[petsc-users] Troubles installing PETSc
Justin Dong (Me)
jsd1 at rice.edu
Thu Nov 21 03:43:59 CST 2013
Here is the error message:
> $ make ex2
> cc ex2.c -o ex2
> ex2.c:13:10: fatal error: 'petscsys.h' file not found
> #include <petscsys.h>
> ^
> 1 error generated.
> make: *** [ex2] Error 1
and this is the entire makefile. It’s long but it’s literally a copy paste from the exercises. Also, I’ve fixed the issue with the PETSC_ARCH so it’s set to linux-gnu now. And when I do cd $PETSC_DIR, I’m moved to the correct directory.
> ALL:
>
> CFLAGS =
> FFLAGS = -I${PETSC_DIR}/include/finclude
> CPPFLAGS =
> FPPFLAGS =
> LOCDIR = src/sys/examples/tutorials/
> EXAMPLESC = ex1.c ex2.c ex3.c ex4.c ex5.c ex6.c ex7.c ex9.c ex11.c
> EXAMPLESF = ex3f.F ex4f.F ex4f90.F90 ex5f90.F90 ex8f90.F90 ex10f90.F90
> MANSEC = Sys
> CLEANFILES = binaryoutput binaryoutput.info
>
> include ${PETSC_DIR}/conf/variables
> include ${PETSC_DIR}/conf/rules
>
> ex1: ex1.o chkopts
> -${CLINKER} -o ex1 ex1.o ${PETSC_SYS_LIB}
> ${RM} -f ex1.o
>
> ex2: ex2.o chkopts
> -${CLINKER} -o ex2 ex2.o ${PETSC_SYS_LIB}
> ${RM} -f ex2.o
>
> ex3: ex3.o chkopts
> -${CLINKER} -o ex3 ex3.o ${PETSC_SYS_LIB}
> ${RM} -f ex3.o
>
> ex3f: ex3f.o chkopts
> -${FLINKER} -o ex3f ex3f.o ${PETSC_SYS_LIB}
> ${RM} -f ex3f.o
>
> ex4: ex4.o chkopts
> -${CLINKER} -o ex4 ex4.o ${PETSC_SYS_LIB}
> ${RM} -f ex4.o
>
> ex4f: ex4f.o chkopts
> -${FLINKER} -o ex4f ex4f.o ${PETSC_SYS_LIB}
> ${RM} -f ex4f.o
>
> ex4f90: ex4f90.o chkopts
> -${FLINKER} -o ex4f90 ex4f90.o ${PETSC_SYS_LIB}
> ${RM} -f ex4f90.o
>
> ex5: ex5.o chkopts
> -${CLINKER} -o ex5 ex5.o ${PETSC_SYS_LIB}
> ${RM} -f ex5.o
>
> ex5f90: ex5f90.o chkopts
> -${FLINKER} -o ex5f90 ex5f90.o ${PETSC_SYS_LIB}
> ${RM} ex5f90.o
>
> ex6: ex6.o chkopts
> -${CLINKER} -o ex6 ex6.o ${PETSC_SYS_LIB}
> ${RM} -f ex6.o
>
> ex7: ex7.o chkopts
> -${CLINKER} -o ex7 ex7.o ${PETSC_SYS_LIB}
> ${RM} -f ex7.o
>
> ex8f90: ex8f90.o chkopts
> -${FLINKER} -o ex8f90 ex8f90.o ${PETSC_SYS_LIB}
> ${RM} ex8f90.o
>
> ex9: ex9.o chkopts
> -${CLINKER} -o ex9 ex9.o ${PETSC_SYS_LIB}
> ${RM} -f ex9.o
>
> ex10f90: ex10f90.o chkopts
> -${FLINKER} -o ex10f90 ex10f90.o ${PETSC_SYS_LIB}
> ${RM} -f ex10f90.o
>
> ex11: ex11.o chkopts
> -${CLINKER} -o ex11 ex11.o ${PETSC_SYS_LIB}
> ${RM} -f ex11.o
> #
> # ------------------------------------------------------------------------
> #
> runex1:
> -@${MPIEXEC} -n 1 ./ex1 > ex1_1.tmp 2>&1; \
> if (${DIFF} output/ex1_1.out ex1_1.tmp) then true; \
> else echo ${PWD} ; echo "Possible problem with with ex1_1, diffs above \n========================================="; fi; \
> ${RM} -f ex1_1.tmp
>
> runex2:
> -@${MPIEXEC} -n 1 ./ex2 > ex2_1.tmp 2>&1; \
> if (${DIFF} output/ex2_1.out ex2_1.tmp) then true; \
> else echo ${PWD} ; echo "Possible problem with with ex2_1, diffs above \n========================================="; fi; \
> ${RM} -f ex2_1.tmp
>
> runex3:
> -@${MPIEXEC} -n 1 ./ex3
>
> runex3f:
> -@${MPIEXEC} -n 1 ./ex3f
>
> runex4:
> -@${MPIEXEC} -n 5 ./ex4 | sort > ex4_1.tmp 2>&1; \
> if (${DIFF} output/ex4_1.out ex4_1.tmp) then true; \
> else echo ${PWD} ; echo "Possible problem with with ex4_1, diffs above \n========================================="; fi; \
> ${RM} -f ex4_1.tmp
>
> runex4f:
> -@${MPIEXEC} -n 5 ./ex4f | sort > ex4f_1.tmp 2>&1; \
> if (${DIFF} output/ex4f_1.out ex4f_1.tmp) then true; \
> else echo ${PWD} ; echo "Possible problem with with ex4f_1, diffs above \n========================================="; fi; \
> ${RM} -f ex4f_1.tmp
>
> runex4f90:
> -@${MPIEXEC} -n 1 ./ex4f90 > ex4f90_1.tmp 5>&1; \
> if (${DIFF} output/ex4f90_1.out ex4f90_1.tmp) then true; \
> else echo ${PWD} ; echo "Possible problem with with ex4f90_1, diffs above \n========================================="; fi; \
> ${RM} -f ex4f90_1.tmp
>
> runex5:
> -@${MPIEXEC} -n 1 ./ex5 -pbag_rho 44 -pbag_do_output true > ex5_1.tmp 5>&1; \
> if (${DIFF} output/ex5_1.out ex5_1.tmp) then true; \
> else echo ${PWD} ; echo "Possible problem with with ex5_1, diffs above \n========================================="; fi; \
> ${RM} -f ex5_1.tmp
>
> runex5f90:
> -@${MPIEXEC} -n 1 ./ex5f90 -pbag_rarray 4,5,88 > ex5f90_1.tmp 5>&1; \
> if (${DIFF} output/ex5f90_1.out ex5f90_1.tmp) then true; \
> else echo ${PWD} ; echo "Possible problem with with ex5f90_1, diffs above \n========================================="; fi; \
> ${RM} -f ex5f90_1.tmp
>
> runex6:
> -@${MPIEXEC} -n 1 ./ex6
>
> runex8f90:
> -@${MPIEXEC} -n 1 ./ex8f90 -joe_jeff b456 > ex8f90_1.tmp 8>&1; \
> if (${DIFF} output/ex8f90_1.out ex8f90_1.tmp) then true; \
> else echo ${PWD} ; echo "Possible problem with with ex8f90_1, diffs above \n========================================="; fi; \
> ${RM} -f ex8f90_1.tmp
>
> runex9_1:
> - at PETSC_OPTIONS= ${MPIEXEC} -n 1 ./ex9 -f petsc.yml > ex9_1.tmp 5>&1; \
> if (${DIFF} output/ex9_1.out ex9_1.tmp) then true; \
> else echo ${PWD} ; echo "Possible problem with with ex9_1, diffs above \n========================================="; fi; \
> ${RM} -f ex9_1.tmp
>
> runex9_2:
> - at PETSC_OPTIONS= ${MPIEXEC} -n 1 ./ex9 -options_file_yaml petsc.yml > ex9_2.tmp 5>&1; \
> if (${DIFF} output/ex9_2.out ex9_2.tmp) then true; \
> else echo ${PWD} ; echo "Possible problem with with ex9_2, diffs above \n========================================="; fi; \
> ${RM} -f ex9_2.tmp
>
> runex10f90_1:
> - at PETSC_OPTIONS= ${MPIEXEC} -n 1 ./ex10f90 -f petsc.yml > ex10f90_1.tmp 8>&1; \
> if (${DIFF} output/ex10f90_1.out ex10f90_1.tmp) then true; \
> else echo ${PWD} ; echo "Possible problem with with ex10f90_1, diffs above \n========================================="; fi; \
> ${RM} -f ex10f90_1.tmp
>
> runex10f90_2:
> - at PETSC_OPTIONS= ${MPIEXEC} -n 1 ./ex10f90 -options_file_yaml petsc.yml > ex10f90_2.tmp 8>&1; \
> if (${DIFF} output/ex10f90_2.out ex10f90_2.tmp) then true; \
> else echo ${PWD} ; echo "Possible problem with with ex10f90_2, diffs above \n========================================="; fi; \
> ${RM} -f ex10f90_2.tmp
>
> runex11:
> -@${MPIEXEC} -n 1 ./ex11
>
> TESTEXAMPLES_C = ex1.PETSc runex1 ex1.rm ex2.PETSc runex2 ex2.rm \
> ex3.PETSc runex3 ex3.rm ex4.PETSc runex4 ex4.rm ex6.PETSc runex6 ex6.rm ex11.PETSc runex11 ex11.rm
> TESTEXAMPLES_C_NOCOMPLEX = ex5.PETSc runex5 ex5.rm
> TESTEXAMPLES_C_X_MPIUNI = ex1.PETSc runex1 ex1.rm ex2.PETSc runex2 ex2.rm \
> ex3.PETSc runex3 ex3.rm
> TESTEXAMPLES_FORTRAN = ex3f.PETSc runex3f ex3f.rm ex4f.PETSc runex4f ex4f.rm
> TESTEXAMPLES_F90 = ex4f90.PETSc runex4f90 ex4f90.rm
> TESTEXAMPLES_F2003 = ex5f90.PETSc runex5f90 ex5f90.rm ex8f90.PETSc runex8f90 ex8f90.rm
> TESTEXAMPLES_YAML = ex9.PETSc runex9_1 runex9_2 ex9.rm ex10f90.PETSc runex10f90_1 runex10f90_2 ex10f90.rm
> include ${PETSC_DIR}/conf/test
On Nov 20, 2013, at 8:05 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:
> "Justin Dong (Me)" <jsd1 at rice.edu> writes:
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