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examples/shallow_sphere gives segmentation fault #642
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I got it to work with 5.7, what seg fault were you seeing? |
Not very informative:
Googling |
Ug, wish we had better error codes with this stuff. I will try and see if I can reproduce this again then and report back. |
If you remove the |
Just some new gfortran warnings similar to what I get these days with the fortran code...
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Have you tried using gdb to find the error? You wouldn’t need to know much gdb - just run it in gdb and when it crashes, look at the backtrace - “(gdb) bt”.
This said, I have found that most development tools (including gdb) on OSX are becoming more and more unusable. So I often have resorted using a Linux VM for debugging.
-----------------------------------
Donna Calhoun
Associate Professor
Department of Mathematics, Mathematics Bldg 241A
Boise State University
1910 University Drive
Boise, ID 83725-1555
(208) 426-3386
http://math.boisestate.edu/~calhoun
-----------------------------------
… On Apr 22, 2020, at 6:33 PM, Randall J. LeVeque ***@***.***> wrote:
Just some new gfortran warnings similar to what I get these days with the fortran code...
(geo5) [shallow_sphere] como $ python Rossby_wave.py
/Users/rjl/clawpack_src/clawpack_master/clawpack/pyclaw/util.py:78: UserWarning: missing extension modules
warnings.warn("missing extension modules")
/Users/rjl/clawpack_src/clawpack_master/clawpack/pyclaw/util.py:79: UserWarning: running python setup.py build_ext -i in /Users/rjl/clawpack_src/clawpack_master/clawpack/pyclaw/examples/shallow_sphere
warnings.warn("running python setup.py build_ext -i in %s" % working_dir)
running build_ext
running build_src
build_src
building extension "shallow_sphere.classic2" sources
f2py options: []
adding 'build/src.macosx-10.7-x86_64-3.6/build/src.macosx-10.7-x86_64-3.6/shallow_sphere/fortranobject.c' to sources.
adding 'build/src.macosx-10.7-x86_64-3.6/build/src.macosx-10.7-x86_64-3.6/shallow_sphere' to include_dirs.
adding 'build/src.macosx-10.7-x86_64-3.6/shallow_sphere/classic2-f2pywrappers.f' to sources.
building extension "shallow_sphere.problem" sources
f2py options: []
adding 'build/src.macosx-10.7-x86_64-3.6/build/src.macosx-10.7-x86_64-3.6/shallow_sphere/fortranobject.c' to sources.
adding 'build/src.macosx-10.7-x86_64-3.6/build/src.macosx-10.7-x86_64-3.6/shallow_sphere' to include_dirs.
build_src: building npy-pkg config files
customize UnixCCompiler
customize UnixCCompiler using build_ext
get_default_fcompiler: matching types: '['gnu95', 'nag', 'absoft', 'ibm', 'intel', 'gnu', 'g95', 'pg']'
customize Gnu95FCompiler
Found executable /usr/local/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'shallow_sphere.classic2' extension
compiling C sources
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/rjl/miniconda/envs/geo5/include -arch x86_64 -I/Users/rjl/miniconda/envs/geo5/include -arch x86_64
compile options: '-Ibuild/src.macosx-10.7-x86_64-3.6/build/src.macosx-10.7-x86_64-3.6/shallow_sphere -I/Users/rjl/miniconda/envs/geo5/lib/python3.6/site-packages/numpy/core/include -I/Users/rjl/miniconda/envs/geo5/include/python3.6m -c'
compiling Fortran sources
Fortran f77 compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -arch x86_64 -fPIC -O2 -fopenmp -O3 -funroll-loops
Fortran f90 compiler: /usr/local/bin/gfortran -Wall -g -fno-second-underscore -arch x86_64 -fPIC -O2 -fopenmp -O3 -funroll-loops
Fortran fix compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -arch x86_64 -fPIC -O2 -fopenmp -O3 -funroll-loops
compile options: '-Ibuild/src.macosx-10.7-x86_64-3.6/build/src.macosx-10.7-x86_64-3.6/shallow_sphere -I/Users/rjl/miniconda/envs/geo5/lib/python3.6/site-packages/numpy/core/include -I/Users/rjl/miniconda/envs/geo5/include/python3.6m -c'
gfortran:f90: ./step2qcor.f90
gfortran:f90: ./qcor.f90
./qcor.f90:2:27:
2 | subroutine qcor(ixy,i,m,aux,q,maxm,num_eqn,num_ghost,qc)
| 1
Warning: Unused dummy argument 'm' at (1) [-Wunused-dummy-argument]
gfortran:f90: /Users/rjl/clawpack_src/clawpack_master/pyclaw/src/pyclaw/classic/limiter.f90
gfortran:f90: /Users/rjl/clawpack_src/clawpack_master/pyclaw/src/pyclaw/classic/philim.f90
gfortran:f90: /Users/rjl/clawpack_src/clawpack_master/pyclaw/src/pyclaw/classic/flux2.f90
gfortran:f90: /Users/rjl/clawpack_src/clawpack_master/pyclaw/src/pyclaw/classic/step2ds.f90
/Users/rjl/clawpack_src/clawpack_master/pyclaw/src/pyclaw/classic/step2ds.f90:111:55:
111 | do 23 i = 1-num_ghost, mx+num_ghost
| 1
Warning: Fortran 2018 deleted feature: Shared DO termination label 23 at (1)
/Users/rjl/clawpack_src/clawpack_master/pyclaw/src/pyclaw/classic/step2ds.f90:117:59:
117 | do 24 i = 1-num_ghost, mx+num_ghost
| 1
Warning: Fortran 2018 deleted feature: Shared DO termination label 24 at (1)
/Users/rjl/clawpack_src/clawpack_master/pyclaw/src/pyclaw/classic/step2ds.f90:124:59:
124 | do 25 i = 1-num_ghost, mx+num_ghost
| 1
Warning: Fortran 2018 deleted feature: Shared DO termination label 25 at (1)
/Users/rjl/clawpack_src/clawpack_master/pyclaw/src/pyclaw/classic/step2ds.f90:193:55:
193 | do 73 j = 1-num_ghost, my+num_ghost
| 1
Warning: Fortran 2018 deleted feature: Shared DO termination label 73 at (1)
/Users/rjl/clawpack_src/clawpack_master/pyclaw/src/pyclaw/classic/step2ds.f90:199:59:
199 | do 74 j = 1-num_ghost, my+num_ghost
| 1
Warning: Fortran 2018 deleted feature: Shared DO termination label 74 at (1)
/Users/rjl/clawpack_src/clawpack_master/pyclaw/src/pyclaw/classic/step2ds.f90:206:59:
206 | do 75 j = 1-num_ghost, my+num_ghost
| 1
Warning: Fortran 2018 deleted feature: Shared DO termination label 75 at (1)
gfortran:f77: build/src.macosx-10.7-x86_64-3.6/shallow_sphere/classic2-f2pywrappers.f
/usr/local/bin/gfortran -Wall -g -arch x86_64 -Wall -g -undefined dynamic_lookup -bundle build/temp.macosx-10.7-x86_64-3.6/build/src.macosx-10.7-x86_64-3.6/shallow_sphere/classic2module.o build/temp.macosx-10.7-x86_64-3.6/build/src.macosx-10.7-x86_64-3.6/build/src.macosx-10.7-x86_64-3.6/shallow_sphere/fortranobject.o build/temp.macosx-10.7-x86_64-3.6/step2qcor.o build/temp.macosx-10.7-x86_64-3.6/qcor.o build/temp.macosx-10.7-x86_64-3.6/Users/rjl/clawpack_src/clawpack_master/pyclaw/src/pyclaw/classic/limiter.o build/temp.macosx-10.7-x86_64-3.6/Users/rjl/clawpack_src/clawpack_master/pyclaw/src/pyclaw/classic/philim.o build/temp.macosx-10.7-x86_64-3.6/Users/rjl/clawpack_src/clawpack_master/pyclaw/src/pyclaw/classic/flux2.o build/temp.macosx-10.7-x86_64-3.6/Users/rjl/clawpack_src/clawpack_master/pyclaw/src/pyclaw/classic/step2ds.o build/temp.macosx-10.7-x86_64-3.6/build/src.macosx-10.7-x86_64-3.6/shallow_sphere/classic2-f2pywrappers.o -L/usr/local/Cellar/gcc/9.2.0_3/lib/gcc/9/gcc/x86_64-apple-darwin18/9.2.0 -L/usr/local/Cellar/gcc/9.2.0_3/lib/gcc/9/gcc/x86_64-apple-darwin18/9.2.0/../../.. -L/usr/local/Cellar/gcc/9.2.0_3/lib/gcc/9/gcc/x86_64-apple-darwin18/9.2.0/../../.. -lgfortran -o ./classic2.cpython-36m-darwin.so
building 'shallow_sphere.problem' extension
compiling C sources
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/rjl/miniconda/envs/geo5/include -arch x86_64 -I/Users/rjl/miniconda/envs/geo5/include -arch x86_64
compile options: '-Ibuild/src.macosx-10.7-x86_64-3.6/build/src.macosx-10.7-x86_64-3.6/shallow_sphere -I/Users/rjl/miniconda/envs/geo5/lib/python3.6/site-packages/numpy/core/include -I/Users/rjl/miniconda/envs/geo5/include/python3.6m -c'
compiling Fortran sources
Fortran f77 compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -arch x86_64 -fPIC -O2 -fopenmp -O3 -funroll-loops
Fortran f90 compiler: /usr/local/bin/gfortran -Wall -g -fno-second-underscore -arch x86_64 -fPIC -O2 -fopenmp -O3 -funroll-loops
Fortran fix compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -arch x86_64 -fPIC -O2 -fopenmp -O3 -funroll-loops
compile options: '-Ibuild/src.macosx-10.7-x86_64-3.6/build/src.macosx-10.7-x86_64-3.6/shallow_sphere -I/Users/rjl/miniconda/envs/geo5/lib/python3.6/site-packages/numpy/core/include -I/Users/rjl/miniconda/envs/geo5/include/python3.6m -c'
gfortran:f90: ./mapc2p.f90
gfortran:f90: ./setaux.f90
./setaux.f90:76:42:
76 | do 15 i=1-num_ghost,mx+num_ghost+1
| 1
Warning: Fortran 2018 deleted feature: Shared DO termination label 15 at (1)
./setaux.f90:104:40:
104 | do 20 i=1-num_ghost,mx+num_ghost
| 1
Warning: Fortran 2018 deleted feature: Shared DO termination label 20 at (1)
gfortran:f90: ./qinit.f90
./qinit.f90:43:20:
43 | do 20 j=1,my
| 1
Warning: Fortran 2018 deleted feature: Shared DO termination label 20 at (1)
./qinit.f90:3:23:
3 | dx,dy,q,num_aux,aux,Rsphere)
| 1
Warning: Unused dummy argument 'aux' at (1) [-Wunused-dummy-argument]
./qinit.f90:50:0:
50 | theta = dasin(yp/rad)
|
Warning: 'theta' may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran:f90: ./src2.f90
./src2.f90:2:25:
2 | subroutine src2(maxmx,maxmy,num_eqn,num_ghost,mx,my,xlower,ylower, &
| 1
Warning: Unused dummy argument 'maxmx' at (1) [-Wunused-dummy-argument]
./src2.f90:2:31:
2 | subroutine src2(maxmx,maxmy,num_eqn,num_ghost,mx,my,xlower,ylower, &
| 1
Warning: Unused dummy argument 'maxmy' at (1) [-Wunused-dummy-argument]
./src2.f90:2:49:
2 | subroutine src2(maxmx,maxmy,num_eqn,num_ghost,mx,my,xlower,ylower, &
| 1
Warning: Unused dummy argument 'num_ghost' at (1) [-Wunused-dummy-argument]
./src2.f90:3:25:
3 | dx,dy,q,num_aux,aux,t,dt,Rsphere)
| 1
Warning: Unused dummy argument 't' at (1) [-Wunused-dummy-argument]
/usr/local/bin/gfortran -Wall -g -arch x86_64 -Wall -g -undefined dynamic_lookup -bundle build/temp.macosx-10.7-x86_64-3.6/build/src.macosx-10.7-x86_64-3.6/shallow_sphere/problemmodule.o build/temp.macosx-10.7-x86_64-3.6/build/src.macosx-10.7-x86_64-3.6/build/src.macosx-10.7-x86_64-3.6/shallow_sphere/fortranobject.o build/temp.macosx-10.7-x86_64-3.6/mapc2p.o build/temp.macosx-10.7-x86_64-3.6/setaux.o build/temp.macosx-10.7-x86_64-3.6/qinit.o build/temp.macosx-10.7-x86_64-3.6/src2.o -L/usr/local/Cellar/gcc/9.2.0_3/lib/gcc/9/gcc/x86_64-apple-darwin18/9.2.0 -L/usr/local/Cellar/gcc/9.2.0_3/lib/gcc/9/gcc/x86_64-apple-darwin18/9.2.0/../../.. -L/usr/local/Cellar/gcc/9.2.0_3/lib/gcc/9/gcc/x86_64-apple-darwin18/9.2.0/../../.. -lgfortran -o ./problem.cpython-36m-darwin.so
/Users/rjl/clawpack_src/clawpack_master/clawpack/pyclaw/util.py:84: UserWarning: successfully executed python setup.py build_ext -i in /Users/rjl/clawpack_src/clawpack_master/clawpack/pyclaw/examples/shallow_sphere
warnings.warn("successfully executed python setup.py build_ext -i in %s" % working_dir)
Segmentation fault: 11
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I wonder if those "shared DO termination label"s are actually a problem? We should get rid of them anyway. I'll do that later today. |
I haven't run into problems with GeoClaw with the termination label warnings, but I agree we need to eventually clean it all up. Also @mjberger recently noticed you can add the gfortran flag |
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I cleaned up all the loop labels in #643. |
I'm trying to build the pyclaw galleries and everything works fine with v5.7.0rc except in
examples/shallow_sphere
where runningRossby_wave.py
ortest_shallow_sphere.py
gives a segmentation fault.The text was updated successfully, but these errors were encountered: