[petsc-users] Tweaking my code for CUDA
Manuel Valera
mvalera-w at mail.sdsu.edu
Wed Mar 14 13:19:31 CDT 2018
Yes, this is the system installation that is being correctly linked (the
linear solver and model are not linking the correct installation idk why
yet) i configured with only CUDA this time because of the message Karl Rupp
posted on my installation thread, where he says only one type of library
will work at a time, anyway this is what i got:
[valera at node50 tutorials]$ ./ex19 -dm_vec_type seqcuda -dm_mat_type
seqaijcusp
lid velocity = 0.0625, prandtl # = 1., grashof # = 1.
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Unknown type. Check for miss-spelling or missing package:
http://www.mcs.anl.gov/petsc/documentation/installation.html#external
[0]PETSC ERROR: Unknown Mat type given: seqaijcusp
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.8.3-2027-g045eeab GIT
Date: 2018-03-12 13:30:25 -0500
[0]PETSC ERROR: ./ex19 on a named node50 by valera Wed Mar 14 11:17:25 2018
[0]PETSC ERROR: Configure options
--prefix=/usr/local/petsc.cod/petsc-install
--with-mpi-dir=/usr/lib64/openmpi --with-blaslapack-dir=/usr/lib64
COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2 --with-shared-libraries=0
--download-hypre --with-debugging=0 --with-cuda=1 --with-cuda-arch=sm_60
[0]PETSC ERROR: #1 MatSetType() line 61 in
/home/valera/testpetsc/src/mat/interface/matreg.c
[0]PETSC ERROR: #2 DMCreateMatrix_DA() line 693 in
/home/valera/testpetsc/src/dm/impls/da/fdda.c
[0]PETSC ERROR: #3 DMCreateMatrix() line 1199 in
/home/valera/testpetsc/src/dm/interface/dm.c
[0]PETSC ERROR: #4 SNESSetUpMatrices() line 646 in
/home/valera/testpetsc/src/snes/interface/snes.c
[0]PETSC ERROR: #5 SNESSetUp_NEWTONLS() line 296 in
/home/valera/testpetsc/src/snes/impls/ls/ls.c
[0]PETSC ERROR: #6 SNESSetUp() line 2795 in
/home/valera/testpetsc/src/snes/interface/snes.c
[0]PETSC ERROR: #7 SNESSolve() line 4187 in
/home/valera/testpetsc/src/snes/interface/snes.c
[0]PETSC ERROR: #8 main() line 161 in
/home/valera/testpetsc/src/snes/examples/tutorials/ex19.c
[0]PETSC ERROR: PETSc Option Table entries:
[0]PETSC ERROR: -dm_mat_type seqaijcusp
[0]PETSC ERROR: -dm_vec_type seqcuda
[0]PETSC ERROR: ----------------End of Error Message -------send entire
error message to petsc-maint at mcs.anl.gov----------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 86.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
On Wed, Mar 14, 2018 at 11:16 AM, Matthew Knepley <knepley at gmail.com> wrote:
> On Thu, Mar 15, 2018 at 3:12 AM, Manuel Valera <mvalera-w at mail.sdsu.edu>
> wrote:
>
>> Thanks, got this error:
>>
>
> Did you not configure with CUSP? It looks like you have CUDA, so use
>
> -dm_vec_type seqcuda
>
> Thanks,
>
> Matt
>
>
>> [valera at node50 testpetsc]$ cd src/snes/examples/tutorials/
>> [valera at node50 tutorials]$ PETSC_ARCH="" make ex19
>> /usr/lib64/openmpi/bin/mpicc -o ex19.o -c -Wall -Wwrite-strings
>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector
>> -fvisibility=hidden -O2 -I/home/valera/testpetsc/include
>> -I/home/valera/testpetsc/arch-linux2-c-opt/include
>> -I/usr/local/petsc.cod/petsc-install/include -I/usr/local/cuda/include
>> -I/usr/lib64/openmpi/include `pwd`/ex19.c
>> /usr/lib64/openmpi/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing
>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O2 -o ex19
>> ex19.o -L/home/valera/testpetsc/arch-linux2-c-opt/lib
>> -Wl,-rpath,/usr/local/petsc.cod/petsc-install/lib
>> -L/usr/local/petsc.cod/petsc-install/lib -Wl,-rpath,/usr/lib64
>> -L/usr/lib64 -Wl,-rpath,/usr/local/cuda/lib64 -L/usr/local/cuda/lib64
>> -L/usr/lib64/openmpi/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5
>> -Wl,-rpath,/usr/lib64/openmpi/lib -lpetsc -lHYPRE -llapack -lblas -lm
>> -lcufft -lcublas -lcudart -lcusparse -lX11 -lstdc++ -ldl -lmpi_usempi
>> -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath
>> -lpthread -lstdc++ -ldl
>> /usr/bin/rm -f ex19.o
>> [valera at node50 tutorials]$ ./ex19 -dm_vec_type seqcusp -dm_mat_type
>> seqaijcusp
>> lid velocity = 0.0625, prandtl # = 1., grashof # = 1.
>> [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [0]PETSC ERROR: Unknown type. Check for miss-spelling or missing package:
>> http://www.mcs.anl.gov/petsc/documentation/installation.html#external
>> [0]PETSC ERROR: Unknown vector type: seqcusp
>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [0]PETSC ERROR: Petsc Development GIT revision: v3.8.3-2027-g045eeab GIT
>> Date: 2018-03-12 13:30:25 -0500
>> [0]PETSC ERROR: ./ex19 on a named node50 by valera Wed Mar 14 11:12:11
>> 2018
>> [0]PETSC ERROR: Configure options --prefix=/usr/local/petsc.cod/petsc-install
>> --with-mpi-dir=/usr/lib64/openmpi --with-blaslapack-dir=/usr/lib64
>> COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2 --with-shared-libraries=0
>> --download-hypre --with-debugging=0 --with-cuda=1 --with-cuda-arch=sm_60
>> [0]PETSC ERROR: #1 VecSetType() line 42 in /home/valera/testpetsc/src/vec
>> /vec/interface/vecreg.c
>> [0]PETSC ERROR: #2 DMCreateGlobalVector_DA() line 39 in
>> /home/valera/testpetsc/src/dm/impls/da/dadist.c
>> [0]PETSC ERROR: #3 DMCreateGlobalVector() line 865 in
>> /home/valera/testpetsc/src/dm/interface/dm.c
>> [0]PETSC ERROR: #4 main() line 158 in /home/valera/testpetsc/src/sne
>> s/examples/tutorials/ex19.c
>> [0]PETSC ERROR: PETSc Option Table entries:
>> [0]PETSC ERROR: -dm_mat_type seqaijcusp
>> [0]PETSC ERROR: -dm_vec_type seqcusp
>> [0]PETSC ERROR: ----------------End of Error Message -------send entire
>> error message to petsc-maint at mcs.anl.gov----------
>> ------------------------------------------------------------
>> --------------
>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>> with errorcode 86.
>>
>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> You may or may not see output from other processes, depending on
>> exactly when Open MPI kills them.
>> ------------------------------------------------------------
>> --------------
>> [valera at node50 tutorials]$
>>
>>
>> On Wed, Mar 14, 2018 at 11:10 AM, Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> On Thu, Mar 15, 2018 at 2:46 AM, Manuel Valera <mvalera-w at mail.sdsu.edu>
>>> wrote:
>>>
>>>> Ok lets try that, if i go to /home/valera/testpetsc/arch
>>>> -linux2-c-opt/tests/src/snes/examples/tutorials there is runex19.sh
>>>> and a lot of other ex19 variantes, but if i run that i get:
>>>>
>>>
>>> knepley/feature-plex-functionals *$:/PETSc3/petsc/petsc-dev$ pushd
>>> src/snes/examples/tutorials/
>>> knepley/feature-plex-functionals *$:/PETSc3/petsc/petsc-dev/src/snes/examples/tutorials$
>>> PETSC_ARCH=arch-master-debug make ex19
>>> knepley/feature-plex-functionals *$:/PETSc3/petsc/petsc-dev/src/snes/examples/tutorials$
>>> ./ex19 -dm_vec_type seqcusp -dm_mat_type seqaijcusp
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>>> [valera at node50 tutorials]$ ./runex19.sh
>>>> not ok snes_tutorials-ex19_1
>>>> # ------------------------------------------------------------
>>>> --------------
>>>> # mpiexec was unable to launch the specified application as it could
>>>> not access
>>>> # or execute an executable:
>>>> #
>>>> # Executable: ../ex19
>>>> # Node: node50
>>>> #
>>>> # while attempting to start process rank 0.
>>>> # ------------------------------------------------------------
>>>> --------------
>>>> # 2 total processes failed to start
>>>> ok snes_tutorials-ex19_1 # SKIP Command failed so no diff
>>>>
>>>> is this the one i should be running ?
>>>>
>>>>
>>>> On Wed, Mar 14, 2018 at 10:39 AM, Matthew Knepley <knepley at gmail.com>
>>>> wrote:
>>>>
>>>>> On Thu, Mar 15, 2018 at 2:27 AM, Manuel Valera <
>>>>> mvalera-w at mail.sdsu.edu> wrote:
>>>>>
>>>>>> Ok thanks Matt, i made a smaller case with only the linear solver and
>>>>>> a 25x25 matrix, the error i have in this case is:
>>>>>>
>>>>>
>>>>> Ah, it appears that not all parts of your problem are taking the type
>>>>> options. If you want the
>>>>> linear algebra objects to change type, you need to have
>>>>>
>>>>> VecSetFromOptions() and MatSetFromOptions()
>>>>>
>>>>> called after you create them, but before sizes are set and data is
>>>>> entered. However, it should
>>>>> not be possible to have a seq Vec with the seqcusp AXPY routine set.
>>>>> Something else is wrong...
>>>>> Did you try a PETSc example, such as SNES ex19, with this?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>> [valera at node50 alone]$ mpirun -n 1 ./linsolve -vec_type cusp
>>>>>> -mat_type aijcusparse
>>>>>> laplacian.petsc !
>>>>>> TrivSoln loaded, size: 125 / 125
>>>>>> RHS loaded, size: 125 / 125
>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>> --------------------------------------------------------------
>>>>>> [0]PETSC ERROR: Null argument, when expecting valid pointer
>>>>>> [0]PETSC ERROR: Null Pointer: Parameter # 4
>>>>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/d
>>>>>> ocumentation/faq.html for trouble shooting.
>>>>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.8.3-1817-g96b6f8a
>>>>>> GIT Date: 2018-02-28 10:19:08 -0600
>>>>>> [0]PETSC ERROR: ./linsolve on a cuda named node50 by valera Wed Mar
>>>>>> 14 10:24:35 2018
>>>>>> [0]PETSC ERROR: Configure options PETSC_ARCH=cuda --with-cc=mpicc
>>>>>> --with-cxx=mpic++ --with-fc=mpifort --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3
>>>>>> --FOPTFLAGS=-O3 --with-shared-libraries=1 --with-debugging=1 --with-cuda=1
>>>>>> --with-cuda-arch=sm_60 --with-cusp=1 --with-cusp-dir=/home/valera/cusp
>>>>>> --with-vienacl=1 --download-fblaslapack=1 --download-hypre
>>>>>> [0]PETSC ERROR: #1 VecSetValues() line 851 in
>>>>>> /home/valera/petsc/src/vec/vec/interface/rvector.c
>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>> --------------------------------------------------------------
>>>>>> [0]PETSC ERROR: Invalid argument
>>>>>> [0]PETSC ERROR: Object (seq) is not seqcusp or mpicusp
>>>>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/d
>>>>>> ocumentation/faq.html for trouble shooting.
>>>>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.8.3-1817-g96b6f8a
>>>>>> GIT Date: 2018-02-28 10:19:08 -0600
>>>>>> [0]PETSC ERROR: ./linsolve on a cuda named node50 by valera Wed Mar
>>>>>> 14 10:24:35 2018
>>>>>> [0]PETSC ERROR: Configure options PETSC_ARCH=cuda --with-cc=mpicc
>>>>>> --with-cxx=mpic++ --with-fc=mpifort --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3
>>>>>> --FOPTFLAGS=-O3 --with-shared-libraries=1 --with-debugging=1 --with-cuda=1
>>>>>> --with-cuda-arch=sm_60 --with-cusp=1 --with-cusp-dir=/home/valera/cusp
>>>>>> --with-vienacl=1 --download-fblaslapack=1 --download-hypre
>>>>>> [0]PETSC ERROR: #2 VecCUSPGetArrayRead() line 1792 in
>>>>>> /home/valera/petsc/src/vec/vec/impls/seq/seqcusp/veccusp2.cu
>>>>>> [0]PETSC ERROR: #3 VecAXPY_SeqCUSP() line 314 in
>>>>>> /home/valera/petsc/src/vec/vec/impls/seq/seqcusp/veccusp2.cu
>>>>>> [0]PETSC ERROR: #4 VecAXPY() line 612 in
>>>>>> /home/valera/petsc/src/vec/vec/interface/rvector.c
>>>>>> [0]PETSC ERROR: #5 KSPSolve_GCR_cycle() line 60 in
>>>>>> /home/valera/petsc/src/ksp/ksp/impls/gcr/gcr.c
>>>>>> [0]PETSC ERROR: #6 KSPSolve_GCR() line 114 in
>>>>>> /home/valera/petsc/src/ksp/ksp/impls/gcr/gcr.c
>>>>>> [0]PETSC ERROR: #7 KSPSolve() line 669 in
>>>>>> /home/valera/petsc/src/ksp/ksp/interface/itfunc.c
>>>>>> soln maxval: 0.0000000000000000
>>>>>> soln minval: 0.0000000000000000
>>>>>> Norm: 11.180339887498949
>>>>>> Its: 0
>>>>>> WARNING! There are options you set that were not used!
>>>>>> WARNING! could be spelling mistake, etc!
>>>>>> Option left: name:-mat_type value: aijcusparse
>>>>>> [valera at node50 alone]$
>>>>>>
>>>>>>
>>>>>> I also see the configure options are not correct, so i guess is still
>>>>>> linking a different petsc installation, but maybe we can try to make it
>>>>>> work as it is, i will let you know if i am able to link the correct petsc
>>>>>> installation here,
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Sun, Mar 11, 2018 at 9:00 AM, Matthew Knepley <knepley at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> On Fri, Mar 9, 2018 at 3:05 AM, Manuel Valera <
>>>>>>> mvalera-w at mail.sdsu.edu> wrote:
>>>>>>>
>>>>>>>> Hello all,
>>>>>>>>
>>>>>>>> I am working on porting a linear solver into GPUs for timing
>>>>>>>> purposes, so far i've been able to compile and run the CUSP libraries and
>>>>>>>> compile PETSc to be used with CUSP and ViennaCL, after the initial runs i
>>>>>>>> noticed some errors, they are different for different flags and i would
>>>>>>>> appreciate any help interpreting them,
>>>>>>>>
>>>>>>>> The only elements in this program that use PETSc are the laplacian
>>>>>>>> matrix (sparse), the RHS and X vectors and a scatter petsc object, so i
>>>>>>>> would say it's safe to pass the command line arguments for the
>>>>>>>> Mat/VecSetType()s instead of changing the source code,
>>>>>>>>
>>>>>>>> If i use *-vec_type cuda -mat_type aijcusparse* or *-vec_type
>>>>>>>> viennacl -mat_type aijviennacl *i get the following:
>>>>>>>>
>>>>>>>
>>>>>>> These systems do not properly propagate errors. My only advice is to
>>>>>>> run a smaller problem and see.
>>>>>>>
>>>>>>>
>>>>>>>> [0]PETSC ERROR: ------------------------------
>>>>>>>> ------------------------------------------
>>>>>>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
>>>>>>>> Violation, probably memory access out of range
>>>>>>>> [0]PETSC ERROR: Try option -start_in_debugger or
>>>>>>>> -on_error_attach_debugger
>>>>>>>> [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>>>>>>>> ocumentation/faq.html#valgrind
>>>>>>>> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple
>>>>>>>> Mac OS X to find memory corruption errors
>>>>>>>> [0]PETSC ERROR: likely location of problem given in stack below
>>>>>>>> [0]PETSC ERROR: --------------------- Stack Frames
>>>>>>>> ------------------------------------
>>>>>>>> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
>>>>>>>> available,
>>>>>>>> [0]PETSC ERROR: INSTEAD the line number of the start of the
>>>>>>>> function
>>>>>>>> [0]PETSC ERROR: is given.
>>>>>>>> [0]PETSC ERROR: [0] VecSetValues line 847
>>>>>>>> /home/valera/petsc/src/vec/vec/interface/rvector.c
>>>>>>>> [0]PETSC ERROR: [0] VecSetType line 36
>>>>>>>> /home/valera/petsc/src/vec/vec/interface/vecreg.c
>>>>>>>> [0]PETSC ERROR: [0] VecSetTypeFromOptions_Private line 1230
>>>>>>>> /home/valera/petsc/src/vec/vec/interface/vector.c
>>>>>>>> [0]PETSC ERROR: [0] VecSetFromOptions line 1271
>>>>>>>> /home/valera/petsc/src/vec/vec/interface/vector.c
>>>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>>>> --------------------------------------------------------------
>>>>>>>> [0]PETSC ERROR: Signal received
>>>>>>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/d
>>>>>>>> ocumentation/faq.html for trouble shooting.
>>>>>>>> [0]PETSC ERROR: Petsc Development GIT revision:
>>>>>>>> v3.8.3-1817-g96b6f8a GIT Date: 2018-02-28 10:19:08 -0600
>>>>>>>> [0]PETSC ERROR: ./gcmSeamount on a cuda named node50 by valera Thu
>>>>>>>> Mar 8 09:50:51 2018
>>>>>>>> [0]PETSC ERROR: Configure options PETSC_ARCH=cuda --with-cc=mpicc
>>>>>>>> --with-cxx=mpic++ --with-fc=mpifort --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3
>>>>>>>> --FOPTFLAGS=-O3 --with-shared-libraries=1 --with-debugging=1 --with-cuda=1
>>>>>>>> --with-cuda-arch=sm_60 --with-cusp=1 --with-cusp-dir=/home/valera/cusp
>>>>>>>> --with-vienacl=1 --download-fblaslapack=1 --download-hypre
>>>>>>>> [0]PETSC ERROR: #5 User provided function() line 0 in unknown file
>>>>>>>> ------------------------------------------------------------
>>>>>>>> --------------
>>>>>>>>
>>>>>>>> This seems to be a memory out of range, maybe my vector is too big
>>>>>>>> for my CUDA system? how do i assess that?
>>>>>>>>
>>>>>>>>
>>>>>>>> Next, if i use *-vec_type cusp -mat_type aijcusparse *i get
>>>>>>>> something different and more interesting:
>>>>>>>>
>>>>>>>
>>>>>>> We need to see the entire error message, since it has the stack.
>>>>>>>
>>>>>>> This seems like a logic error, but could definitely be on our end.
>>>>>>> Here is how I think about these:
>>>>>>>
>>>>>>> 1) We have nightly test solves, so at least some solver
>>>>>>> configuration works
>>>>>>>
>>>>>>> 2) Some vector which is marked read-only (happens for input to
>>>>>>> solvers), but someone is trying to update it.
>>>>>>> The stack will tell me where this is happening.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Matt
>>>>>>>
>>>>>>>
>>>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>>>> --------------------------------------------------------------
>>>>>>>> [0]PETSC ERROR: Object is in wrong state
>>>>>>>> [0]PETSC ERROR: Vec is locked read only, argument # 3
>>>>>>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/d
>>>>>>>> ocumentation/faq.html for trouble shooting.
>>>>>>>> [0]PETSC ERROR: Petsc Development GIT revision:
>>>>>>>> v3.8.3-1817-g96b6f8a GIT Date: 2018-02-28 10:19:08 -0600
>>>>>>>> [0]PETSC ERROR: ./gcmSeamount on a cuda named node50 by valera Thu
>>>>>>>> Mar 8 10:02:19 2018
>>>>>>>> [0]PETSC ERROR: Configure options PETSC_ARCH=cuda --with-cc=mpicc
>>>>>>>> --with-cxx=mpic++ --with-fc=mpifort --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3
>>>>>>>> --FOPTFLAGS=-O3 --with-shared-libraries=1 --with-debugging=1 --with-cuda=1
>>>>>>>> --with-cuda-arch=sm_60 --with-cusp=1 --with-cusp-dir=/home/valera/cusp
>>>>>>>> --with-vienacl=1 --download-fblaslapack=1 --download-hypre
>>>>>>>> [0]PETSC ERROR: #48 KSPSolve() line 615 in
>>>>>>>> /home/valera/petsc/src/ksp/ksp/interface/itfunc.c
>>>>>>>> PETSC_SOLVER_ONLY 6.8672990892082453E-005 s
>>>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>>>> --------------------------------------------------------------
>>>>>>>> [0]PETSC ERROR: Invalid argument
>>>>>>>> [0]PETSC ERROR: Object (seq) is not seqcusp or mpicusp
>>>>>>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/d
>>>>>>>> ocumentation/faq.html for trouble shooting.
>>>>>>>> [0]PETSC ERROR: Petsc Development GIT revision:
>>>>>>>> v3.8.3-1817-g96b6f8a GIT Date: 2018-02-28 10:19:08 -0600
>>>>>>>> [0]PETSC ERROR: ./gcmSeamount on a cuda named node50 by valera Thu
>>>>>>>> Mar 8 10:02:19 2018
>>>>>>>> [0]PETSC ERROR: Configure options PETSC_ARCH=cuda --with-cc=mpicc
>>>>>>>> --with-cxx=mpic++ --with-fc=mpifort --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3
>>>>>>>> --FOPTFLAGS=-O3 --with-shared-libraries=1 --with-debugging=1 --with-cuda=1
>>>>>>>> --with-cuda-arch=sm_60 --with-cusp=1 --with-cusp-dir=/home/valera/cusp
>>>>>>>> --with-vienacl=1 --download-fblaslapack=1 --download-hypre
>>>>>>>> [0]PETSC ERROR: #49 VecCUSPGetArrayReadWrite() line 1718 in
>>>>>>>> /home/valera/petsc/src/vec/vec/impls/seq/seqcusp/veccusp2.cu
>>>>>>>> [0]PETSC ERROR: #50 VecScatterCUSP_StoS() line 269 in
>>>>>>>> /home/valera/petsc/src/vec/vec/impls/seq/seqcusp/vecscattercusp.cu
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> And it yields a "solution" to the system and also a log at the end:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ./gcmSeamount on a cuda named node50 with 1 processor, by valera
>>>>>>>> Thu Mar 8 10:02:24 2018
>>>>>>>> Using Petsc Development GIT revision: v3.8.3-1817-g96b6f8a GIT
>>>>>>>> Date: 2018-02-28 10:19:08 -0600
>>>>>>>>
>>>>>>>> Max Max/Min Avg Total
>>>>>>>> Time (sec): 4.573e+00 1.00000 4.573e+00
>>>>>>>> Objects: 8.100e+01 1.00000 8.100e+01
>>>>>>>> Flop: 3.492e+07 1.00000 3.492e+07 3.492e+07
>>>>>>>> Flop/sec: 7.637e+06 1.00000 7.637e+06 7.637e+06
>>>>>>>> Memory: 2.157e+08 1.00000 2.157e+08
>>>>>>>> MPI Messages: 0.000e+00 0.00000 0.000e+00 0.000e+00
>>>>>>>> MPI Message Lengths: 0.000e+00 0.00000 0.000e+00 0.000e+00
>>>>>>>> MPI Reductions: 0.000e+00 0.00000
>>>>>>>>
>>>>>>>> Flop counting convention: 1 flop = 1 real number operation of type
>>>>>>>> (multiply/divide/add/subtract)
>>>>>>>> e.g., VecAXPY() for real vectors of
>>>>>>>> length N --> 2N flop
>>>>>>>> and VecAXPY() for complex vectors of
>>>>>>>> length N --> 8N flop
>>>>>>>>
>>>>>>>> Summary of Stages: ----- Time ------ ----- Flop ----- ---
>>>>>>>> Messages --- -- Message Lengths -- -- Reductions --
>>>>>>>> Avg %Total Avg %Total counts
>>>>>>>> %Total Avg %Total counts %Total
>>>>>>>> 0: Main Stage: 4.5729e+00 100.0% 3.4924e+07 100.0%
>>>>>>>> 0.000e+00 0.0% 0.000e+00 0.0% 0.000e+00 0.0%
>>>>>>>>
>>>>>>>> ------------------------------------------------------------
>>>>>>>> ------------------------------------------------------------
>>>>>>>> See the 'Profiling' chapter of the users' manual for details on
>>>>>>>> interpreting output.
>>>>>>>> Phase summary info:
>>>>>>>> Count: number of times phase was executed
>>>>>>>> Time and Flop: Max - maximum over all processors
>>>>>>>> Ratio - ratio of maximum to minimum over all
>>>>>>>> processors
>>>>>>>> Mess: number of messages sent
>>>>>>>> Avg. len: average message length (bytes)
>>>>>>>> Reduct: number of global reductions
>>>>>>>> Global: entire computation
>>>>>>>> Stage: stages of a computation. Set stages with
>>>>>>>> PetscLogStagePush() and PetscLogStagePop().
>>>>>>>> %T - percent time in this phase %F - percent flop in
>>>>>>>> this phase
>>>>>>>> %M - percent messages in this phase %L - percent message
>>>>>>>> lengths in this phase
>>>>>>>> %R - percent reductions in this phase
>>>>>>>> Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max
>>>>>>>> time over all processors)
>>>>>>>> ------------------------------------------------------------
>>>>>>>> ------------------------------------------------------------
>>>>>>>>
>>>>>>>>
>>>>>>>> ##########################################################
>>>>>>>> # #
>>>>>>>> # WARNING!!! #
>>>>>>>> # #
>>>>>>>> # This code was compiled with a debugging option, #
>>>>>>>> # To get timing results run ./configure #
>>>>>>>> # using --with-debugging=no, the performance will #
>>>>>>>> # be generally two or three times faster. #
>>>>>>>> # #
>>>>>>>> ##########################################################
>>>>>>>>
>>>>>>>>
>>>>>>>> Event Count Time (sec) Flop
>>>>>>>> --- Global --- --- Stage --- Total
>>>>>>>> Max Ratio Max Ratio Max Ratio Mess
>>>>>>>> Avg len Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s
>>>>>>>> ------------------------------------------------------------
>>>>>>>> ------------------------------------------------------------
>>>>>>>>
>>>>>>>> --- Event Stage 0: Main Stage
>>>>>>>>
>>>>>>>> MatLUFactorNum 1 1.0 4.9502e-02 1.0 3.49e+07 1.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 1100 0 0 0 1100 0 0 0 706
>>>>>>>> MatILUFactorSym 1 1.0 1.9642e-02 1.0 0.00e+00 0.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>> MatAssemblyBegin 2 1.0 6.9141e-06 1.0 0.00e+00 0.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>> MatAssemblyEnd 2 1.0 2.6612e-01 1.0 0.00e+00 0.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 6 0 0 0 0 6 0 0 0 0 0
>>>>>>>> MatGetRowIJ 1 1.0 5.0068e-06 1.0 0.00e+00 0.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>> MatGetOrdering 1 1.0 1.7186e-02 1.0 0.00e+00 0.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>> MatLoad 1 1.0 1.1575e-01 1.0 0.00e+00 0.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 3 0 0 0 0 3 0 0 0 0 0
>>>>>>>> MatView 1 1.0 8.0877e-02 1.0 0.00e+00 0.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 0
>>>>>>>> MatCUSPCopyTo 1 1.0 2.4664e-01 1.0 0.00e+00 0.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 5 0 0 0 0 5 0 0 0 0 0
>>>>>>>> VecSet 68 1.0 5.1665e-02 1.0 0.00e+00 0.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0
>>>>>>>> VecAssemblyBegin 17 1.0 5.2691e-05 1.0 0.00e+00 0.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>> VecAssemblyEnd 17 1.0 4.3631e-05 1.0 0.00e+00 0.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>> VecScatterBegin 15 1.0 1.5345e-03 1.0 0.00e+00 0.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>> VecCUSPCopyFrom 1 1.0 1.1199e-03 1.0 0.00e+00 0.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>> KSPSetUp 1 1.0 5.1929e-02 1.0 0.00e+00 0.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0
>>>>>>>> PCSetUp 2 1.0 8.6590e-02 1.0 3.49e+07 1.0 0.0e+00
>>>>>>>> 0.0e+00 0.0e+00 2100 0 0 0 2100 0 0 0 403
>>>>>>>> ------------------------------------------------------------
>>>>>>>> ------------------------------------------------------------
>>>>>>>>
>>>>>>>> Memory usage is given in bytes:
>>>>>>>>
>>>>>>>> Object Type Creations Destructions Memory
>>>>>>>> Descendants' Mem.
>>>>>>>> Reports information only for process 0.
>>>>>>>>
>>>>>>>> --- Event Stage 0: Main Stage
>>>>>>>>
>>>>>>>> Matrix 3 1 52856972 0.
>>>>>>>> Matrix Null Space 1 1 608 0.
>>>>>>>> Vector 66 3 3414600 0.
>>>>>>>> Vector Scatter 1 1 680 0.
>>>>>>>> Viewer 3 2 1680 0.
>>>>>>>> Krylov Solver 1 0 0 0.
>>>>>>>> Preconditioner 2 1 864 0.
>>>>>>>> Index Set 4 1 800 0.
>>>>>>>> ============================================================
>>>>>>>> ============================================================
>>>>>>>> Average time to get PetscTime(): 9.53674e-08
>>>>>>>> #PETSc Option Table entries:
>>>>>>>> -ksp_view
>>>>>>>> -log_view
>>>>>>>> -mat_type aijcusparse
>>>>>>>> -matload_block_size 1
>>>>>>>> -vec_type cusp
>>>>>>>> #End of PETSc Option Table entries
>>>>>>>> Compiled without FORTRAN kernels
>>>>>>>> Compiled with full precision matrices (default)
>>>>>>>> sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8
>>>>>>>> sizeof(PetscScalar) 8 sizeof(PetscInt) 4
>>>>>>>> Configure options: PETSC_ARCH=cuda --with-cc=mpicc
>>>>>>>> --with-cxx=mpic++ --with-fc=mpifort --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3
>>>>>>>> --FOPTFLAGS=-O3 --with-shared-libraries=1 --with-debugging=1 --with-cuda=1
>>>>>>>> --with-cuda-arch=sm_60 --with-cusp=1 --with-cusp-dir=/home/valera/cusp
>>>>>>>> --with-vienacl=1 --download-fblaslapack=1 --download-hypre
>>>>>>>> -----------------------------------------
>>>>>>>> Libraries compiled on Mon Mar 5 16:37:18 2018 on node50
>>>>>>>> Machine characteristics: Linux-3.10.0-693.17.1.el7.x86_
>>>>>>>> 64-x86_64-with-centos-7.2.1511-Core
>>>>>>>> Using PETSc directory: /home/valera/petsc
>>>>>>>> Using PETSc arch: cuda
>>>>>>>> -----------------------------------------
>>>>>>>>
>>>>>>>> Using C compiler: mpicc -fPIC -Wall -Wwrite-strings
>>>>>>>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector
>>>>>>>> -fvisibility=hidden -O3
>>>>>>>> Using Fortran compiler: mpifort -fPIC -Wall -ffree-line-length-0
>>>>>>>> -Wno-unused-dummy-argument -O3
>>>>>>>> -----------------------------------------
>>>>>>>>
>>>>>>>> Using include paths: -I/home/valera/petsc/cuda/include
>>>>>>>> -I/home/valera/petsc/include -I/home/valera/petsc/include
>>>>>>>> -I/home/valera/petsc/cuda/include -I/home/valera/cusp/
>>>>>>>> -I/usr/local/cuda/include
>>>>>>>> -----------------------------------------
>>>>>>>>
>>>>>>>> Using C linker: mpicc
>>>>>>>> Using Fortran linker: mpifort
>>>>>>>> Using libraries: -Wl,-rpath,/home/valera/petsc/cuda/lib
>>>>>>>> -L/home/valera/petsc/cuda/lib -lpetsc -Wl,-rpath,/home/valera/petsc/cuda/lib
>>>>>>>> -L/home/valera/petsc/cuda/lib -Wl,-rpath,/usr/local/cuda/lib64
>>>>>>>> -L/usr/local/cuda/lib64 -Wl,-rpath,/usr/lib64/openmpi/lib
>>>>>>>> -L/usr/lib64/openmpi/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5
>>>>>>>> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -lHYPRE -lflapack -lfblas
>>>>>>>> -lm -lcufft -lcublas -lcudart -lcusparse -lX11 -lstdc++ -ldl -lmpi_usempi
>>>>>>>> -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath
>>>>>>>> -lpthread -lstdc++ -ldl
>>>>>>>> -----------------------------------------
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks for your help,
>>>>>>>>
>>>>>>>> Manuel
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> 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
>>>>>>>
>>>>>>> https://www.cse.buffalo.edu/~knepley/
>>>>>>> <http://www.caam.rice.edu/~mk51/>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>> https://www.cse.buffalo.edu/~knepley/
>>>>> <http://www.caam.rice.edu/~mk51/>
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> 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
>>>
>>> https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
>>>
>>
>>
>
>
> --
> 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
>
> https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
>
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