On 06/26/2016 02:24 AM, Satish Balay wrote: > 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.
Yes. > >>>>>>>>>>> > + 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? > Yes, no rpaths for the serial libraries, so 'libpetsc.so' and 'libpetsc64.so' (renamed for mine needs). Test reported is for PETSc (32 bit integer) serial library: libpetsc.so -- --- Antonio Trande mailto: sagitter 'at' fedoraproject 'dot' org http://fedoraos.wordpress.com/ https://fedoraproject.org/wiki/User:Sagitter GPG Key: 0x6CE6D08A Check on https://keys.fedoraproject.org/
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