[petsc-users] make error on cluster

[Sijie Zhang]

Hi,

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

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
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