[petsc-users] make error on cluster

[Matthew Knepley]

On Fri, Nov 25, 2022 at 11:49 PM Sijie Zhang <zhan2355 at purdue.edu> wrote:

> Hi,
>
>
>
> When I try to install petsc, I got the following error. Can you help me
> with that?
>

This is an issue with your MPI, which I am guessing was installed by the
admin. I would send them this output.
However, I did find a suggestion on StackExchange:


https://stackoverflow.com/questions/45910849/shmget-operation-not-permitted

   Thanks,

     Matt


>
>
> Thanks.
>
>
>
> Sijie
>
>
>
>
> ================================================================================================
>
>
>
> Running check examples to verify correct installation
>
> Using PETSC_DIR=/home/tools/a/zhan2355/petsc-3.18.1 and
> PETSC_ARCH=arch-linux-c-debug
>
> *******************Error detected during compile or
> link!*******************
>
> See https://petsc.org/release/faq/
>
> /home/tools/a/zhan2355/petsc-3.18.1/src/snes/tutorials ex19
>
>
> *********************************************************************************
>
> mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas
> -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -g3 -O0
> -I/home/tools/a/zhan2355/petsc-3.18.1/include
> -I/home/tools/a/zhan2355/petsc-3.18.1/arch-linux-c-debug/include
> -export-dynamic ex19.c
> -Wl,-rpath,/home/tools/a/zhan2355/petsc-3.18.1/arch-linux-c-debug/lib
> -L/home/tools/a/zhan2355/petsc-3.18.1/arch-linux-c-debug/lib
> -Wl,-rpath,/usr/lib64/openmpi3/lib -L/usr/lib64/openmpi3/lib
> -Wl,-rpath,/package/gcc/8.3.0/lib/gcc/x86_64-pc-linux-gnu/8.3.0
> -L/package/gcc/8.3.0/lib/gcc/x86_64-pc-linux-gnu/8.3.0
> -Wl,-rpath,/package/gcc/8.3.0/lib/gcc -L/package/gcc/8.3.0/lib/gcc
> -Wl,-rpath,/package/gcc/8.3.0/lib64 -L/package/gcc/8.3.0/lib64
> -Wl,-rpath,/package/gcc/8.3.0/lib -L/package/gcc/8.3.0/lib -lpetsc -llapack
> -lblas -lm -lX11 -lstdc++ -ldl -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran
> -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl -o
> ex19
>
> /usr/bin/ld: warning: libgfortran.so.3, needed by
> /lib/../lib64/liblapack.so, may conflict with libgfortran.so.5
>
> /usr/bin/ld: warning: libgfortran.so.3, needed by
> /lib/../lib64/liblapack.so, may conflict with libgfortran.so.5
>
> Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process
>
> See https://petsc.org/release/faq/
>
> [1669441660.650232] [nut:40436:0]            sys.c:618  UCX  ERROR
> shmget(size=2097152 flags=0xfb0) for mm_recv_desc failed: Operation not
> permitted, please check shared memory limits by 'ipcs -l'
>
> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
>
> Number of SNES iterations = 2
>
> Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes
>
> See https://petsc.org/release/faq/
>
> [1669441661.708168] [nut:40467:0]            sys.c:618  UCX  ERROR
> shmget(size=2097152 flags=0xfb0) for mm_recv_desc failed: Operation not
> permitted, please check shared memory limits by 'ipcs -l'
>
> [1669441661.713950] [nut:40466:0]            sys.c:618  UCX  ERROR
> shmget(size=2097152 flags=0xfb0) for mm_recv_desc failed: Operation not
> permitted, please check shared memory limits by 'ipcs -l'
>
> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
>
> Number of SNES iterations = 2
>
> *******************Error detected during compile or
> link!*******************
>
> See https://petsc.org/release/faq/
>
> /home/tools/a/zhan2355/petsc-3.18.1/src/snes/tutorials ex5f
>
> *********************************************************
>
> mpif90 -fPIC -Wall -ffree-line-length-none -ffree-line-length-0
> -Wno-lto-type-mismatch -Wno-unused-dummy-argument -g -O0
> -I/home/tools/a/zhan2355/petsc-3.18.1/include
> -I/home/tools/a/zhan2355/petsc-3.18.1/arch-linux-c-debug/include
> ex5f.F90
> -Wl,-rpath,/home/tools/a/zhan2355/petsc-3.18.1/arch-linux-c-debug/lib
> -L/home/tools/a/zhan2355/petsc-3.18.1/arch-linux-c-debug/lib
> -Wl,-rpath,/usr/lib64/openmpi3/lib -L/usr/lib64/openmpi3/lib
> -Wl,-rpath,/package/gcc/8.3.0/lib/gcc/x86_64-pc-linux-gnu/8.3.0
> -L/package/gcc/8.3.0/lib/gcc/x86_64-pc-linux-gnu/8.3.0
> -Wl,-rpath,/package/gcc/8.3.0/lib/gcc -L/package/gcc/8.3.0/lib/gcc
> -Wl,-rpath,/package/gcc/8.3.0/lib64 -L/package/gcc/8.3.0/lib64
> -Wl,-rpath,/package/gcc/8.3.0/lib -L/package/gcc/8.3.0/lib -lpetsc -llapack
> -lblas -lm -lX11 -lstdc++ -ldl -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran
> -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl -o
> ex5f
>
> /usr/bin/ld: warning: libgfortran.so.3, needed by
> /lib/../lib64/liblapack.so, may conflict with libgfortran.so.5
>
> /usr/bin/ld: warning: libgfortran.so.3, needed by
> /lib/../lib64/liblapack.so, may conflict with libgfortran.so.5
>
> /usr/bin/ld: warning: libgfortran.so.3, needed by
> /lib/../lib64/liblapack.so, may conflict with libgfortran.so.5
>
> /usr/bin/ld: warning: libgfortran.so.3, needed by
> /lib/../lib64/liblapack.so, may conflict with libgfortran.so.5
>
> Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI
> process
>
> See https://petsc.org/release/faq/
>
> [1669441665.341407] [nut:40669:0]            sys.c:618  UCX  ERROR
> shmget(size=2097152 flags=0xfb0) for mm_recv_desc failed: Operation not
> permitted, please check shared memory limits by 'ipcs -l'
>
> Number of SNES iterations =     3
>
> Completed test examples
>
> Error while running make check
>
> make[1]: *** [check] Error 1
>
> make: *** [check] Error 2
>


-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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