Hello, I recently started receiving the following error when trying to compile anything... makefile:16: /conf/variables: No such file or directory makefile:17: /conf/rules: No such file or directory makefile:858: /conf/test: No such file or directory make: *** No rule to make target `/conf/test'. Stop. The errors seem to be related to one another. I tried to hardcode this path, but the makefile is not picking up the path. I can't recall changing anything major Thanks! Mark
You have not set your PETSC_ARCH and PETSC_DIR On Nov 12, 2010, at 9:43 AM, Nunion wrote:
Hello,
I recently started receiving the following error when trying to compile anything...
makefile:16: /conf/variables: No such file or directory makefile:17: /conf/rules: No such file or directory makefile:858: /conf/test: No such file or directory make: *** No rule to make target `/conf/test'. Stop.
The errors seem to be related to one another. I tried to hardcode this path, but the makefile is not picking up the path. I can't recall changing anything major
Thanks!
Mark
Initially, I thought that was the case as well. However, I saved some output from installation; =============================================================================== Configuring PETSc to compile on your system =============================================================================== TESTING: alternateConfigureLibrary from PETSc.packages.petsc4py(config/PETSc/packages/petsc4py.py:64) Compilers: C Compiler: mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -g3 Fortran Compiler: mpif90 -g Linkers: Static linker: /usr/bin/ar cr Dynamic linker: mpicc -shared -Wall -Wwrite-strings -Wno-strict-aliasing -g3 MPI: Includes: -I/home/walker/MPI/mpich2-1.0.8-install/include X11: Includes: Library: -lX11 BLAS/LAPACK: -llapack -lblas PETSc: PETSC_ARCH: linux-gnu-c-debug PETSC_DIR: /home/walker/Desktop/PETSc/LITE/petsc-3.1-p4 Clanguage: C shared libraries: disabled dynamic libraries: disabled Scalar type: real Precision: double Memory alignment: 16 xxx=========================================================================xxx Configure stage complete. Now build PETSc libraries with: make PETSC_DIR=/home/walker/Desktop/PETSc/LITE/petsc-3.1-p4 PETSC_ARCH=linux-gnu-c-debug all xxx=========================================================================xxx Is this the same information that would be contained in the log file for the configuration? On Fri, Nov 12, 2010 at 10:07 AM, Barry Smith <[email protected]> wrote:
You have not set your PETSC_ARCH and PETSC_DIR
On Nov 12, 2010, at 9:43 AM, Nunion wrote:
Hello,
I recently started receiving the following error when trying to compile anything...
makefile:16: /conf/variables: No such file or directory makefile:17: /conf/rules: No such file or directory makefile:858: /conf/test: No such file or directory make: *** No rule to make target `/conf/test'. Stop.
The errors seem to be related to one another. I tried to hardcode this path, but the makefile is not picking up the path. I can't recall changing anything major
Thanks!
Mark
On Fri, 12 Nov 2010, Nunion wrote:
Initially, I thought that was the case as well. However, I saved some output from installation;
????? Why don't you try the provided suggestion - and say if it worked or - not? and if it didn't - furnish further relavent info - like the command used, errors obtained, makefile used? And how and where exactly did you set PETSC_ARCH and PETSC_DIR? BTW: The log you qouted mentiones one way of using PETSC_ARCH and PETSC_DIR with 'make'
make PETSC_DIR=/home/walker/Desktop/PETSc/LITE/petsc-3.1-p4 PETSC_ARCH=linux-gnu-c-debug all
Satish
On Fri, Nov 12, 2010 at 10:07 AM, Barry Smith <[email protected]> wrote:
You have not set your PETSC_ARCH and PETSC_DIR
On Nov 12, 2010, at 9:43 AM, Nunion wrote:
Hello,
I recently started receiving the following error when trying to compile anything...
makefile:16: /conf/variables: No such file or directory makefile:17: /conf/rules: No such file or directory makefile:858: /conf/test: No such file or directory make: *** No rule to make target `/conf/test'. Stop.
The errors seem to be related to one another. I tried to hardcode this path, but the makefile is not picking up the path. I can't recall changing anything major
Thanks!
Mark
Hello, While compiling one of my code with ifort , I have the following error pointing towards petscvec.h . Any idea about this posssible kind of error please ? Any option of ifort to use ? Many thanks Tahar ifort -assume byterecl -I/usr/local/petsc/ -I/usr/local/petsc//include -I/usr/local/petsc//include/finclude -I/usr/local/petsc//macx/include -I/usr/X11R6/include/X11 -DPETSC_HAVE_PARMETIS -DPETSC_USE_DEBUG -DPETSC_USE_LOG -DPETSC_USE_BOPT_g -DPETSC_USE_STACK -DPETSC_AVOID_MPIF_H -c petsc.fpp /usr/local/petsc//include/finclude/petscvec.h(10): error #6418: This name has already been assigned a data type. [NORM_1] integer(kind=selected_int_kind(5)) NORM_1 -------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
Looks like this is related to the following: http://www.mcs.anl.gov/petsc/petsc-as/documentation/changes/31.html # petsc.h and petscdef.h are replaced with petscsys.h and petscsysdef.h; while petsc.h now includes ALL PETSc include files. Try removing all includes other than 'petsc.h' from your code. Satish On Fri, 12 Nov 2010, Tahar Amari wrote:
Hello,
While compiling one of my code with ifort , I have the following error pointing towards petscvec.h .
Any idea about this posssible kind of error please ? Any option of ifort to use ?
Many thanks
Tahar
ifort -assume byterecl -I/usr/local/petsc/ -I/usr/local/petsc//include -I/usr/local/petsc//include/finclude -I/usr/local/petsc//macx/include -I/usr/X11R6/include/X11 -DPETSC_HAVE_PARMETIS -DPETSC_USE_DEBUG -DPETSC_USE_LOG -DPETSC_USE_BOPT_g -DPETSC_USE_STACK -DPETSC_AVOID_MPIF_H -c petsc.fpp /usr/local/petsc//include/finclude/petscvec.h(10): error #6418: This name has already been assigned a data type. [NORM_1] integer(kind=selected_int_kind(5)) NORM_1
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
Many thanks. This is solved. Now at link I have the library not found. Any idea ? -L/usr/local/petsc/macx/lib -lpetscsnes -lpetscvec -lpetscmat -lpetsccontrib -lpetscts -lpetscdm -lpetscksp -lpetsc -lmpich -lpmpich -lfmpich -lmpichf90 -lparmetis -lmetis -lfblas -lflapack ld: library not found for -lpetscsnes Tahar Le 12 nov. 2010 à 18:17, Satish Balay a écrit :
Looks like this is related to the following: http://www.mcs.anl.gov/petsc/petsc-as/documentation/changes/31.html # petsc.h and petscdef.h are replaced with petscsys.h and petscsysdef.h; while petsc.h now includes ALL PETSc include files.
Try removing all includes other than 'petsc.h' from your code.
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
Hello,
While compiling one of my code with ifort , I have the following error pointing towards petscvec.h .
Any idea about this posssible kind of error please ? Any option of ifort to use ?
Many thanks
Tahar
ifort -assume byterecl -I/usr/local/petsc/ -I/usr/local/petsc//include -I/usr/local/petsc//include/finclude -I/usr/local/petsc//macx/include -I/usr/X11R6/include/X11 -DPETSC_HAVE_PARMETIS -DPETSC_USE_DEBUG -DPETSC_USE_LOG -DPETSC_USE_BOPT_g -DPETSC_USE_STACK -DPETSC_AVOID_MPIF_H -c petsc.fpp /usr/local/petsc//include/finclude/petscvec.h(10): error #6418: This name has already been assigned a data type. [NORM_1] integer(kind=selected_int_kind(5)) NORM_1
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
Looks like you are not using PETSc makefiles - and upgrading from older release to petsc-3.1 Currently there is only one library for petsc [-lpetsc] Check: cd $PETSC_DIR make getincludedirs getlinklibs Satish On Fri, 12 Nov 2010, Tahar Amari wrote:
Many thanks. This is solved.
Now at link I have the library not found. Any idea ?
-L/usr/local/petsc/macx/lib -lpetscsnes -lpetscvec -lpetscmat -lpetsccontrib -lpetscts -lpetscdm -lpetscksp -lpetsc -lmpich -lpmpich -lfmpich -lmpichf90 -lparmetis -lmetis -lfblas -lflapack ld: library not found for -lpetscsnes
Tahar
Le 12 nov. 2010 à 18:17, Satish Balay a écrit :
Looks like this is related to the following: http://www.mcs.anl.gov/petsc/petsc-as/documentation/changes/31.html # petsc.h and petscdef.h are replaced with petscsys.h and petscsysdef.h; while petsc.h now includes ALL PETSc include files.
Try removing all includes other than 'petsc.h' from your code.
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
Hello,
While compiling one of my code with ifort , I have the following error pointing towards petscvec.h .
Any idea about this posssible kind of error please ? Any option of ifort to use ?
Many thanks
Tahar
ifort -assume byterecl -I/usr/local/petsc/ -I/usr/local/petsc//include -I/usr/local/petsc//include/finclude -I/usr/local/petsc//macx/include -I/usr/X11R6/include/X11 -DPETSC_HAVE_PARMETIS -DPETSC_USE_DEBUG -DPETSC_USE_LOG -DPETSC_USE_BOPT_g -DPETSC_USE_STACK -DPETSC_AVOID_MPIF_H -c petsc.fpp /usr/local/petsc//include/finclude/petscvec.h(10): error #6418: This name has already been assigned a data type. [NORM_1] integer(kind=selected_int_kind(5)) NORM_1
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
You are right. Here is what I got timac> make getincludedirs getlinklibs -I/Data/Poub1/petsc-3.1-p5/macx/include -I/Data/Poub1/petsc-3.1-p5/include -I/Data/Poub1/petsc-3.1-p5/macx/include -L/Data/Poub1/petsc-3.1-p5/macx/lib -L/Data/Poub1/petsc-3.1-p5/macx/lib -L/Data/Poub1/petsc-3.1-p5/macx/lib -lpetsc -L/usr/X11R6/lib -lX11 -L/Data/Poub1/petsc-3.1-p5/macx/lib -lparmetis -lmetis -lflapack -lfblas -L/Data/Poub1/petsc-3.1-p5/macx/lib -L/usr/lib/gcc/i686-apple-darwin10/4.2.1/x86_64 -L/usr/lib/i686-apple-darwin10/4.2.1 -L/opt/intel/Compiler/11.1/088/lib -L/opt/intel/Compiler/11.1/088/Frameworks/mkl/lib/em64t -L/usr/lib/gcc/i686-apple-darwin10/4.2.1 -ldl -lpmpich -lmpich -lSystem -lmpichf90 -lifport -lifcore -limf -lsvml -lipgo -lgcc_s.10.5 -lSystemStubs -lmx -lirc -lpthread -ldl -lpmpich -lmpich -lSystem -ldl What does it mean please for me to change in my makefiles ? Do you mean that I should remove any link other than -lpetsc ? Great thanks Tahar Le 12 nov. 2010 à 18:26, Satish Balay a écrit :
Looks like you are not using PETSc makefiles - and upgrading from older release to petsc-3.1
Currently there is only one library for petsc [-lpetsc]
Check: cd $PETSC_DIR make getincludedirs getlinklibs
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
Many thanks. This is solved.
Now at link I have the library not found. Any idea ?
-L/usr/local/petsc/macx/lib -lpetscsnes -lpetscvec -lpetscmat -lpetsccontrib -lpetscts -lpetscdm -lpetscksp -lpetsc -lmpich -lpmpich -lfmpich -lmpichf90 -lparmetis -lmetis -lfblas -lflapack ld: library not found for -lpetscsnes
Tahar
Le 12 nov. 2010 à 18:17, Satish Balay a écrit :
Looks like this is related to the following: http://www.mcs.anl.gov/petsc/petsc-as/documentation/changes/31.html # petsc.h and petscdef.h are replaced with petscsys.h and petscsysdef.h; while petsc.h now includes ALL PETSc include files.
Try removing all includes other than 'petsc.h' from your code.
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
Hello,
While compiling one of my code with ifort , I have the following error pointing towards petscvec.h .
Any idea about this posssible kind of error please ? Any option of ifort to use ?
Many thanks
Tahar
ifort -assume byterecl -I/usr/local/petsc/ -I/usr/local/petsc//include -I/usr/local/petsc//include/finclude -I/usr/local/petsc//macx/include -I/usr/X11R6/include/X11 -DPETSC_HAVE_PARMETIS -DPETSC_USE_DEBUG -DPETSC_USE_LOG -DPETSC_USE_BOPT_g -DPETSC_USE_STACK -DPETSC_AVOID_MPIF_H -c petsc.fpp /usr/local/petsc//include/finclude/petscvec.h(10): error #6418: This name has already been assigned a data type. [NORM_1] integer(kind=selected_int_kind(5)) NORM_1
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
Make sure your compiles have all the flags listed here.. Its best to use petsc makefile formats so that this info is automatically picked up from the petsc config files. [and not tweak user makefiles for every install of petsc..] Satish On Fri, 12 Nov 2010, Tahar Amari wrote:
You are right.
Here is what I got
timac> make getincludedirs getlinklibs -I/Data/Poub1/petsc-3.1-p5/macx/include -I/Data/Poub1/petsc-3.1-p5/include -I/Data/Poub1/petsc-3.1-p5/macx/include -L/Data/Poub1/petsc-3.1-p5/macx/lib -L/Data/Poub1/petsc-3.1-p5/macx/lib -L/Data/Poub1/petsc-3.1-p5/macx/lib -lpetsc -L/usr/X11R6/lib -lX11 -L/Data/Poub1/petsc-3.1-p5/macx/lib -lparmetis -lmetis -lflapack -lfblas -L/Data/Poub1/petsc-3.1-p5/macx/lib -L/usr/lib/gcc/i686-apple-darwin10/4.2.1/x86_64 -L/usr/lib/i686-apple-darwin10/4.2.1 -L/opt/intel/Compiler/11.1/088/lib -L/opt/intel/Compiler/11.1/088/Frameworks/mkl/lib/em64t -L/usr/lib/gcc/i686-apple-darwin10/4.2.1 -ldl -lpmpich -lmpich -lSystem -lmpichf90 -lifport -lifcore -limf -lsvml -lipgo -lgcc_s.10.5 -lSystemStubs -lmx -lirc -lpthread -ldl -lpmpich -lmpich -lSystem -ldl
What does it mean please for me to change in my makefiles ?
Do you mean that I should remove any link other than -lpetsc ?
Great thanks
Tahar
Le 12 nov. 2010 à 18:26, Satish Balay a écrit :
Looks like you are not using PETSc makefiles - and upgrading from older release to petsc-3.1
Currently there is only one library for petsc [-lpetsc]
Check: cd $PETSC_DIR make getincludedirs getlinklibs
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
Many thanks. This is solved.
Now at link I have the library not found. Any idea ?
-L/usr/local/petsc/macx/lib -lpetscsnes -lpetscvec -lpetscmat -lpetsccontrib -lpetscts -lpetscdm -lpetscksp -lpetsc -lmpich -lpmpich -lfmpich -lmpichf90 -lparmetis -lmetis -lfblas -lflapack ld: library not found for -lpetscsnes
Tahar
Le 12 nov. 2010 à 18:17, Satish Balay a écrit :
Looks like this is related to the following: http://www.mcs.anl.gov/petsc/petsc-as/documentation/changes/31.html # petsc.h and petscdef.h are replaced with petscsys.h and petscsysdef.h; while petsc.h now includes ALL PETSc include files.
Try removing all includes other than 'petsc.h' from your code.
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
Hello,
While compiling one of my code with ifort , I have the following error pointing towards petscvec.h .
Any idea about this posssible kind of error please ? Any option of ifort to use ?
Many thanks
Tahar
ifort -assume byterecl -I/usr/local/petsc/ -I/usr/local/petsc//include -I/usr/local/petsc//include/finclude -I/usr/local/petsc//macx/include -I/usr/X11R6/include/X11 -DPETSC_HAVE_PARMETIS -DPETSC_USE_DEBUG -DPETSC_USE_LOG -DPETSC_USE_BOPT_g -DPETSC_USE_STACK -DPETSC_AVOID_MPIF_H -c petsc.fpp /usr/local/petsc//include/finclude/petscvec.h(10): error #6418: This name has already been assigned a data type. [NORM_1] integer(kind=selected_int_kind(5)) NORM_1
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
Great thanks, it seems that -lpetsc alone works . I will follow this advice regarding the makefile, for the reason you gave. Where should I get a typical makefile to modify please ? Tahar Le 12 nov. 2010 à 18:34, Satish Balay a écrit :
Make sure your compiles have all the flags listed here..
Its best to use petsc makefile formats so that this info is automatically picked up from the petsc config files. [and not tweak user makefiles for every install of petsc..]
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
You are right.
Here is what I got
timac> make getincludedirs getlinklibs -I/Data/Poub1/petsc-3.1-p5/macx/include -I/Data/Poub1/petsc-3.1-p5/include -I/Data/Poub1/petsc-3.1-p5/macx/include -L/Data/Poub1/petsc-3.1-p5/macx/lib -L/Data/Poub1/petsc-3.1-p5/macx/lib -L/Data/Poub1/petsc-3.1-p5/macx/lib -lpetsc -L/usr/X11R6/lib -lX11 -L/Data/Poub1/petsc-3.1-p5/macx/lib -lparmetis -lmetis -lflapack -lfblas -L/Data/Poub1/petsc-3.1-p5/macx/lib -L/usr/lib/gcc/i686-apple-darwin10/4.2.1/x86_64 -L/usr/lib/i686-apple-darwin10/4.2.1 -L/opt/intel/Compiler/11.1/088/lib -L/opt/intel/Compiler/11.1/088/Frameworks/mkl/lib/em64t -L/usr/lib/gcc/i686-apple-darwin10/4.2.1 -ldl -lpmpich -lmpich -lSystem -lmpichf90 -lifport -lifcore -limf -lsvml -lipgo -lgcc_s.10.5 -lSystemStubs -lmx -lirc -lpthread -ldl -lpmpich -lmpich -lSystem -ldl
What does it mean please for me to change in my makefiles ?
Do you mean that I should remove any link other than -lpetsc ?
Great thanks
Tahar
Le 12 nov. 2010 à 18:26, Satish Balay a écrit :
Looks like you are not using PETSc makefiles - and upgrading from older release to petsc-3.1
Currently there is only one library for petsc [-lpetsc]
Check: cd $PETSC_DIR make getincludedirs getlinklibs
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
Many thanks. This is solved.
Now at link I have the library not found. Any idea ?
-L/usr/local/petsc/macx/lib -lpetscsnes -lpetscvec -lpetscmat -lpetsccontrib -lpetscts -lpetscdm -lpetscksp -lpetsc -lmpich -lpmpich -lfmpich -lmpichf90 -lparmetis -lmetis -lfblas -lflapack ld: library not found for -lpetscsnes
Tahar
Le 12 nov. 2010 à 18:17, Satish Balay a écrit :
Looks like this is related to the following: http://www.mcs.anl.gov/petsc/petsc-as/documentation/changes/31.html # petsc.h and petscdef.h are replaced with petscsys.h and petscsysdef.h; while petsc.h now includes ALL PETSc include files.
Try removing all includes other than 'petsc.h' from your code.
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
Hello,
While compiling one of my code with ifort , I have the following error pointing towards petscvec.h .
Any idea about this posssible kind of error please ? Any option of ifort to use ?
Many thanks
Tahar
ifort -assume byterecl -I/usr/local/petsc/ -I/usr/local/petsc//include -I/usr/local/petsc//include/finclude -I/usr/local/petsc//macx/include -I/usr/X11R6/include/X11 -DPETSC_HAVE_PARMETIS -DPETSC_USE_DEBUG -DPETSC_USE_LOG -DPETSC_USE_BOPT_g -DPETSC_USE_STACK -DPETSC_AVOID_MPIF_H -c petsc.fpp /usr/local/petsc//include/finclude/petscvec.h(10): error #6418: This name has already been assigned a data type. [NORM_1] integer(kind=selected_int_kind(5)) NORM_1
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
Attaching a minimal sample makefile. The additional info it would need is PETSC_DIR, PETSC_ARCH values for your install of PETSc. All example/tests,tutorial dirs have makefiles in petsc format.. Satish On Fri, 12 Nov 2010, Tahar Amari wrote:
Great thanks, it seems that -lpetsc alone works .
I will follow this advice regarding the makefile, for the reason you gave. Where should I get a typical makefile to modify please ?
Tahar
Le 12 nov. 2010 à 18:34, Satish Balay a écrit :
Make sure your compiles have all the flags listed here..
Its best to use petsc makefile formats so that this info is automatically picked up from the petsc config files. [and not tweak user makefiles for every install of petsc..]
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
You are right.
Here is what I got
timac> make getincludedirs getlinklibs -I/Data/Poub1/petsc-3.1-p5/macx/include -I/Data/Poub1/petsc-3.1-p5/include -I/Data/Poub1/petsc-3.1-p5/macx/include -L/Data/Poub1/petsc-3.1-p5/macx/lib -L/Data/Poub1/petsc-3.1-p5/macx/lib -L/Data/Poub1/petsc-3.1-p5/macx/lib -lpetsc -L/usr/X11R6/lib -lX11 -L/Data/Poub1/petsc-3.1-p5/macx/lib -lparmetis -lmetis -lflapack -lfblas -L/Data/Poub1/petsc-3.1-p5/macx/lib -L/usr/lib/gcc/i686-apple-darwin10/4.2.1/x86_64 -L/usr/lib/i686-apple-darwin10/4.2.1 -L/opt/intel/Compiler/11.1/088/lib -L/opt/intel/Compiler/11.1/088/Frameworks/mkl/lib/em64t -L/usr/lib/gcc/i686-apple-darwin10/4.2.1 -ldl -lpmpich -lmpich -lSystem -lmpichf90 -lifport -lifcore -limf -lsvml -lipgo -lgcc_s.10.5 -lSystemStubs -lmx -lirc -lpthread -ldl -lpmpich -lmpich -lSystem -ldl
What does it mean please for me to change in my makefiles ?
Do you mean that I should remove any link other than -lpetsc ?
Great thanks
Tahar
Le 12 nov. 2010 à 18:26, Satish Balay a écrit :
Looks like you are not using PETSc makefiles - and upgrading from older release to petsc-3.1
Currently there is only one library for petsc [-lpetsc]
Check: cd $PETSC_DIR make getincludedirs getlinklibs
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
Many thanks. This is solved.
Now at link I have the library not found. Any idea ?
-L/usr/local/petsc/macx/lib -lpetscsnes -lpetscvec -lpetscmat -lpetsccontrib -lpetscts -lpetscdm -lpetscksp -lpetsc -lmpich -lpmpich -lfmpich -lmpichf90 -lparmetis -lmetis -lfblas -lflapack ld: library not found for -lpetscsnes
Tahar
Le 12 nov. 2010 à 18:17, Satish Balay a écrit :
Looks like this is related to the following: http://www.mcs.anl.gov/petsc/petsc-as/documentation/changes/31.html # petsc.h and petscdef.h are replaced with petscsys.h and petscsysdef.h; while petsc.h now includes ALL PETSc include files.
Try removing all includes other than 'petsc.h' from your code.
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
Hello,
While compiling one of my code with ifort , I have the following error pointing towards petscvec.h .
Any idea about this posssible kind of error please ? Any option of ifort to use ?
Many thanks
Tahar
ifort -assume byterecl -I/usr/local/petsc/ -I/usr/local/petsc//include -I/usr/local/petsc//include/finclude -I/usr/local/petsc//macx/include -I/usr/X11R6/include/X11 -DPETSC_HAVE_PARMETIS -DPETSC_USE_DEBUG -DPETSC_USE_LOG -DPETSC_USE_BOPT_g -DPETSC_USE_STACK -DPETSC_AVOID_MPIF_H -c petsc.fpp /usr/local/petsc//include/finclude/petscvec.h(10): error #6418: This name has already been assigned a data type. [NORM_1] integer(kind=selected_int_kind(5)) NORM_1
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
Thank you very much for your efficient help. Tahar Le 12 nov. 2010 à 18:44, Satish Balay a écrit :
Attaching a minimal sample makefile. The additional info it would need is PETSC_DIR, PETSC_ARCH values for your install of PETSc.
All example/tests,tutorial dirs have makefiles in petsc format..
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
Great thanks, it seems that -lpetsc alone works .
I will follow this advice regarding the makefile, for the reason you gave. Where should I get a typical makefile to modify please ?
Tahar
Le 12 nov. 2010 à 18:34, Satish Balay a écrit :
Make sure your compiles have all the flags listed here..
Its best to use petsc makefile formats so that this info is automatically picked up from the petsc config files. [and not tweak user makefiles for every install of petsc..]
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
You are right.
Here is what I got
timac> make getincludedirs getlinklibs -I/Data/Poub1/petsc-3.1-p5/macx/include -I/Data/Poub1/petsc-3.1-p5/include -I/Data/Poub1/petsc-3.1-p5/macx/include -L/Data/Poub1/petsc-3.1-p5/macx/lib -L/Data/Poub1/petsc-3.1-p5/macx/lib -L/Data/Poub1/petsc-3.1-p5/macx/lib -lpetsc -L/usr/X11R6/lib -lX11 -L/Data/Poub1/petsc-3.1-p5/macx/lib -lparmetis -lmetis -lflapack -lfblas -L/Data/Poub1/petsc-3.1-p5/macx/lib -L/usr/lib/gcc/i686-apple-darwin10/4.2.1/x86_64 -L/usr/lib/i686-apple-darwin10/4.2.1 -L/opt/intel/Compiler/11.1/088/lib -L/opt/intel/Compiler/11.1/088/Frameworks/mkl/lib/em64t -L/usr/lib/gcc/i686-apple-darwin10/4.2.1 -ldl -lpmpich -lmpich -lSystem -lmpichf90 -lifport -lifcore -limf -lsvml -lipgo -lgcc_s.10.5 -lSystemStubs -lmx -lirc -lpthread -ldl -lpmpich -lmpich -lSystem -ldl
What does it mean please for me to change in my makefiles ?
Do you mean that I should remove any link other than -lpetsc ?
Great thanks
Tahar
Le 12 nov. 2010 à 18:26, Satish Balay a écrit :
Looks like you are not using PETSc makefiles - and upgrading from older release to petsc-3.1
Currently there is only one library for petsc [-lpetsc]
Check: cd $PETSC_DIR make getincludedirs getlinklibs
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
Many thanks. This is solved.
Now at link I have the library not found. Any idea ?
-L/usr/local/petsc/macx/lib -lpetscsnes -lpetscvec -lpetscmat -lpetsccontrib -lpetscts -lpetscdm -lpetscksp -lpetsc -lmpich -lpmpich -lfmpich -lmpichf90 -lparmetis -lmetis -lfblas -lflapack ld: library not found for -lpetscsnes
Tahar
Le 12 nov. 2010 à 18:17, Satish Balay a écrit :
Looks like this is related to the following: http://www.mcs.anl.gov/petsc/petsc-as/documentation/changes/31.html # petsc.h and petscdef.h are replaced with petscsys.h and petscsysdef.h; while petsc.h now includes ALL PETSc include files.
Try removing all includes other than 'petsc.h' from your code.
Satish
On Fri, 12 Nov 2010, Tahar Amari wrote:
Hello,
While compiling one of my code with ifort , I have the following error pointing towards petscvec.h .
Any idea about this posssible kind of error please ? Any option of ifort to use ?
Many thanks
Tahar
ifort -assume byterecl -I/usr/local/petsc/ -I/usr/local/petsc//include -I/usr/local/petsc//include/finclude -I/usr/local/petsc//macx/include -I/usr/X11R6/include/X11 -DPETSC_HAVE_PARMETIS -DPETSC_USE_DEBUG -DPETSC_USE_LOG -DPETSC_USE_BOPT_g -DPETSC_USE_STACK -DPETSC_AVOID_MPIF_H -c petsc.fpp /usr/local/petsc//include/finclude/petscvec.h(10): error #6418: This name has already been assigned a data type. [NORM_1] integer(kind=selected_int_kind(5)) NORM_1
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
<makefile.txt>
-------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
Hello, I have written a C/C++ code on unstructured mesh (tetrahedra) , using pthreads but not MPI. 1 Is it a good idea to use petsc as a framework as an easier high level library for interface to MPI in order to parallelize the code 2. If yes. I have fields on various location on my mesh ; some variables are defined at cell center, otheres on edges, and others on faces. Does petsc allow to avoid to deal with low level MPI routines to get and set the ghost values between partitions to evaluate some functions such as fluxes at cell faces which needs different variables which may lie on different partitions ? (I have seen on the talk http://www.mcs.anl.gov/petsc/petsc-as/documentation/tutorials/ARSC2010.pdf page 81 some code lines which suggest that it is simple /∗ Code to communicate nonlocal ghost point data ∗/ VecGetArray(F, &f ); /∗ Code to compute local function components ∗/ VecRestoreArray(F, &f ); return 0; Would it be possible to get some advice please ? Thanks Tahar -------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
Hello, Reading the doc files, I saw that the DA frameworks contains very interesting functions which allow to specify various stencils for ghost cells and fields. I read that those cannot be used for unstructured meshes. HOwever is there some equivalent for unstructured mesh. This would be very useful. Tahar -------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 42 52 fax: 33 1 69 33 49 49 email: <mailto:[email protected]> URL : http://www.cpht.polytechnique.fr/cpht/amari
Hi, I have a modified makefile originally given to me by the PETSc team. It worked well but there's a small problem. Sometimes, when I have edited a fortran file and tries to rebuild, it gives this error: /opt/openmpi-1.4.1/bin/mpif90 -r8 -w95 -c -O3 -save airfoil.f90 /opt/openmpi-1.4.1/bin/mpif90 -w95 -c -O3 -save grid.f90 m2c -o cell_data.o cell_data.mod make: m2c: Command not found make: *** [cell_data.o] Error 127 However, if I delete all the *.o and *.mod files and build clean, there's no such problems. Is there anyway to solve this problem? I have attached the makefile Thanks! Yours sincerely, TAY wee-beng
On 15/11/10 09:54, TAY wee-beng wrote:
Hi,
I have a modified makefile originally given to me by the PETSc team. It worked well but there's a small problem. Sometimes, when I have edited a fortran file and tries to rebuild, it gives this error:
/opt/openmpi-1.4.1/bin/mpif90 -r8 -w95 -c -O3 -save airfoil.f90 /opt/openmpi-1.4.1/bin/mpif90 -w95 -c -O3 -save grid.f90 m2c -o cell_data.o cell_data.mod make: m2c: Command not found make: *** [cell_data.o] Error 127
However, if I delete all the *.o and *.mod files and build clean, there's no such problems. Is there anyway to solve this problem?
I have attached the makefile
Thanks!
Yours sincerely,
TAY wee-beng
This is caused by a built-in implicit make rule that tells make it can make object files from modula-2 .mod files by running m2c - obviously not what you want. You can override it by adding the following line to your makefile: %.o: %.mod Make sure the next line doesn't start with a tab. Cheers Stephan
Hi Stephan, Thanks, it worked! Yours sincerely, TAY wee-beng On 15-11-2010 12:41, Stephan Kramer wrote:
On 15/11/10 09:54, TAY wee-beng wrote:
Hi,
I have a modified makefile originally given to me by the PETSc team. It worked well but there's a small problem. Sometimes, when I have edited a fortran file and tries to rebuild, it gives this error:
/opt/openmpi-1.4.1/bin/mpif90 -r8 -w95 -c -O3 -save airfoil.f90 /opt/openmpi-1.4.1/bin/mpif90 -w95 -c -O3 -save grid.f90 m2c -o cell_data.o cell_data.mod make: m2c: Command not found make: *** [cell_data.o] Error 127
However, if I delete all the *.o and *.mod files and build clean, there's no such problems. Is there anyway to solve this problem?
I have attached the makefile
Thanks!
Yours sincerely,
TAY wee-beng
This is caused by a built-in implicit make rule that tells make it can make object files from modula-2 .mod files by running m2c - obviously not what you want. You can override it by adding the following line to your makefile:
%.o: %.mod
Make sure the next line doesn't start with a tab.
Cheers Stephan
Hi, I have a modified makefile originally given to me by the PETSc team. It worked well but now I want to change some of the options of the compiler, like using -O3 or -ipo etc instead of -O. I tried to add -O3 in and the compiling command becomes: /opt/openmpi-1.4.1/bin/mpif90 -O3 -c -g -r8 -save -w90 -w -w95 -O -I/home/wtay/Lib/petsc-3.1-p5/include .... So now there's -O3 and -O. How can I change it to only -O3 or -ipo? I have attached the makefile too. Thank you very much Yours sincerely, TAY wee-beng
Edit $PETSC_ARCH/conf/petscvariables and remove the options you don't want from everywhere in that file. Barry On Nov 19, 2010, at 8:15 AM, TAY wee-beng wrote:
Hi,
I have a modified makefile originally given to me by the PETSc team. It worked well but now I want to change some of the options of the compiler, like using -O3 or -ipo etc instead of -O.
I tried to add -O3 in and the compiling command becomes:
/opt/openmpi-1.4.1/bin/mpif90 -O3 -c -g -r8 -save -w90 -w -w95 -O -I/home/wtay/Lib/petsc-3.1-p5/include ....
So now there's -O3 and -O. How can I change it to only -O3 or -ipo?
I have attached the makefile too.
Thank you very much
Yours sincerely,
TAY wee-beng
<makefile.txt>
Hi Barry, Thanks! Yours sincerely, Wee-Beng Tay On 19/11/2010 6:37 PM, Barry Smith wrote:
Edit $PETSC_ARCH/conf/petscvariables and remove the options you don't want from everywhere in that file.
Barry
On Nov 19, 2010, at 8:15 AM, TAY wee-beng wrote:
Hi,
I have a modified makefile originally given to me by the PETSc team. It worked well but now I want to change some of the options of the compiler, like using -O3 or -ipo etc instead of -O.
I tried to add -O3 in and the compiling command becomes:
/opt/openmpi-1.4.1/bin/mpif90 -O3 -c -g -r8 -save -w90 -w -w95 -O -I/home/wtay/Lib/petsc-3.1-p5/include ....
So now there's -O3 and -O. How can I change it to only -O3 or -ipo?
I have attached the makefile too.
Thank you very much
Yours sincerely,
TAY wee-beng
<makefile.txt>
participants (7)
-
Barry Smith -
Nunion -
Satish Balay -
Stephan Kramer -
Tahar Amari -
TAY wee-beng -
Wee-Beng Tay