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

Wed Apr 17 09:17:22 CDT 2024

I looked at it before and checked again, and still see
https://urldefense.us/v3/__https://docs.nvidia.com/deeplearning/nccl/user-guide/docs/mpi.html*inter-gpu-communication-with-cuda-aware-mpi__;Iw!!G_uCfscf7eWS!aoebw25LunX6PlUYyVIti_VNLojOyz8MwWS3U-t5NHMMb4GnFUFV-nGq1LbjnigF72oKfDjmLXk9vUwkcYZpFTq0PgLl$ 
 > Using both MPI and NCCL to perform transfers between the same sets of
CUDA devices concurrently is therefore not guaranteed to be safe.

I was scared by it.  It means we have to replace all MPI device
communications (what if they are from a third-party library?) with NCCL.

--Junchao Zhang

On Wed, Apr 17, 2024 at 8:27 AM Sreeram R Venkat <srvenkat at utexas.edu>
wrote:

> Yes, I saw this paper
> https://urldefense.us/v3/__https://www.sciencedirect.com/science/article/abs/pii/S016781912100079X__;!!G_uCfscf7eWS!aoebw25LunX6PlUYyVIti_VNLojOyz8MwWS3U-t5NHMMb4GnFUFV-nGq1LbjnigF72oKfDjmLXk9vUwkcYZpFWw9ViCb$ 
> that mentioned it, and I heard in Barry's talk at SIAM PP this year about
> the need for stream-aware MPI, so I was wondering if NCCL would be used in
> PETSc to do GPU-GPU communication.
>
> On Wed, Apr 17, 2024, 7:58 AM Junchao Zhang <junchao.zhang at gmail.com>
> wrote:
>
>>
>>
>>
>>
>> On Wed, Apr 17, 2024 at 7:51 AM Sreeram R Venkat <srvenkat at utexas.edu>
>> wrote:
>>
>>> Do you know if there are plans for NCCL support in PETSc?
>>>
>> What is your need?  Do you mean using NCCL for the MPI communication?
>>
>>
>>>
>>> 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
>>>>> ZjQcmQRYFpfptBannerStart
>>>>> This Message Is From an External Sender
>>>>> This message came from outside your organization.
>>>>>
>>>>> ZjQcmQRYFpfptBannerEnd
>>>>> 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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