And, building in my home directory looks fine. Looks like a problem with the scratch directory.
On Fri, Jan 28, 2022 at 1:15 PM Mark Adams <[email protected]> wrote: > Something is very messed up on Crusher. I've never seen this "Cannot > allocate memory", but see it for everything: > > 13:11 1 main= crusher:/gpfs/alpine/csc314/scratch/adams/petsc2$ ll > ls: cannot read symbolic link 'configure.log.bkp': Cannot allocate memory > ls: cannot read symbolic link 'make.log': Cannot allocate memory > ls: cannot read symbolic link 'configure.log': Cannot allocate memory > total 25637 > drwxr-xr-x 8 adams adams 4096 Jan 20 08:51 arch-olcf-crusher > drwxr-xr-x 8 adams adams 4096 Jan 18 20:23 arch-spock-amd > drwxrwxr-x 5 adams adams 4096 Jan 26 19:10 arch-summit-dbg-gnu-cuda > .... > > and > > 13:11 main= crusher:/gpfs/alpine/csc314/scratch/adams/petsc2$ git fetch > remote: Enumerating objects: 648, done. > remote: Counting objects: 100% (547/547), done. > remote: Compressing objects: 100% (238/238), done. > remote: Total 648 (delta 379), reused 442 (delta 308), pack-reused 101 > Receiving objects: 100% (648/648), 591.28 KiB | 1.38 MiB/s, done. > Resolving deltas: 100% (402/402), completed with 114 local objects. > error: cannot update the ref 'refs/remotes/origin/main': unable to append > to '.git/logs/refs/remotes/origin/main': Cannot allocate memory > From https://gitlab.com/petsc/petsc > > On Fri, Jan 28, 2022 at 1:07 PM Mark Adams <[email protected]> wrote: > >> Crusher has been giving me fits and now I get this error (empty log) >> >> 13:01 main *= crusher:/gpfs/alpine/csc314/scratch/adams/petsc$ >> ../arch-olcf-crusher.py >> Traceback (most recent call last): >> File "../arch-olcf-crusher.py", line 55, in <module> >> configure.petsc_configure(configure_options) >> AttributeError: module 'configure' has no attribute 'petsc_configure' >> >> This is a modified version of the repo configure file. This was working >> this AM. >> Any idea what could cause this? >> >> Thanks, >> Mark >> >> #!/usr/bin/python3 >> >> # Modules loaded by default (on login to Crusher): >> # >> # 1) craype-x86-trento 9) cce/13.0.0 >> # 2) libfabric/1.13.0.0 10) craype/2.7.13 >> # 3) craype-network-ofi 11) cray-dsmml/0.2.2 >> # 4) perftools-base/21.12.0 12) cray-libsci/21.08.1.2 >> # 5) xpmem/2.3.2-2.2_1.16__g9ea452c.shasta 13) PrgEnv-cray/8.2.0 >> # 6) cray-pmi/6.0.16 14) DefApps/default >> # 7) cray-pmi-lib/6.0.16 15) rocm/4.5.0 >> # 8) tmux/3.2a 16) cray-mpich/8.1.12 >> # >> # We use Cray Programming Environment, Cray compilers, Cray-mpich. >> # To enable GPU-aware MPI, one has to also set this environment variable >> # >> # export MPICH_GPU_SUPPORT_ENABLED=1 >> # >> # Additional note: If "craype-accel-amd-gfx90a" module is loaded (that is >> # needed for "OpenMP offload") - it causes link errors when using 'cc or >> hipcc' >> # with fortran objs, hence not used >> # >> >> if __name__ == '__main__': >> import sys >> import os >> sys.path.insert(0, os.path.abspath('config')) >> import configure >> configure_options = [ >> '--with-cc=cc', >> '--with-cxx=CC', >> '--with-fc=ftn', >> '--COPTFLAGS=-g -ggdb', >> '--CXXOPTFLAGS=-g -ggdb', >> '--FOPTFLAGS=-g', >> '--with-fortran-bindings=0', >> 'LIBS=-L{x}/gtl/lib >> -lmpi_gtl_hsa'.format(x=os.environ['CRAY_MPICH_ROOTDIR']), >> '--with-debugging=1', >> #'--with-64-bit-indices=1', >> '--with-mpiexec=srun -p batch -N 1 -A csc314_crusher -t 00:10:00', >> '--with-hip', >> '--with-hipc=hipcc', >> '--download-hypre', >> #'--download-hypre-commit=HEAD', >> #'--download-hypre-configure-arguments=--enable-unified-memory', >> #'--with-hypre-gpuarch=gfx90a', >> '--with-hip-arch=gfx90a', >> '--download-kokkos', >> '--download-kokkos-kernels', >> #'--with-kokkos-kernels-tpl=1', >> >> #'--prefix=/gpfs/alpine/world-shared/geo127/petsc/arch-crusher-opt-cray', # >> /gpfs/alpine/phy122/proj-shared/petsc/current/arch-opt-amd-hypre', >> ] >> configure.petsc_configure(configure_options) >> >> >>
