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error when install

Issue #120 resolved
Ji Zhang created an issue

I get some error during the install.

the following is the error message:

#!

running build
running build_src
running build_py
running build_ext
PETSC_DIR:    /scratch/zhang/python/petsc-3.10.3
PETSC_ARCH:   linux-openmpi-opblas
version:      3.10.3 release
integer-size: 32-bit
scalar-type:  real
precision:    double
language:     CONLY
compiler:     /scratch/zhang/python/openmpi-2.1.1/build/bin/mpicc
linker:       /scratch/zhang/python/openmpi-2.1.1/build/bin/mpicc
building 'PETSc' extension
/scratch/zhang/python/openmpi-2.1.1/build/bin/mpicc -pthread -B /scratch/zhang/anaconda3/compiler_compat -Wl,--sysroot=/ -O3 -fPIC -fPIC -Wsign-compare -DNDEBUG -g -fwrapv-O3 -Wall -DPETSC_DIR=/scratch/zhang/python/petsc-3.10.3 -I/scratch/zhang/python/openmpi-2.1.1/build/include -I/scratch/zhang/python/hdf5-1.10.4/build/include -I/scratch/zhang/python/petsc-3.10.3/linux-openmpi-opblas/include -I/scratch/zhang/python/petsc-3.10.3/include -Isrc/include -I/scratch/zhang/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/scratch/zhang/anaconda3/include/python3.7m -c src/PETSc.c -o build/temp.linux-x86_64-3.7/linux-openmpi-opblas/src/PETSc.o
In file included from src/PETSc.c:4:0:
src/petsc4py.PETSc.c: In function ‘PyInit_PETSc’:
src/petsc4py.PETSc.c:284319:43: error: ‘SNESTEST’ undeclared (first use in this function)
   __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(SNESTEST); if (unlikely(!__pyx_t_7)) __PYX_ERR(37, 7, __pyx_L1_error)
                                           ^
src/petsc4py.PETSc.c:284319:43: note: each undeclared identifier is reported only once for each function it appears in
error: command '/scratch/zhang/python/openmpi-2.1.1/build/bin/mpicc' failed with exitstatus 1

can any one give me some help? Thanks.

Comments (11)

  1. Lisandro Dalcin

    This is an unfortunate consequence of a change in PETSc patch release 3.10.3, for the time being, you should use branch maint of petsc4py's git repository, commit a013d13 fixes this issue.

    @BarryFSmith I understand and welcome cleanups, but IMHO patch releases is not the place to make them.

  5. Drew Parsons

    Belay that. The Debian build tools must have taken some of Barry's eggnog. pdebuild is not updating petsc4py.PETSc.c (so build fails), but dpkg-buildpackage is (so build succeeds). Not petsc4py's problem :)

  6. Lisandro Dalcin

    @drewparsons I should really make a new petsc4py patch release, but right now I'm in vacations until end of January. In the mean time, I would recommend to apply the following patch on top of petsc4py 3.10 release tarball.

    diff --git a/src/PETSc.c b/src/PETSc.c
index c6124b5..c60270a 100644
--- a/src/PETSc.c
+++ b/src/PETSc.c
@@ -1,4 +1,5 @@
 #define MPICH_SKIP_MPICXX 1
 #define OMPI_SKIP_MPICXX 1
 #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
+#define SNESTEST "test"
 #include "petsc4py.PETSc.c"
  7. Drew Parsons

    Hi @dalcinl, I did get commit a013d13 to work (the Debian build just needed to trigger autoreconf, I found the debhelper tools to do that). So it's all good in Debian, no need for the local definition of SNESTEST.

  10. 欧阳涛

    i still met the problem when install the new release 3.10.1 running build running build_src running build_py running build_ext PETSC_DIR: /home/geophyx/PETGEM/PETSc/petsc-3.9.4 PETSC_ARCH: Linux_gnu version: 3.9.4 release integer-size: 32-bit scalar-type: real precision: double language: CONLY compiler: /home/geophyx/PETGEM/MPI/bin/mpicc linker: /home/geophyx/PETGEM/MPI/bin/mpicc building 'PETSc' extension /home/geophyx/PETGEM/MPI/bin/mpicc -pthread -B /home/geophyx/anaconda3/compiler_compat -Wl,--sysroot=/ -fPIC -wd1572 -g -fPIC -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -DPETSC_DIR=/home/geophyx/PETGEM/PETSc/petsc-3.9.4 -I/home/geophyx/PETGEM/MPI/include -I/home/geophyx/PETGEM/PETSc/petsc-3.9.4/Linux_gnu/include -I/home/geophyx/PETGEM/PETSc/petsc-3.9.4/include -Isrc/include -I/home/geophyx/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/home/geophyx/anaconda3/include/python3.7m -c src/PETSc.c -o build/temp.linux-x86_64-3.7/Linux_gnu/src/PETSc.o icc: command line warning #10006: ignoring unknown option '-fwrapv' src/petsc4py.PETSc.c(145369): warning #266: function "MatISFixLocalEmpty" declared implicitly __pyx_t_2 = __pyx_f_8petsc4py_5PETSc_CHKERR(MatISFixLocalEmpty(__pyx_v_self->mat, __pyx_v_cfix)); if (unlikely(__pyx_t_2 == ((int)-1))) __PYX_ERR(34, 1400, __pyx_L1_error) ^

    src/petsc4py.PETSc.c(275338): error: identifier "PETSCVIEWERADIOS" is undefined __pyx_t_4 = __pyx_f_8petsc4py_5PETSc_S_(PETSCVIEWERADIOS); if (unlikely(!__pyx_t_4)) __PYX_ERR(27, 16, __pyx_L1_error) ^

    src/petsc4py.PETSc.c(275350): error: identifier "PETSCVIEWERADIOS2" is undefined __pyx_t_4 = __pyx_f_8petsc4py_5PETSc_S_(PETSCVIEWERADIOS2); if (unlikely(!__pyx_t_4)) __PYX_ERR(27, 17, __pyx_L1_error) ^

    src/petsc4py.PETSc.c(275736): error: identifier "PETSC_VIEWER_HDF5_XDMF" is undefined __pyx_t_4 = __Pyx_PyInt_From_PetscViewerFormat(PETSC_VIEWER_HDF5_XDMF); if (unlikely(!__pyx_t_4)) __PYX_ERR(27, 49, __pyx_L1_error) ^

    src/petsc4py.PETSc.c(277868): error: identifier "MATLMVM" is undefined __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(MATLMVM); if (unlikely(!__pyx_t_7)) __PYX_ERR(34, 67, __pyx_L1_error) ^

    src/petsc4py.PETSc.c(279829): error: identifier "PCLMVM" is undefined __pyx_t_7 = __pyx_f_8petsc4py_5PETSc_S_(PCLMVM); if (unlikely(!__pyx_t_7)) __PYX_ERR(35, 47, __pyx_L1_error) ^

    src/petsc4py.PETSc.c(283974): error: identifier "TAOBQNLS" is undefined __pyx_t_1 = __pyx_f_8petsc4py_5PETSc_S_(TAOBQNLS); if (unlikely(!__pyx_t_1)) __PYX_ERR(39, 16, __pyx_L1_error) ^

    src/petsc4py.PETSc.c(283998): error: identifier "TAOBNLS" is undefined __pyx_t_1 = __pyx_f_8petsc4py_5PETSc_S_(TAOBNLS); if (unlikely(!__pyx_t_1)) __PYX_ERR(39, 18, __pyx_L1_error) ^

    src/petsc4py.PETSc.c(284010): error: identifier "TAOBNTR" is undefined __pyx_t_1 = __pyx_f_8petsc4py_5PETSc_S_(TAOBNTR); if (unlikely(!__pyx_t_1)) __PYX_ERR(39, 19, __pyx_L1_error) ^

    src/petsc4py.PETSc.c(284022): error: identifier "TAOBNTL" is undefined __pyx_t_1 = __pyx_f_8petsc4py_5PETSc_S_(TAOBNTL); if (unlikely(!__pyx_t_1)) __PYX_ERR(39, 20, __pyx_L1_error) ^

    src/petsc4py.PETSc.c(284034): error: identifier "TAOBQNKLS" is undefined __pyx_t_1 = __pyx_f_8petsc4py_5PETSc_S_(TAOBQNKLS); if (unlikely(!__pyx_t_1)) __PYX_ERR(39, 21, __pyx_L1_error) ^

    src/petsc4py.PETSc.c(284046): error: identifier "TAOBQNKTR" is undefined __pyx_t_1 = __pyx_f_8petsc4py_5PETSc_S_(TAOBQNKTR); if (unlikely(!__pyx_t_1)) __PYX_ERR(39, 22, __pyx_L1_error) ^

    src/petsc4py.PETSc.c(284058): error: identifier "TAOBQNKTL" is undefined __pyx_t_1 = __pyx_f_8petsc4py_5PETSc_S_(TAOBQNKTL); if (unlikely(!__pyx_t_1)) __PYX_ERR(39, 23, __pyx_L1_error) ^

    compilation aborted for src/PETSc.c (code 2) error: command '/home/geophyx/PETGEM/MPI/bin/mpicc' failed with exit status 2

  11. Lisandro Dalcin

    @geophyx You have to use a PETSc 3.10 release to build petsc4py 3.10. It seems you are using PETSc 3.9.

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