[petsc-users] Compiling PETSc in Polaris with gnu

[Satish Balay]

Perhaps you need to:

module load craype-accel-nvidia80

And then rebuild PETSc, your application

And have the same list of modules loaded at runtime.

Satish

On Thu, 2 May 2024, Vanella, Marcos (Fed) via petsc-users wrote:

> Thank you Satish and Junchao! I was able to compile PETSc with your configure options + suitesparse and hypre, and then compile my fortran code linking to PETSc.
> But when I try to run my test run I'm picking up an error at the very beginning:
> 
> MPICH ERROR [Rank 0] [job id 01eb3c4a-28a7-4178-aced-512b4fb704c6] [Thu May  2 20:44:26 2024] [x3006c0s19b1n0] - Abort(-1) (rank 0 in comm 0): MPIDI_CRAY_init: GPU_SUPPORT_ENABLED is requested, but GTL library is not linked
>  (Other MPI error)
> 
> aborting job:
> MPIDI_CRAY_init: GPU_SUPPORT_ENABLED is requested, but GTL library is not linked
> 
> It says in the Polaris user guide that:
> 
> The environment variable MPICH_GPU_SUPPORT_ENABLED=1 needs to be set if your application requires MPI-GPU support whereby the MPI library sends and receives data directly from GPU buffers. In this case, it will be important to have the craype-accel-nvidia80  module loaded both when compiling your application and during runtime to correctly link against a GPU Transport Layer (GTL) MPI library. Otherwise, you'll likely see GPU_SUPPORT_ENABLED is requested, but GTL library is not linked errors during runtime.
> 
> I tried adding loading this module (also needed to add nvhpc-mixed) in my submission script but I get the same result.
> I'll get in touch with alcf help on this.
> 
> 
> 
> ________________________________
> From: Satish Balay <balay at mcs.anl.gov>
> Sent: Thursday, May 2, 2024 11:58 AM
> To: Junchao Zhang <junchao.zhang at gmail.com>
> Cc: petsc-users <petsc-users at mcs.anl.gov>; Vanella, Marcos (Fed) <marcos.vanella at nist.gov>; Mueller, Eric V. (Fed) <eric.mueller at nist.gov>
> Subject: Re: [petsc-users] Compiling PETSc in Polaris with gnu
> 
> I just tried a build  (used default versions) - and the following builds for me [on the login node].
> 
> 
> module use /soft/modulefiles
> module load PrgEnv-gnu
> module load cudatoolkit-standalone
> module load cray-libsci
> ./configure --with-cc=cc --with-fc=ftn --with-cxx=CC --with-make-np=4 --with-cuda=1 --with-cudac=nvcc --with-cuda-arch=80 \
>   --with-debugging=0 COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2 CUDAOPTFLAGS=-O2 --download-kokkos --download-kokkos-kernels
> make
> 
> Satish
> 
> ---
> 
> balay at polaris-login-01:~> module list
> 
> Currently Loaded Modules:
>   1) libfabric/1.15.2.0       4) darshan/3.4.4     7) cray-dsmml/0.2.2   10) cray-pals/1.3.4     13) PrgEnv-gnu/8.5.0
>   2) craype-network-ofi       5) gcc-native/12.3   8) cray-mpich/8.1.28  11) cray-libpals/1.3.4  14) cudatoolkit-standalone/12.2.2
>   3) perftools-base/23.12.0   6) craype/2.7.30     9) cray-pmi/6.1.13    12) craype-x86-milan    15) cray-libsci/23.12.5
> 
> 
> On Thu, 2 May 2024, Junchao Zhang wrote:
> 
> > I used cudatoolkit-standalone/12.4.1 and gcc-12.3.
> >
> > Be sure to use the latest petsc/main or petsc/release, which contains fixes
> > for Polaris.
> >
> > --Junchao Zhang
> >
> >
> > On Thu, May 2, 2024 at 10:23 AM Satish Balay via petsc-users <
> > petsc-users at mcs.anl.gov> wrote:
> >
> > > Try:
> > >
> > > module use /soft/modulefiles
> > >
> > > Satish
> > >
> > > On Thu, 2 May 2024, Vanella, Marcos (Fed) via petsc-users wrote:
> > >
> > > > Hi all, it seems the modules in Polaris have changed (can't find
> > > cudatoolkit-standalone anymore).
> > > > Does anyone have recent experience compiling the library with gnu and
> > > cuda in the machine?
> > > > Thank you!
> > > > Marcos
> > > >
> > >
> > >
> >
>