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

Fri Apr 19 11:54:57 CDT 2024

I talked to the MVAPICH people, and they told me to try adding
/path/to/mvapich2-gdr/lib64/libmpi.so to LD_PRELOAD (apparently, they've
had this issue before). This seemed to do the trick; I can build everything
with MVAPICH2-GDR and run with it now. Not sure if this is something you
want to add to the docs.

Thanks,
Sreeram

On Wed, Apr 17, 2024 at 9:17 AM Junchao Zhang <junchao.zhang at gmail.com>
wrote:

> 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!bE42LoNqiOoD5Yu05BdtZqAHbFHxkuFy6S8ljr09QRqymgFnne-nbxx-xywoOtRzBGA3fRvcsOyyVgNDLWPRbI84MA$ 
>  > 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!bE42LoNqiOoD5Yu05BdtZqAHbFHxkuFy6S8ljr09QRqymgFnne-nbxx-xywoOtRzBGA3fRvcsOyyVgNDLWMNhkqWSA$ 
>> 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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