[petsc-users] ex52_integrateElement.cu

David Fuentes fuentesdt at gmail.com
Wed Mar 28 11:45:14 CDT 2012 

The example seems to be running on cpu with '-batch' but i'm getting errors
in line 323 with the '-gpu' option

[0]PETSC ERROR: IntegrateElementBatchGPU() line 323 in
src/snes/examples/tutorials/ex52_integrateElement.cu

should this possibly be PetscScalar ?

-  ierr = cudaMalloc((void**) &d_coefficients,         Ne*N_bt *
sizeof(float));CHKERRQ(ierr);
+  ierr = cudaMalloc((void**) &d_coefficients,         Ne*N_bt *
sizeof(PetscScalar));CHKERRQ(ierr);


SCRGP2$ python $PETSC_DIR/bin/pythonscripts/PetscGenerateFEMQuadrature.py 2
1 1 1 laplacian ex52.h
['/opt/apps/PETSC/petsc-dev/bin/pythonscripts/PetscGenerateFEMQuadrature.py',
'2', '1', '1', '1', 'laplacian', 'ex52.h']
2 1 1 1 laplacian
[{(-1.0, -1.0): [(1.0, ())]}, {(1.0, -1.0): [(1.0, ())]}, {(-1.0, 1.0):
[(1.0, ())]}]
{0: {0: [0], 1: [1], 2: [2]}, 1: {0: [], 1: [], 2: []}, 2: {0: []}}
Perm: [0, 1, 2]
Creating /home/fuentes/snestutorial/ex52.h
Creating /home/fuentes/snestutorial/ex52_gpu.h
[{(-1.0, -1.0): [(1.0, ())]}, {(1.0, -1.0): [(1.0, ())]}, {(-1.0, 1.0):
[(1.0, ())]}]
{0: {0: [0], 1: [1], 2: [2]}, 1: {0: [], 1: [], 2: []}, 2: {0: []}}
Perm: [0, 1, 2]
Creating /home/fuentes/snestutorial/ex52_gpu_inline.h

SCRGP2$ make ex52
/usr/bin/mpicxx -o ex52.o -c -O0 -g -fPIC
-I/opt/apps/PETSC/petsc-dev/include
-I/opt/apps/PETSC/petsc-dev/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include
-I/opt/apps/cuda/4.1/cuda/include -I/opt/apps/PETSC/petsc-dev/include/sieve
-I/opt/MATLAB/R2011a/extern/include -I/usr/include
-I/opt/apps/PETSC/petsc-dev/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/cbind/include
-I/opt/apps/PETSC/petsc-dev/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/forbind/include
-I/usr/include/mpich2 -D__INSDIR__=src/snes/examples/tutorials/ ex52.c
nvcc -O0 -g -arch=sm_20  -c --compiler-options="-O0 -g   -fPIC
 -I/opt/apps/PETSC/petsc-dev/include
-I/opt/apps/PETSC/petsc-dev/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/include
-I/opt/apps/cuda/4.1/cuda/include -I/opt/apps/PETSC/petsc-dev/include/sieve
-I/opt/MATLAB/R2011a/extern/include -I/usr/include
-I/opt/apps/PETSC/petsc-dev/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/cbind/include
-I/opt/apps/PETSC/petsc-dev/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/forbind/include
-I/usr/include/mpich2    -D__INSDIR__=src/snes/examples/tutorials/"
 ex52_integrateElement.cu
ex52_gpu_inline.h(7): warning: variable "points_0" was declared but never
referenced

ex52_gpu_inline.h(21): warning: variable "Basis_0" was declared but never
referenced

ex52_gpu_inline.h(7): warning: variable "points_0" was declared but never
referenced

ex52_gpu_inline.h(13): warning: variable "weights_0" was declared but never
referenced

ex52_gpu_inline.h(21): warning: variable "Basis_0" was declared but never
referenced

ex52_gpu_inline.h(28): warning: variable "BasisDerivatives_0" was declared
but never referenced

ex52_gpu_inline.h(7): warning: variable "points_0" was declared but never
referenced

ex52_gpu_inline.h(21): warning: variable "Basis_0" was declared but never
referenced

ex52_gpu_inline.h(7): warning: variable "points_0" was declared but never
referenced

ex52_gpu_inline.h(13): warning: variable "weights_0" was declared but never
referenced

ex52_gpu_inline.h(21): warning: variable "Basis_0" was declared but never
referenced

ex52_gpu_inline.h(28): warning: variable "BasisDerivatives_0" was declared
but never referenced

/usr/bin/mpicxx -O0 -g   -o ex52 ex52.o ex52_integrateElement.o
 -Wl,-rpath,/opt/apps/PETSC/petsc-dev/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib
-L/opt/apps/PETSC/petsc-dev/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib  -lpetsc
-Wl,-rpath,/opt/apps/PETSC/petsc-dev/gcc-4.4.3-mpich2-1.2-epd-sm_20-dbg/lib
-ltriangle -lX11 -lpthread -lsuperlu_dist_3.0 -lcmumps -ldmumps -lsmumps
-lzmumps -lmumps_common -lpord -lparmetis -lmetis -lscalapack -lblacs
-Wl,-rpath,/opt/apps/cuda/4.1/cuda/lib64 -L/opt/apps/cuda/4.1/cuda/lib64
-lcufft -lcublas -lcudart -lcusparse
-Wl,-rpath,/opt/MATLAB/R2011a/sys/os/glnxa64:/opt/MATLAB/R2011a/bin/glnxa64:/opt/MATLAB/R2011a/extern/lib/glnxa64
-L/opt/MATLAB/R2011a/bin/glnxa64 -L/opt/MATLAB/R2011a/extern/lib/glnxa64
-leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc
-Wl,-rpath,/opt/epd-7.1-2-rh5-x86_64/lib -L/opt/epd-7.1-2-rh5-x86_64/lib
-lmkl_rt -lmkl_intel_thread -lmkl_core -liomp5 -lexoIIv2for -lexodus
-lnetcdf_c++ -lnetcdf -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.4.3
-L/usr/lib/gcc/x86_64-linux-gnu/4.4.3 -ldl -lmpich -lopa -lpthread -lrt
-lgcc_s -lmpichf90 -lgfortran -lm -lm -lmpichcxx -lstdc++ -lmpichcxx
-lstdc++ -ldl -lmpich -lopa -lpthread -lrt -lgcc_s -ldl
/bin/rm -f ex52.o ex52_integrateElement.o


SCRGP2$ ./ex52 -dim 2 -compute_function -show_residual -batch
Residual:
Vector Object: 1 MPI processes
  type: seq
-0.25
-0.5
0.25
-0.5
-1
0.5
0.25
0.5
0.75
SCRGP2$ ./ex52 -dim 2 -compute_function -show_residual -batch -gpu
[0]PETSC ERROR: IntegrateElementBatchGPU() line 323 in
src/snes/examples/tutorials/ex52_integrateElement.cu
[0]PETSC ERROR: FormFunctionLocalBatch() line 679 in
src/snes/examples/tutorials/ex52.c
[0]PETSC ERROR: SNESDMComplexComputeFunction() line 431 in
src/snes/utils/damgsnes.c
[0]PETSC ERROR: main() line 1021 in src/snes/examples/tutorials/ex52.c
application called MPI_Abort(MPI_COMM_WORLD, 35) - process 0


On Tue, Mar 27, 2012 at 8:37 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Tue, Mar 27, 2012 at 2:10 PM, Blaise Bourdin <bourdin at lsu.edu> wrote:
>
>>
>> On Mar 27, 2012, at 1:23 PM, Matthew Knepley wrote:
>>
>> On Tue, Mar 27, 2012 at 12:58 PM, David Fuentes <fuentesdt at gmail.com>wrote:
>>
>>> Hi,
>>>
>>> I had a question about the status of example 52.
>>>
>>>
>>> http://petsc.cs.iit.edu/petsc/petsc-dev/file/a8e2f2c19319/src/snes/examples/tutorials/ex52.c
>>>
>>> http://petsc.cs.iit.edu/petsc/petsc-dev/file/a8e2f2c19319/src/snes/examples/tutorials/ex52_integrateElement.cu
>>>
>>>
>>> Can this example be used with a DM object created from an unstructured
>>> exodusII mesh, DMMeshCreateExodus, And the FEM assembly done on GPU ?
>>>
>>
>> 1) I have pushed many more tests for it now. They can be run using the
>> Python build system
>>
>>   ./config/builder2.py check src/snes/examples/tutorials/ex52.c
>>
>>   in fact, you can build any set of files this way.
>>
>> 2) The Exodus creation has to be converted to DMComplex from DMMesh. That
>> should not take me very long. Blaise maintains that
>>      so maybe there will be help :) You will just replace
>> DMComplexCreateBoxMesh() with DMComplexCreateExodus(). If you request
>>      it, I will bump it up the list.
>>
>>
>> DMMeshCreateExodusNG is much more flexible than DMMeshCreateExodus in
>> that it can read meshes with multiple element types and should have a much
>> lower memory footprint. The code should be fairly easy to read. you can
>> email me directly if you have specific questions. I had looked at creating
>> a DMComplex and it did not look too difficult, as long as interpolation is
>> not needed. I have plans to write DMComplexCreateExodus, but haven't had
>> time too so far. Updating the Vec viewers and readers may be a bit more
>> involved. In perfect world, one would write an EXODUS viewer following the
>> lines of the VTK and HDF5 ones.
>>
>
> David and Blaise,  I have converted this function, now
> DMComplexCreateExodus(). Its not tested, but I think
> Blaise has some stuff we can use to test it.
>
>   Thanks,
>
>      Matt
>
>
>> Blaise
>>
>>
>>
>> Let me know if you can run the tests.
>>
>>   Thanks
>>
>>      Matt
>>
>>
>>> Thanks,
>>> David
>>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>>
>>  --
>> Department of Mathematics and Center for Computation & Technology
>> Louisiana State University, Baton Rouge, LA 70803, USA
>> Tel. +1 (225) 578 1612, Fax  +1 (225) 578 4276
>> http://www.math.lsu.edu/~bourdin
>>
>>
>>
>>
>>
>>
>>
>>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
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