@carlosal1015: I assume you solved it, at least I saw in your Kokkos package '' -DKokkos_ENABLE_OPENMP=OFF''
We could also try to enable openMP in PETSc, but I think that is normally not recommended.
Git Clone URL: | https://aur.archlinux.org/petsc.git (read-only, click to copy) |
---|---|
Package Base: | petsc |
Description: | Portable, extensible toolkit for scientific computation |
Upstream URL: | https://petsc.org |
Keywords: | computing scientific |
Licenses: | BSD |
Provides: | petsc4py |
Submitter: | heitzmann |
Maintainer: | MartinDiehl |
Last Packager: | MartinDiehl |
Votes: | 19 |
Popularity: | 0.000003 |
First Submitted: | 2018-02-24 11:36 (UTC) |
Last Updated: | 2024-09-01 08:58 (UTC) |
@carlosal1015: I assume you solved it, at least I saw in your Kokkos package '' -DKokkos_ENABLE_OPENMP=OFF''
We could also try to enable openMP in PETSc, but I think that is normally not recommended.
I have the following message error
CC linux-c-opt/obj/src/vec/is/sf/interface/ftn-custom/zvscat.o
CXX linux-c-opt/obj/src/sys/objects/kokkos/kinit.o
In file included from /usr/include/OpenMP/Kokkos_OpenMP.hpp:203,
from /usr/include/decl/Kokkos_Declare_OPENMP.hpp:21,
from /usr/include/KokkosCore_Config_DeclareBackend.hpp:22,
from /usr/include/Kokkos_Core.hpp:45,
from /tmp/makepkg/petsc/src/petsc-3.21.5/include/petsc/private/kokkosimpl.hpp:6,
from /tmp/makepkg/petsc/src/petsc-3.21.5/src/sys/objects/kokkos/kinit.kokkos.cxx:2:
/usr/include/OpenMP/Kokkos_OpenMP_Instance.hpp:23:2: error: #error "You enabled Kokkos OpenMP support without enabling OpenMP in the compiler!"
23 | #error \
| ^~~~~
make[3]: *** [gmakefile:200: linux-c-opt/obj/src/sys/objects/kokkos/kinit.o] Error 1
make[3]: *** Waiting for unfinished jobs....
CC linux-c-opt/obj/src/vec/is/section/interface/sectionhdf5.o
CC linux-c-opt/obj/src/vec/is/sf/interface/ftn-custom/zsf.o
CC linux-c-opt/obj/src/vec/is/sf/impls/basic/neighbor/sfneighbor.o
CC linux-c-opt/obj/src/vec/is/sf/interface/sfregi.o
CC linux-c-opt/obj/src/vec/is/sf/utils/f90-custom/zsfutilsf90.o
CC linux-c-opt/obj/src/vec/is/is/impls/general/general.o
CC linux-c-opt/obj/src/vec/is/sf/impls/basic/allgatherv/sfallgatherv.o
CC linux-c-opt/obj/src/vec/is/sf/interface/sftype.o
CC linux-c-opt/obj/src/vec/is/is/utils/iscoloring.o
CC linux-c-opt/obj/src/vec/is/is/utils/isdiff.o
CC linux-c-opt/obj/src/vec/is/sf/impls/basic/sfbasic.o
CC linux-c-opt/obj/src/sys/objects/options.o
CC linux-c-opt/obj/src/vec/is/sf/impls/window/sfwindow.o
CC linux-c-opt/obj/src/vec/is/sf/interface/vscat.o
CC linux-c-opt/obj/src/vec/is/is/interface/index.o
CC linux-c-opt/obj/src/vec/is/sf/interface/sf.o
CC linux-c-opt/obj/src/vec/is/section/interface/section.o
CC linux-c-opt/obj/src/sys/logging/handler/impls/default/logdefault.o
CC linux-c-opt/obj/src/vec/is/sf/impls/basic/sfpack.o
make[3]: Leaving directory '/tmp/makepkg/petsc/src/petsc-3.21.5'
make[2]: *** [/tmp/makepkg/petsc/src/petsc-3.21.5/lib/petsc/conf/rules_doc.mk:5: libs] Error 2
make[2]: Leaving directory '/tmp/makepkg/petsc/src/petsc-3.21.5'
**************************ERROR*************************************
Error during compile, check linux-c-opt/lib/petsc/conf/make.log
Send it and linux-c-opt/lib/petsc/conf/configure.log to petsc-maint@mcs.anl.gov
********************************************************************
make[1]: *** [makefile:44: all] Error 1
make: *** [GNUmakefile:9: all] Error 2
==> ERROR: A failure occurred in build().
full log: https://0x0.st/XEmY.bin
TLDR: I had kokkos
installed before run makepkg. Something is wrong from kokkos's PKGBUILD side or PETSc configuration?
@carlosal1915: I get the same error in a non-Python code that uses OpenMPI and PETSc. I think it is an upstream issue in either OpenMPI or PETSc.
Hi, I have the following warning/error? message
>>> from petsc4py.PETSc import ScalarType
[5161bd26d9fc:00008] shmem: mmap: an error occurred while determining whether or not /tmp/ompi.5161bd26d9fc.33333/jf.0/2252865536/shared_mem_cuda_pool.5161bd26d9fc could be created.
[5161bd26d9fc:00008] create_and_attach: unable to create shared memory BTL coordinating structure :: size 134217728
Maybe related with https://github.com/open-mpi/ompi/issues/12307
@lahwaacz Getting the same error.
The tests fail to build:
*******************Error detected during compile or link!*******************
See https://petsc.org/release/faq/
/build/petsc/src/petsc-3.21.0/src/snes/tutorials ex19
*********************************************************************************
/usr/bin/mpicc -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-z,pack-relative-relocs -flto=auto -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/petsc/src=/usr/src/debug/petsc -flto=auto -fPIC -I/build/petsc/src/petsc-3.21.0/include -I/build/petsc/src/petsc-3.21.0/arch-linux-c-opt/include -I/usr/include/hypre -I/usr/include/suitesparse -I/usr/include/superlu -I/usr/include/superlu_dist -I/usr/include -Wl,-export-dynamic ex19.c -Wl,-rpath,/opt/petsc/linux-c-opt/lib -L/opt/petsc/linux-c-opt/lib -Wl,-rpath,/usr/lib/gcc/x86_64-pc-linux-gnu/13.2.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/13.2.1 -lpetsc /usr/lib/libHYPRE.so -lamd -lbtf -lcamd -lccolamd -lcholmod -lcolamd -lcxsparse -lgraphblas -lklu -lklu_cholmod -llagraph -llagraphx -lldl -lparu -lrbio -lspex -lspqr -lsuitesparse_mongoose -lsuitesparseconfig -lumfpack -ldmumps -lmumps_common -lpord -lpthread -lscalapack -lsuperlu -lsuperlu_dist -lml -lfftw3_mpi -lfftw3 -lkokkoscontainers -lkokkoscore -lkokkossimd -llapack -lblas -lzfp -lzoltan -lptesmumps -lptscotchparmetisv3 -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lparmetis -lmetis -lnetcdf -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -ltriangle -lm -lz -lgsl -lgslcblas -ljpeg -lyaml -lX11 -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -o ex19
/usr/bin/ld: cannot find -lpetsc: No such file or directory
collect2: error: ld returned 1 exit status
make[4]: *** [<builtin>: ex19] Error 1
It uses -L/opt/petsc/linux-c-opt/lib
but of course the package is not installed there yet.
@gpettinello Have you rebuilt trilinos with openmpi version 5? See what ldd /usr/lib/libml.so
shows.
Same problem to compile as written below about ml libraries. Only solution was to pecify --with-ml = 0 in test_optdepens.sh
You can also remove export OMPI_MCA_plm_rsh_agent=sh
, since openmpi
has had a hard dependency on openssh
since 4.1.5-1 and it will be solved in a better way by https://gitlab.archlinux.org/archlinux/packaging/packages/prrte/-/merge_requests/2
Pinned Comments
MartinDiehl commented on 2022-10-06 10:26 (UTC)
@jrohwer
When building PETSc (more specifically, petsc4py), one test (ex100 from ksp) will fail if a previous (major) version is installed. I could not figure out why this happens. The solution would be to build in a clean root (which is a little bit complicated due to dependency on other AUR packages) or simply uninstall the old version before.
Any help to solve this issue is welcomed.