[petsc-users] ex52_integrateElement.cu

David Fuentes fuentesdt at gmail.com
Wed Mar 28 16:12:25 CDT 2012 

works!

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-single-dbg/include
-I/opt/apps/cuda/4.0/cuda/include -I/usr/include -I/usr/include/mpich2
-D__INSDIR__=src/snes/examples/tutorials/ ex52.c
nvcc -G -O0 -g -arch=sm_10  -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-single-dbg/include
-I/opt/apps/cuda/4.0/cuda/include -I/usr/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-single-dbg/lib
-L/opt/apps/PETSC/petsc-dev/gcc-4.4.3-mpich2-1.2-epd-sm_20-single-dbg/lib
 -lpetsc
-Wl,-rpath,/opt/apps/PETSC/petsc-dev/gcc-4.4.3-mpich2-1.2-epd-sm_20-single-dbg/lib
-ltriangle -lX11 -lpthread -lmetis -Wl,-rpath,/opt/apps/cuda/4.0/cuda/lib64
-L/opt/apps/cuda/4.0/cuda/lib64 -lcufft -lcublas -lcudart -lcusparse
-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
-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


SCRGP2$ ./ex52 -dim 2 -compute_function -show_residual -batch -gpu
GPU layout grid(1,2,1) block(3,1,1) with 1 batches
 N_t: 3, N_cb: 1
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
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





On Wed, Mar 28, 2012 at 1:37 PM, David Fuentes <fuentesdt at gmail.com> wrote:

> sure. will do.
>
>
> On Wed, Mar 28, 2012 at 1:23 PM, Matthew Knepley <knepley at gmail.com>wrote:
>
>> On Wed, Mar 28, 2012 at 1:14 PM, David Fuentes <fuentesdt at gmail.com>wrote:
>>
>>> thanks! its running, but I seem to be getting different answer for
>>> cpu/gpu ?
>>> i had some floating point problems on this Tesla M2070 gpu before, but
>>> adding the '-arch=sm_20' option seemed to fix it last time.
>>>
>>>
>>> is the assembly in single precision ? my 'const PetscReal
>>> jacobianInverse' being passed in are doubles
>>>
>>
>> Yep, that is the problem. I have not tested anything in double. I have
>> not decided exactly how to handle it. Can you
>> make another ARCH --with-precision=single and make sure it works, and
>> then we can fix the double issue?
>>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> SCRGP2$ ./ex52 -dim 2 -compute_function -show_residual -batch -gpu
>>> GPU layout grid(1,2,1) block(3,1,1) with 1 batches
>>>  N_t: 3, N_cb: 1
>>> Residual:
>>> Vector Object: 1 MPI processes
>>>   type: seq
>>> 0
>>> 755712
>>> 0
>>> -58720
>>> -2953.13
>>> 0.375
>>> 1.50323e+07
>>> 0.875
>>> 0
>>> SCRGP2$
>>> 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
>>>
>>>
>>>
>>>
>>>
>>> On Wed, Mar 28, 2012 at 11:55 AM, Matthew Knepley <knepley at gmail.com>wrote:
>>>
>>>> On Wed, Mar 28, 2012 at 11:45 AM, David Fuentes <fuentesdt at gmail.com>wrote:
>>>>
>>>>> 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 ?
>>>>>
>>>>
>>>> No.
>>>>
>>>>
>>>>> -  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
>>>>>
>>>>
>>>> This is failing on cudaMalloc(), which means your card is not available
>>>> for running. Are you trying to run on your laptop?
>>>> If so, applications like Preview can lock up the GPU. I know of no way
>>>> to test this in CUDA while running. I just close
>>>> apps until it runs.
>>>>
>>>>   Thanks,
>>>>
>>>>      Matt
>>>>
>>>>
>>>>>
>>>>> 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
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> 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
>>>>
>>>
>>>
>>
>>
>> --
>> 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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