<div dir="ltr"><div dir="ltr">On Fri, Nov 25, 2022 at 11:49 PM Sijie Zhang <<a href="mailto:zhan2355@purdue.edu">zhan2355@purdue.edu</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg8394480161216283128">
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<p class="MsoNormal">Hi,</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">When I try to install petsc, I got the following error. Can you help me with that?</p></div></div></div></blockquote><div><br></div><div>This is an issue with your MPI, which I am guessing was installed by the admin. I would send them this output.</div><div>However, I did find a suggestion on StackExchange:</div><div><br></div><div> <a href="https://stackoverflow.com/questions/45910849/shmget-operation-not-permitted">https://stackoverflow.com/questions/45910849/shmget-operation-not-permitted</a></div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg8394480161216283128"><div lang="EN-US" style="overflow-wrap: break-word;"><div class="m_8394480161216283128WordSection1"><p class="MsoNormal"> </p><p class="MsoNormal"><u></u></p>
<p class="MsoNormal">Thanks.</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Sijie</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">================================================================================================</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Running check examples to verify correct installation</p>
<p class="MsoNormal">Using PETSC_DIR=/home/tools/a/zhan2355/petsc-3.18.1 and PETSC_ARCH=arch-linux-c-debug</p>
<p class="MsoNormal">*******************Error detected during compile or link!*******************</p>
<p class="MsoNormal">See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a></p>
<p class="MsoNormal">/home/tools/a/zhan2355/petsc-3.18.1/src/snes/tutorials ex19</p>
<p class="MsoNormal">*********************************************************************************</p>
<p class="MsoNormal">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</p>
<p class="MsoNormal">/usr/bin/ld: warning: libgfortran.so.3, needed by /lib/../lib64/liblapack.so, may conflict with libgfortran.so.5</p>
<p class="MsoNormal">/usr/bin/ld: warning: libgfortran.so.3, needed by /lib/../lib64/liblapack.so, may conflict with libgfortran.so.5</p>
<p class="MsoNormal">Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process</p>
<p class="MsoNormal">See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a></p>
<p class="MsoNormal">[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'</p>
<p class="MsoNormal">lid velocity = 0.0016, prandtl # = 1., grashof # = 1.</p>
<p class="MsoNormal">Number of SNES iterations = 2</p>
<p class="MsoNormal">Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes</p>
<p class="MsoNormal">See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a></p>
<p class="MsoNormal">[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'</p>
<p class="MsoNormal">[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'</p>
<p class="MsoNormal">lid velocity = 0.0016, prandtl # = 1., grashof # = 1.</p>
<p class="MsoNormal">Number of SNES iterations = 2</p>
<p class="MsoNormal">*******************Error detected during compile or link!*******************</p>
<p class="MsoNormal">See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a></p>
<p class="MsoNormal">/home/tools/a/zhan2355/petsc-3.18.1/src/snes/tutorials ex5f</p>
<p class="MsoNormal">*********************************************************</p>
<p class="MsoNormal">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</p>
<p class="MsoNormal">/usr/bin/ld: warning: libgfortran.so.3, needed by /lib/../lib64/liblapack.so, may conflict with libgfortran.so.5</p>
<p class="MsoNormal">/usr/bin/ld: warning: libgfortran.so.3, needed by /lib/../lib64/liblapack.so, may conflict with libgfortran.so.5</p>
<p class="MsoNormal">/usr/bin/ld: warning: libgfortran.so.3, needed by /lib/../lib64/liblapack.so, may conflict with libgfortran.so.5</p>
<p class="MsoNormal">/usr/bin/ld: warning: libgfortran.so.3, needed by /lib/../lib64/liblapack.so, may conflict with libgfortran.so.5</p>
<p class="MsoNormal">Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process</p>
<p class="MsoNormal">See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a></p>
<p class="MsoNormal">[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'</p>
<p class="MsoNormal">Number of SNES iterations = 3</p>
<p class="MsoNormal">Completed test examples</p>
<p class="MsoNormal">Error while running make check</p>
<p class="MsoNormal">make[1]: *** [check] Error 1</p>
<p class="MsoNormal">make: *** [check] Error 2</p>
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</div></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>