On Sat, 25 Jun 2016, Antonio Trande wrote: > On 06/25/2016 09:41 PM, Antonio Trande wrote: > > On 06/25/2016 03:59 PM, Matthew Knepley wrote: > >> On Sat, Jun 25, 2016 at 8:21 AM, Antonio Trande <[email protected] > >> <mailto:[email protected]>> wrote: > >> > >> Hi all, > >> > >> is it possible to compile serial PETSc library ? > >> I'm trying to compile PETSc without MPI by configuring with options: > >> > >> --with-mpi=0 --with-mpiuni-fortran-binding=0 > >> > >> but compiler uses -I/.../petsc-3.7.2/include/petsc/mpiuni flag anyway > >> and libpetsc.so contains an "undefined symbol": > >> > >> undefined symbol: mpi_init_ (/usr/lib64/libpetsc.so.3.7.2) > >> > >> How I can fix this issue ? > >> Full log: > >> > >> https://copr-be.cloud.fedoraproject.org/results/sagitter/petsc/fedora-24-x86_64/00362302-petsc/build.log.gz > >> > >> > >> 1) Why are you giving --with-mpiuni-fortran-binding=0 if you still have > >> Fortran turned on? If you want to turn off Fortran, use --with-fc=0. > > > > I did't know what it does. If I active --with-mpiuni-fortran-binding, > > 'undefined symbol' disappears. > > > >> > >> 2) You did not send configure.log which is what I need, not a screen > >> capture. > >> > >> 3) I cannot see the error you sent anywhere. It would be more useful to > >> send the output from 'make test'. > >> > >> Matt > >> > >> > > > > I send you all config.log; petsc-serial, petsc-serial (64bit integer), > > petsc-openmpi and petsc-mpich are compiled from an own fresh source > > directory, respectively from petsc-3.7.2, build64, buildopenmpi_dir, > > buildmpich_dir. > > > > All libraries look compiled fine and related test passed. > > I will send you latest builds log from Fedora Copr build-system. > > > > No, tests not passed with > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > This is a build log from Fedora 24 64 bit: > https://copr-be.cloud.fedoraproject.org/results/sagitter/petsc/fedora-24-x86_64/00362535-petsc/build.log.gz
>>>>>>>> + echo 'Patch #1 (petsc-lib64.patch):' + /usr/bin/patch -p0 --fuzz=0 patching file config/BuildSystem/config/setCompilers.py patching file gmakefile Patch #0 (petsc-3.7-no-rpath.patch): + /usr/bin/patch -p0 --fuzz=0 patching file config/BuildSystem/config/setCompilers.py <<<<<<<<<<< Well looks like there were some modifications done to get the 'multi-variant' build working. >>>>>>>>>> + make test -C petsc-3.7.2 make: Entering directory '/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2' Running test examples to verify correct installation Using PETSC_DIR=/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2 and PETSC_ARCH=x86_64 *******************Error detected during compile or link!******************* See http://www.mcs.anl.gov/petsc/documentation/faq.html /builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/src/snes/examples/tutorials ex19 ********************************************************************************* gcc -o ex19.o -c -O2 -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fopenmp -I/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/include -I/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/x86_64/include -I/usr/include -I/usr/include/suitesparse -I/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/include/petsc/mpiuni `pwd`/ex19.c gcc -Wl,-z,relro -O2 -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fopenmp -o ex19 ex19.o -L/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/x86_64/lib -L/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/x86_64/lib -lpetsc -lmetis -L/usr/lib64 -lumfpack -lklu -lcholmod -lbtf -lccolamd -lcolamd -lcamd -lamd -lsuitesparseconfig -llapack -lblas -lOpenCL -lhwloc -lpapi -lgmp -lpthread -ljpeg -lpng -lm -L/usr/lib/gcc/x86_64-redhat-linux/6.1.1 -lgfortran -lm -lgfortran -lm -lquadmath -lm -lstdc++ -L/usr/lib/gcc/x86_64-redhat-linux/6.1.1 -ldl -lgcc_s -ldl /usr/bin/rm -f ex19.o Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI process See http://www.mcs.anl.gov/petsc/documentation/faq.html [0]PETSC ERROR: #1 PetscLogInitialize() line 219 in /builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/src/sys/logging/plog.c [0]PETSC ERROR: #2 PetscInitialize() line 891 in /builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/src/sys/objects/pinit.c /usr/bin/sh: line 13: 16933 Aborted (core dumped) <<<<<<<<<< So there is no -rpath here. Which -lpetsc variant is getting used at runtime? Satish
