[petsc-users] Installing petsc4py

[Stegmeier, Nicholas]

Hello all,


I was hoping to get some advice on installing petsc4py. Hopefully this is an 
appropriate question as it's my first time emailing the list.


I failed numerous times installing petsc4py on my personal laptop, so I decided 
to use a virtual machine with Ubuntu to try installing from a clean slate.


I followed the steps listed on this webpage: 
https://gist.github.com/mrosemeier/088115b2e34f319b913a

  1.  Install openmpi
  2.  Install anaconda-python
  3.  Install petsc
  4.  Install petsc4py

After doing all this, I entered the petsc4py/demo folder and used make to see 
if all the tests passed. But several of the tests promptly failed. Below are 
some of the errors I received, but I also attached the full error output. Maybe 
I have forgotten to assign some environment variable?

Thank you,
Nicholas Stegmeier

inside .bashrc:
export LD_LIBRARY_PATH=/home/nick/local/openmpi-1.10.5/lib:$LD_LIBRARY_PATH
export PATH=/home/nick/local/openmpi-1.10.5/bin:$PATH
export PATH="/home/nick/local/anaconda2/bin:$PATH"
export PETSC_DIR=/home/nick/local/petsc.git
export PETSC_ARCH=arch-python-linux-i686

nick@nick-VirtualBox:~/local/petsc.git/bin$ echo $PATH
/home/nick/local/anaconda2/bin:/home/nick/local/openmpi-1.10.5/bin:/home/nick/local/anaconda2/bin:/home/nick/local/openmpi-1.10.5/bin:/home/nick/bin:/home/nick/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

nick@nick-VirtualBox:~/local/petsc.git/bin$ echo $PATH
/home/nick/local/anaconda2/bin:/home/nick/local/openmpi-1.10.5/bin:/home/nick/local/anaconda2/bin:/home/nick/local/openmpi-1.10.5/bin:/home/nick/bin:/home/nick/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

sample error output:

make -f makefile.petsc \
        PETSC_DIR=/home/nick/local/petsc.git PETSC_ARCH=arch-python-linux-i686
make[2]: Entering directory '/home/nick/local/petsc4py.git/demo/perftest'
c        App.f90
make[2]: c: Command not found
makefile.petsc:15: recipe for target 'driver.exe' failed
make[2]: [driver.exe] Error 127 (ignored)
/home/nick/local/openmpi-1.10.5/bin/mpicc -c -Wall -Wwrite-strings 
-Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden 
-g -O   -I/home/nick/local/petsc.git/include 
-I/home/nick/local/petsc.git/arch-python-linux-i686/include     `pwd`/driver.c
/home/nick/local/openmpi-1.10.5/bin/mpicc -Wall -Wwrite-strings 
-Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden 
-g -O  -o driver.exe 
-Wl,-rpath,/home/nick/local/petsc.git/arch-python-linux-i686/lib 
-L/home/nick/local/petsc.git/arch-python-linux-i686/lib -lpetsc -llapack -lblas 
-lm -ldl  driver.o App.o
gcc: error: App.o: No such file or directory
makefile.petsc:15: recipe for target 'driver.exe' failed
make[2]: [driver.exe] Error 1 (ignored)

...

./Bratu2D.F90:20:0:

 #include "petsc/finclude/petscdef.h"
 ^
Fatal Error: petsc/finclude/petscdef.h: No such file or directory
compilation terminated.
./Bratu2D.F90:20:0:

 #include "petsc/finclude/petscdef.h"
 ^
Fatal Error: petsc/finclude/petscdef.h: No such file or directory
compilation terminated.
error: Command "/usr/bin/gfortran -Wall -g -fno-second-underscore 
-DF2PY_REPORT_ON_ARRAY_COPY=1 
-I/home/nick/local/petsc.git/arch-python-linux-i686/include 
-I/home/nick/local/petsc.git/include 
-I/home/nick/local/anaconda2/lib/python2.7/site-packages/petsc4py/include -I. 
-Ibuild/src.linux-i686-2.7/. 
-I/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include 
-I/home/nick/local/anaconda2/include/python2.7 -c -c ./Bratu2D.F90 -o 
build/temp.linux-i686-2.7/Bratu2D.o -Jbuild/temp.linux-i686-2.7/ 
-Ibuild/temp.linux-i686-2.7/" failed with exit status 1
makefile:20: recipe for target 'Bratu2D.so' failed
make[1]: *** [Bratu2D.so] Error 1
make[1]: Leaving directory '/home/nick/local/petsc4py.git/demo/wrap-f2py'
makefile:3: recipe for target 'all' failed
make: [all] Error 2 (ignored)

Thank you,
Nicholas Stegmeier

nick@nick-VirtualBox:~/local/petsc4py.git$ cd demo/

nick@nick-VirtualBox:~/local/petsc4py.git/demo$ ls
binary-io  bratu3d  kspsolve  ode       poisson2d  taosolve     wrap-f2py
bratu2d    dmplex   makefile  perftest  poisson3d  wrap-cython  wrap-swig

nick@nick-VirtualBox:~/local/petsc4py.git/demo$ make

make -C binary-io
make[1]: Entering directory '/home/nick/local/petsc4py.git/demo/binary-io'
python matvecio.py
rm -f matrix-*.dat* vector-*.dat*
rm -f *.py[co]
rm -f -r __pycache__
make[1]: Leaving directory '/home/nick/local/petsc4py.git/demo/binary-io'
make -C kspsolve
make[1]: Entering directory '/home/nick/local/petsc4py.git/demo/kspsolve'
python test_mat_cg.py
iterations: 46 residual norm: 0.000303767
iterations: 46 residual norm: 0.000303767
[0]PETSC ERROR: PETSc installed without X windows, Microsoft Graphics, OpenGL 
ES, or GLUT/OpenGL on this machine
proceeding without graphics
python test_mat_ksp.py
[0]PETSC ERROR: PETSc installed without X windows, Microsoft Graphics, OpenGL 
ES, or GLUT/OpenGL on this machine
proceeding without graphics
rm -f *.py[co]
rm -f -r __pycache__
make[1]: Leaving directory '/home/nick/local/petsc4py.git/demo/kspsolve'
make -C bratu2d
make[1]: Entering directory '/home/nick/local/petsc4py.git/demo/bratu2d'
python bratu2d.py -impl python
[0]PETSC ERROR: PETSc installed without X windows, Microsoft Graphics, OpenGL 
ES, or GLUT/OpenGL on this machine
proceeding without graphics
f2py --quiet --noarch --f90flags='' -DF2PY_REPORT_ON_ARRAY_COPY=1 -c 
bratu2df90.f90 -m bratu2df90
In file included from 
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from 
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from 
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /tmp/tmpmgJ0Cg/src.linux-i686-2.7/fortranobject.h:13,
                 from /tmp/tmpmgJ0Cg/src.linux-i686-2.7/bratu2df90module.c:19:
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
 warning: #warning "Using deprecated NumPy API, disable it by " "#defining 
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
/tmp/tmpmgJ0Cg/src.linux-i686-2.7/bratu2df90module.c:112:12: warning: 
‘f2py_size’ defined but not used [-Wunused-function]
 static int f2py_size(PyArrayObject* var, ...)
            ^
In file included from 
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from 
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from 
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /tmp/tmpmgJ0Cg/src.linux-i686-2.7/fortranobject.h:13,
                 from /tmp/tmpmgJ0Cg/src.linux-i686-2.7/fortranobject.c:2:
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
 warning: #warning "Using deprecated NumPy API, disable it by " "#defining 
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
/tmp/tmpmgJ0Cg/src.linux-i686-2.7/fortranobject.c: In function 
‘f2py_report_on_array_copy’:
/tmp/tmpmgJ0Cg/src.linux-i686-2.7/fortranobject.c:556:24: warning: format 
‘%ld’ expects argument of type ‘long int’, but argument 3 has type 
‘npy_intp {aka const int}’ [-Wformat=]
         fprintf(stderr,"copied an array: size=%ld, elsize=%"NPY_INTP_FMT"\n",
                        ^
python bratu2d.py -impl fortran
copied an array: size=1024, elsize=8
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[0]PETSC ERROR: PETSc installed without X windows, Microsoft Graphics, OpenGL 
ES, or GLUT/OpenGL on this machine
proceeding without graphics
rm -f *.py[co] bratu2df90*.so
rm -f -r __pycache__
make[1]: Leaving directory '/home/nick/local/petsc4py.git/demo/bratu2d'
make -C bratu3d
make[1]: Entering directory '/home/nick/local/petsc4py.git/demo/bratu3d'
python bratu3d.py -fd -nx 7 -ny 8 -nz 9
python bratu3d.py -mf -nx 9 -ny 8 -nz 7
rm -f *.py[co]
rm -f -r __pycache__
make[1]: Leaving directory '/home/nick/local/petsc4py.git/demo/bratu3d'
make -C poisson2d
make[1]: Entering directory '/home/nick/local/petsc4py.git/demo/poisson2d'
python poisson2d.py -nx 15 -ny 16
[0]PETSC ERROR: PETSc installed without X windows, Microsoft Graphics, OpenGL 
ES, or GLUT/OpenGL on this machine
proceeding without graphics
rm -f *.py[co]
rm -f -r __pycache__
make[1]: Leaving directory '/home/nick/local/petsc4py.git/demo/poisson2d'
make -C poisson3d
make[1]: Entering directory '/home/nick/local/petsc4py.git/demo/poisson3d'
python poisson3d.py
copied an array: size=32768, elsize=8
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make -f makefile.petsc \
        PETSC_DIR=/home/nick/local/petsc.git PETSC_ARCH=arch-python-linux-i686
make[2]: Entering directory '/home/nick/local/petsc4py.git/demo/poisson3d'
c        del2lib.f90
make[2]: c: Command not found
makefile.petsc:16: recipe for target 'poisson3d.exe' failed
make[2]: [poisson3d.exe] Error 127 (ignored)
/home/nick/local/openmpi-1.10.5/bin/mpicc -c -Wall -Wwrite-strings 
-Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden 
-g -O   -I/home/nick/local/petsc.git/include 
-I/home/nick/local/petsc.git/arch-python-linux-i686/include     
`pwd`/poisson3d.c
/home/nick/local/openmpi-1.10.5/bin/mpicc -Wall -Wwrite-strings 
-Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden 
-g -O  -o poisson3d.exe 
-Wl,-rpath,/home/nick/local/petsc.git/arch-python-linux-i686/lib 
-L/home/nick/local/petsc.git/arch-python-linux-i686/lib -lpetsc -llapack -lblas 
-lm -ldl  poisson3d.o del2lib.o
gcc: error: del2lib.o: No such file or directory
makefile.petsc:16: recipe for target 'poisson3d.exe' failed
make[2]: [poisson3d.exe] Error 1 (ignored)
/bin/rm -f poisson3d.o del2lib.o
make[2]: Leaving directory '/home/nick/local/petsc4py.git/demo/poisson3d'
./poisson3d.exe
make[1]: ./poisson3d.exe: Command not found
makefile:29: recipe for target 'run_cc' failed
make[1]: *** [run_cc] Error 127
make[1]: Leaving directory '/home/nick/local/petsc4py.git/demo/poisson3d'
makefile:3: recipe for target 'all' failed
make: [all] Error 2 (ignored)
make -C perftest
make[1]: Entering directory '/home/nick/local/petsc4py.git/demo/perftest'
python driver.py
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copied an array: size=2197, elsize=8
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copied an array: size=2197, elsize=8
copied an array: size=2197, elsize=8
copied an array: size=2197, elsize=8
copied an array: size=2197, elsize=8
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copied an array: size=2197, elsize=8
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copied an array: size=2197, elsize=8
copied an array: size=2197, elsize=8
copied an array: size=2197, elsize=8
copied an array: size=2197, elsize=8
copied an array: size=2197, elsize=8
copied an array: size=2197, elsize=8
copied an array: size=2197, elsize=8
copied an array: size=2197, elsize=8
copied an array: size=2197, elsize=8
copied an array: size=2197, elsize=8
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Grid  13 x  13 x  13 -> 1.072628  seconds ( 1 samples)
make -f makefile.petsc \
        PETSC_DIR=/home/nick/local/petsc.git PETSC_ARCH=arch-python-linux-i686
make[2]: Entering directory '/home/nick/local/petsc4py.git/demo/perftest'
c        App.f90
make[2]: c: Command not found
makefile.petsc:15: recipe for target 'driver.exe' failed
make[2]: [driver.exe] Error 127 (ignored)
/home/nick/local/openmpi-1.10.5/bin/mpicc -c -Wall -Wwrite-strings 
-Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden 
-g -O   -I/home/nick/local/petsc.git/include 
-I/home/nick/local/petsc.git/arch-python-linux-i686/include     `pwd`/driver.c
/home/nick/local/openmpi-1.10.5/bin/mpicc -Wall -Wwrite-strings 
-Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden 
-g -O  -o driver.exe 
-Wl,-rpath,/home/nick/local/petsc.git/arch-python-linux-i686/lib 
-L/home/nick/local/petsc.git/arch-python-linux-i686/lib -lpetsc -llapack -lblas 
-lm -ldl  driver.o App.o
gcc: error: App.o: No such file or directory
makefile.petsc:15: recipe for target 'driver.exe' failed
make[2]: [driver.exe] Error 1 (ignored)
/bin/rm -f driver.o App.o
make[2]: Leaving directory '/home/nick/local/petsc4py.git/demo/perftest'
./driver.exe
make[1]: ./driver.exe: Command not found
makefile:21: recipe for target 'run_cc' failed
make[1]: *** [run_cc] Error 127
make[1]: Leaving directory '/home/nick/local/petsc4py.git/demo/perftest'
makefile:3: recipe for target 'all' failed
make: [all] Error 2 (ignored)
make -C wrap-swig
make[1]: Entering directory '/home/nick/local/petsc4py.git/demo/wrap-swig'
CC=/home/nick/local/openmpi-1.10.5/bin/mpicc F90= 
LDSHARED='/home/nick/local/openmpi-1.10.5/bin/mpicc -Wall -Wwrite-strings 
-Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden 
-g -O  -shared' \
/home/nick/local/anaconda2/bin/python2 setup.py -q build_ext --inplace
unable to execute 'swig': No such file or directory
error: command 'swig' failed with exit status 1
makefile:20: recipe for target 'Bratu3D.py' failed
make[1]: *** [Bratu3D.py] Error 1
make[1]: Leaving directory '/home/nick/local/petsc4py.git/demo/wrap-swig'
makefile:3: recipe for target 'all' failed
make: [all] Error 2 (ignored)
make -C wrap-f2py
make[1]: Entering directory '/home/nick/local/petsc4py.git/demo/wrap-f2py'
CC=/home/nick/local/openmpi-1.10.5/bin/mpicc F90= LDSHARED= \
/home/nick/local/anaconda2/bin/python2 setup.py -q build_ext --inplace
Reading .f2py_f2cmap ...
        Mapping "integer(kind=HANDLE_KIND)" to "long"
        Mapping "integer(kind=handle_kind)" to "long"
Successfully applied user defined changes from .f2py_f2cmap
In file included from 
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from 
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from 
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from build/src.linux-i686-2.7/./fortranobject.h:13,
                 from build/src.linux-i686-2.7/./fortranobject.c:2:
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
 warning: #warning "Using deprecated NumPy API, disable it by " "#defining 
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
build/src.linux-i686-2.7/./fortranobject.c: In function 
‘f2py_report_on_array_copy’:
build/src.linux-i686-2.7/./fortranobject.c:556:24: warning: format ‘%ld’ 
expects argument of type ‘long int’, but argument 3 has type ‘npy_intp 
{aka const int}’ [-Wformat=]
         fprintf(stderr,"copied an array: size=%ld, elsize=%"NPY_INTP_FMT"\n",
                        ^
In file included from 
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from 
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from 
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from build/src.linux-i686-2.7/./fortranobject.h:13,
                 from ./Bratu2Dmodule.c:18:
/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
 warning: #warning "Using deprecated NumPy API, disable it by " "#defining 
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
./Bratu2D.F90:20:0:

 #include "petsc/finclude/petscdef.h"
 ^
Fatal Error: petsc/finclude/petscdef.h: No such file or directory
compilation terminated.
./Bratu2D.F90:20:0:

 #include "petsc/finclude/petscdef.h"
 ^
Fatal Error: petsc/finclude/petscdef.h: No such file or directory
compilation terminated.
error: Command "/usr/bin/gfortran -Wall -g -fno-second-underscore 
-DF2PY_REPORT_ON_ARRAY_COPY=1 
-I/home/nick/local/petsc.git/arch-python-linux-i686/include 
-I/home/nick/local/petsc.git/include 
-I/home/nick/local/anaconda2/lib/python2.7/site-packages/petsc4py/include -I. 
-Ibuild/src.linux-i686-2.7/. 
-I/home/nick/local/anaconda2/lib/python2.7/site-packages/numpy/core/include 
-I/home/nick/local/anaconda2/include/python2.7 -c -c ./Bratu2D.F90 -o 
build/temp.linux-i686-2.7/Bratu2D.o -Jbuild/temp.linux-i686-2.7/ 
-Ibuild/temp.linux-i686-2.7/" failed with exit status 1
makefile:20: recipe for target 'Bratu2D.so' failed
make[1]: *** [Bratu2D.so] Error 1
make[1]: Leaving directory '/home/nick/local/petsc4py.git/demo/wrap-f2py'
makefile:3: recipe for target 'all' failed
make: [all] Error 2 (ignored)