(/home/matteo/software/petsc/config/PETSc/options/petscclone.py:20)
TESTING: configureInstallationMethod from
PETSc.options.petscclone(config/PETSc/options/petscclone.py:20)
*******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log
for details):
-------------------------------------------------------------------------------
Your petsc source tree is broken. Use "git status" to check, or remove
the entire directory and start all over again
*******************************************************************************
File "./config/configure.py", line 393, in petsc_configure
framework.configure(out = sys.stdout)
File
"/home/matteo/software/petsc/config/BuildSystem/config/framework.py",
line 1097, in configure
self.processChildren()
File
"/home/matteo/software/petsc/config/BuildSystem/config/framework.py",
line 1086, in processChildren
self.serialEvaluation(self.childGraph)
File
"/home/matteo/software/petsc/config/BuildSystem/config/framework.py",
line 1067, in serialEvaluation
child.configure()
File
"/home/matteo/software/petsc/config/PETSc/options/petscclone.py", line
55, in configure
self.executeTest(self.configureInstallationMethod)
File "/home/matteo/software/petsc/config/BuildSystem/config/base.py",
line 126, in executeTest
ret = test(*args,**kargs)
File
"/home/matteo/software/petsc/config/PETSc/options/petscclone.py", line
49, in configureInstallationMethod
raise RuntimeError('Your petsc source tree is broken. Use "git
status" to check, or remove the entire directory and start all over again')
================================================================================
Finishing Configure Run at Wed Nov 8 15:32:58 2017
================================================================================
debian/rules:140: set di istruzioni per l'obiettivo
"override_dh_auto_configure" non riuscito
make[1]: *** [override_dh_auto_configure] Errore 1
make[1]: uscita dalla directory "/home/matteo/software/petsc"
debian/rules:118: set di istruzioni per l'obiettivo "binary" non riuscito
make: *** [binary] Errore 2
Matteo
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