[petsc-users] Configure error while building PETSc with CUDA/MVAPICH2-GDR

Wed Apr 17 07:50:54 CDT 2024

Do you know if there are plans for NCCL support in PETSc?

On Tue, Apr 16, 2024, 10:41 PM Junchao Zhang <junchao.zhang at gmail.com>
wrote:

> Glad to hear you found a way.   Did you use Frontera at TACC?  If yes, I
> could have a try.
>
> --Junchao Zhang
>
>
> On Tue, Apr 16, 2024 at 8:35 PM Sreeram R Venkat <srvenkat at utexas.edu>
> wrote:
>
>> I finally figured out a way to make it work. I had to build PETSc and my
>> application using the (non GPU-aware) Intel MPI. Then, before running, I
>> switch to the MVAPICH2-GDR. I'm not sure why that works, but it's the only
>> way I've
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>> I finally figured out a way to make it work. I had to build PETSc and my
>> application using the (non GPU-aware) Intel MPI. Then, before running, I
>> switch to the MVAPICH2-GDR.
>> I'm not sure why that works, but it's the only way I've found to compile
>> and run successfully without throwing any errors about not having a
>> GPU-aware MPI.
>>
>>
>>
>> On Fri, Dec 8, 2023 at 5:30 PM Mark Adams <mfadams at lbl.gov> wrote:
>>
>>> You may need to set some env variables. This can be system specific so
>>> you might want to look at docs or ask TACC how to run with GPU-aware MPI.
>>>
>>> Mark
>>>
>>> On Fri, Dec 8, 2023 at 5:17 PM Sreeram R Venkat <srvenkat at utexas.edu>
>>> wrote:
>>>
>>>> Actually, when I compile my program with this build of PETSc and run, I
>>>> still get the error:
>>>>
>>>> PETSC ERROR: PETSc is configured with GPU support, but your MPI is not
>>>> GPU-aware. For better performance, please use a GPU-aware MPI.
>>>>
>>>> I have the mvapich2-gdr module loaded and MV2_USE_CUDA=1.
>>>>
>>>> Is there anything else I need to do?
>>>>
>>>> Thanks,
>>>> Sreeram
>>>>
>>>> On Fri, Dec 8, 2023 at 3:29 PM Sreeram R Venkat <srvenkat at utexas.edu>
>>>> wrote:
>>>>
>>>>> Thank you, changing to CUDA 11.4 fixed the issue. The mvapich2-gdr
>>>>> module didn't require CUDA 11.4 as a dependency, so I was using 12.0
>>>>>
>>>>> On Fri, Dec 8, 2023 at 1:15 PM Satish Balay <balay at mcs.anl.gov> wrote:
>>>>>
>>>>>> Executing: mpicc -show
>>>>>> stdout: icc -I/opt/apps/cuda/11.4/include
>>>>>> -I/opt/apps/cuda/11.4/include -lcuda -L/opt/apps/cuda/11.4/lib64/stubs
>>>>>> -L/opt/apps/cuda/11.4/lib64 -lcudart -lrt
>>>>>> -Wl,-rpath,/opt/apps/cuda/11.4/lib64 -Wl,-rpath,XORIGIN/placeholder
>>>>>> -Wl,--build-id -L/opt/apps/cuda/11.4/lib64/ -lm
>>>>>> -I/opt/apps/intel19/mvapich2-gdr/2.3.7/include
>>>>>> -L/opt/apps/intel19/mvapich2-gdr/2.3.7/lib64 -Wl,-rpath
>>>>>> -Wl,/opt/apps/intel19/mvapich2-gdr/2.3.7/lib64 -Wl,--enable-new-dtags -lmpi
>>>>>>
>>>>>>     Checking for program /opt/apps/cuda/12.0/bin/nvcc...found
>>>>>>
>>>>>> Looks like you are trying to mix in 2 different cuda versions in this
>>>>>> build.
>>>>>>
>>>>>> Perhaps you need to use cuda-11.4 - with this install of mvapich..
>>>>>>
>>>>>> Satish
>>>>>>
>>>>>> On Fri, 8 Dec 2023, Matthew Knepley wrote:
>>>>>>
>>>>>> > On Fri, Dec 8, 2023 at 1:54 PM Sreeram R Venkat <
>>>>>> srvenkat at utexas.edu> wrote:
>>>>>> >
>>>>>> > > I am trying to build PETSc with CUDA using the CUDA-Aware
>>>>>> MVAPICH2-GDR.
>>>>>> > >
>>>>>> > > Here is my configure command:
>>>>>> > >
>>>>>> > > ./configure PETSC_ARCH=linux-c-debug-mvapich2-gdr --download-hypre
>>>>>> > >  --with-cuda=true --cuda-dir=$TACC_CUDA_DIR --with-hdf5=true
>>>>>> > > --with-hdf5-dir=$TACC_PHDF5_DIR --download-elemental
>>>>>> --download-metis
>>>>>> > > --download-parmetis --with-cc=mpicc --with-cxx=mpicxx
>>>>>> --with-fc=mpif90
>>>>>> > >
>>>>>> > > which errors with:
>>>>>> > >
>>>>>> > >           UNABLE to CONFIGURE with GIVEN OPTIONS (see
>>>>>> configure.log for
>>>>>> > > details):
>>>>>> > >
>>>>>> > >
>>>>>> ---------------------------------------------------------------------------------------------
>>>>>> > >   CUDA compile failed with arch flags " -ccbin mpic++ -std=c++14
>>>>>> > > -Xcompiler -fPIC
>>>>>> > >   -Xcompiler -fvisibility=hidden -g -lineinfo -gencode
>>>>>> > > arch=compute_80,code=sm_80"
>>>>>> > >   generated from "--with-cuda-arch=80"
>>>>>> > >
>>>>>> > >
>>>>>> > >
>>>>>> > > The same configure command works when I use the Intel MPI and I
>>>>>> can build
>>>>>> > > with CUDA. The full config.log file is attached. Please let me
>>>>>> know if you
>>>>>> > > need any other information. I appreciate your help with this.
>>>>>> > >
>>>>>> >
>>>>>> > The proximate error is
>>>>>> >
>>>>>> > Executing: nvcc -c -o
>>>>>> /tmp/petsc-kn3f29gl/config.packages.cuda/conftest.o
>>>>>> > -I/tmp/petsc-kn3f29gl/config.setCompilers
>>>>>> > -I/tmp/petsc-kn3f29gl/config.types
>>>>>> > -I/tmp/petsc-kn3f29gl/config.packages.cuda  -ccbin mpic++ -std=c++14
>>>>>> > -Xcompiler -fPIC -Xcompiler -fvisibility=hidden -g -lineinfo
>>>>>> -gencode
>>>>>> > arch=compute_80,code=sm_80
>>>>>> /tmp/petsc-kn3f29gl/config.packages.cuda/
>>>>>> > conftest.cu
>>>>>> <https://urldefense.us/v3/__http://conftest.cu__;!!G_uCfscf7eWS!duKUz7pE9N0adJ-FOW7PLZ_1cSZvYlnqh7J0TIcZN0v8RLplcWxh1YE8Vis29K0cuw_zAvjdK-H9H2JYYuUUKRXxlA$>
>>>>>> > stdout:
>>>>>> > /opt/apps/cuda/11.4/include/crt/sm_80_rt.hpp(141): error: more than
>>>>>> one
>>>>>> > instance of overloaded function
>>>>>> "__nv_associate_access_property_impl" has
>>>>>> > "C" linkage
>>>>>> > 1 error detected in the compilation of
>>>>>> > "/tmp/petsc-kn3f29gl/config.packages.cuda/conftest.cu
>>>>>> <https://urldefense.us/v3/__http://conftest.cu__;!!G_uCfscf7eWS!duKUz7pE9N0adJ-FOW7PLZ_1cSZvYlnqh7J0TIcZN0v8RLplcWxh1YE8Vis29K0cuw_zAvjdK-H9H2JYYuUUKRXxlA$>
>>>>>> ".
>>>>>> > Possible ERROR while running compiler: exit code 1
>>>>>> > stderr:
>>>>>> > /opt/apps/cuda/11.4/include/crt/sm_80_rt.hpp(141): error: more than
>>>>>> one
>>>>>> > instance of overloaded function
>>>>>> "__nv_associate_access_property_impl" has
>>>>>> > "C" linkage
>>>>>> >
>>>>>> > 1 error detected in the compilation of
>>>>>> > "/tmp/petsc-kn3f29gl/config.packages.cuda
>>>>>> >
>>>>>> > This looks like screwed up headers to me, but I will let someone
>>>>>> that
>>>>>> > understands CUDA compilation reply.
>>>>>> >
>>>>>> >   Thanks,
>>>>>> >
>>>>>> >      Matt
>>>>>> >
>>>>>> > Thanks,
>>>>>> > > Sreeram
>>>>>> > >
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>
>>>>>
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