[petsc-users] ex52_integrateElement.cu

David Fuentes fuentesdt at gmail.com
Wed Mar 28 13:37:59 CDT 2012 

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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