Compiling manually did the trick. Thanks! —————————————————— Alp Dener
> On Jul 30, 2014, at 9:48 PM, Satish Balay <[email protected]> wrote: > > https://www.alcf.anl.gov/user-guides/compiling-and-linking-faq#how-do-i-compile-and-link-a-shared-library? > > Looks like I need to specify '-Wl,-dy' for the linker to find the shared > library. > > [balay@vestalac1 tutorials]$ make ex2 CFLAGS="-Wl,-dy > -Wl,-rpath,/home/balay/petsc/arch-xl-opt-nopkg/lib" > mpixlc_r -o ex2.o -c -qpic -O3 -qhot=level=0 -qsimd=auto -qmaxmem=-1 -qstrict > -qstrict_induction -Wl,-dy -Wl,-rpath,/home/balay/petsc/arch-xl-opt-nop > kg/lib -I/home/balay/petsc/include > -I/home/balay/petsc/arch-xl-opt-nopkg/include > -I/bgsys/drivers/V1R2M1/ppc64/comm/include -I/bgsys/drivers/V1R2M1/pp > c64/comm/lib/gnu -I/bgsys/drivers/V1R2M1/ppc64 > -I/bgsys/drivers/V1R2M1/ppc64/comm/sys/include > -I/bgsys/drivers/V1R2M1/ppc64/spi/include > -I/bgsys/drivers/V1R2M1/ppc64/spi/include/kernel/cnk `pwd`/ex2.c > mpixlc_r -qpic -O3 -qhot=level=0 -qsimd=auto -qmaxmem=-1 -qstrict > -qstrict_induction -Wl,-dy -Wl,-rpath,/home/balay/petsc/arch-xl-opt-nopkg/lib > -o ex2 ex2.o -L/home/balay/petsc/arch-xl-opt-nopkg/lib -lpetsc > -L/soft/libraries/alcf/current/xl/LAPACK/lib -llapack > -L/soft/libraries/alcf/current/xl/BLAS/lib -lblas -lpthread > -L/bgsys/drivers/V1R2M1/ppc64/comm/lib > -L/bgsys/drivers/V1R2M1/ppc64/comm/lib64 > -L/bgsys/drivers/V1R2M1/ppc64/spi/lib > -L/bgsys/drivers/V1R2M1/ppc64/comm/sys/lib > -L/soft/compilers/ibmcmp-may2014/xlsmp/bg/3.1/bglib64 > -L/soft/compilers/ibmcmp-may2014/xlmass/bg/7.3/bglib64 > -L/soft/compilers/ibmcmp-may2014/vac/bg/12.1/bglib64 > -L/soft/compilers/ibmcmp-may2014/vacpp/bg/12.1/bglib64 > -L/bgsys/drivers/toolchain/V1R2M1_base-efix033/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6 > -L/bgsys/drivers/toolchain/V1R2M1_base-efix033/gnu-linux/lib/gcc > -L/bgsys/drivers/toolchain/V1R2M1_base-efix033/gnu-linux/powerpc64-bgq-linux/lib > -L/soft/compilers/ibmcmp-may2014/xlf/bg/14.1/bglib64 > -Wl,-rpath,/soft/compilers/ibmcmp-may2014/lib64/bg/bglib64 -lmpichf90-gcc > -lxlf90_r -lxlomp_ser -lxlfmath -lm -lmpichcxx-gcc -libmc++ -ldl -lmpich-gcc > -lopa-gcc -lmpl-gcc -lpami-gcc -lSPI -lSPI_cnk -lrt -lpthread -lstdc++ > -lxlopt -lxl -lnss_files -lnss_dns -lresolv -lgcc_eh -ldl > /bin/rm -f ex2.o > [balay@vestalac1 tutorials]$ ldd ex2 > linux-vdso64.so.1 => (0x00000fff8d020000) > libpetsc.so => /home/balay/petsc/arch-xl-opt-nopkg/lib/libpetsc.so > (0x00000fff8bfb0000) > libpthread.so.0 => /lib64/libpthread.so.0 (0x00000fff8bf50000) > libmpichf90-gcc.so.8 => > /bgsys/drivers/ppcfloor/comm/lib/libmpichf90-gcc.so.8 (0x00000fff8be40000) > libxlf90_r.so.1 => > /soft/compilers/ibmcmp-may2014/lib64/bg/bglib64/libxlf90_r.so.1 > (0x00000fff8b7a0000) > libxlomp_ser.so.1 => > /soft/compilers/ibmcmp-may2014/lib64/bg/bglib64/libxlomp_ser.so.1 > (0x00000fff8b690000) > libxlfmath.so.1 => > /soft/compilers/ibmcmp-may2014/lib64/bg/bglib64/libxlfmath.so.1 > (0x00000fff8b580000) > libm.so.6 => /lib64/libm.so.6 (0x00000fff8b480000) > libmpichcxx-gcc.so.8 => > /bgsys/drivers/ppcfloor/comm/lib/libmpichcxx-gcc.so.8 (0x00000fff8b370000) > libibmc++.so.1 => > /soft/compilers/ibmcmp-may2014/lib64/bg/bglib64/libibmc++.so.1 > (0x00000fff8b260000) > libdl.so.2 => /lib64/libdl.so.2 (0x00000fff8b230000) > libmpich-gcc.so.8 => > /bgsys/drivers/ppcfloor/comm/lib/libmpich-gcc.so.8 (0x00000fff8ae90000) > libopa-gcc.so.0 => /bgsys/drivers/ppcfloor/comm/lib/libopa-gcc.so.0 > (0x00000fff8ad80000) > libmpl-gcc.so.1 => /bgsys/drivers/ppcfloor/comm/lib/libmpl-gcc.so.1 > (0x00000fff8ac70000) > libpami-gcc.so => /bgsys/drivers/ppcfloor/comm/lib/libpami-gcc.so > (0x00000fff8a700000) > librt.so.1 => /lib64/librt.so.1 (0x00000fff8a6d0000) > libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000080ea910000) > libnss_files.so.2 => /lib64/libnss_files.so.2 (0x00000fff8a6a0000) > libnss_dns.so.2 => /lib64/libnss_dns.so.2 (0x00000fff8a670000) > libresolv.so.2 => /lib64/libresolv.so.2 (0x00000fff8a630000) > libc.so.6 => /lib64/libc.so.6 (0x00000fff8a440000) > /lib64/bgq/ld64.so.1 => /lib64/ld64.so.1 (0x00000000264e0000) > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000080ea720000) > libgfortran.so.3 => > /bgsys/drivers/toolchain/V1R2M2_base/gnu-linux/powerpc64-bgq-linux/lib/libgfortran.so.3 > (0x00000fff8a220000) > > And I could run this binary successfully.. > > Satish > > On Wed, 30 Jul 2014, Satish Balay wrote: > >> On Wed, 30 Jul 2014, Alp Dener wrote: >> >>> Hi, >>> >>> I’m trying to build PETSc 3.4.5 on an IBM BlueGene/Q at the moment using >>> the XL toolchain. I need to build the PETSc shared library and to >>> accomplish that, I use the following configure options: >>> >>> ./configure \ >>> --with-shared-libraries=1 \ >>> --with-debugging=1 \ >>> --with-fortran-interfaces=1 \ >>> --with-mpi=/bgsys/drivers/ppcfloor/comm \ >>> --with-blas-lib="-L/gpfs/u/software/bgq/lapack/xl/3.5.0/lib -lblas" \ >>> --with-lapack-lib="-L/gpfs/u/software/bgq/lapack/xl/3.5.0/lib -llapack" \ >>> --with-metis-include=/gpfs/u/software/bgq/parmetis/xl/4.0.2/include \ >>> --with-metis-lib="-L/gpfs/u/software/bgq/parmetis/xl/4.0.2/lib -lmetis" \ >>> --with-parmetis-include=/gpfs/u/software/bgq/parmetis/xl/4.0.2/include \ >>> --with-parmetis-lib="-L/gpfs/u/software/bgq/parmetis/xl/4.0.2/lib >>> -lparmetis" \ >>> --download-superlu=/gpfs/u/barn/ODLC/shared/src/PETSc/superlu_4.3.tar.gz >>> \ >>> >>> --download-superlu_dist=/gpfs/u/barn/ODLC/shared/src/PETSc/superlu_dist_3.3.tar.gz >>> \ >>> --prefix=/gpfs/u/barn/ODLC/shared/xl/petsc/3.4.5 \ >>> --PETSC_ARCH=xl-dbg \ >>> FFLAGS="-qextname” >>> >>> Despite specifying the “—with-shared-libraries” option, the configuration >>> report shows “shared libraries : disabled”. The configure log doesn’t >>> appear to contain any warnings or errors about this (or maybe I couldn’t >>> find it). >>> >>> Normally, compiling shared objects with XL compilers require a -qmkshrobj >>> flag. I’ve attempted passing this to PETSc using LDFLAGS but this causes >>> the configuration to fail with an error, stating that it cannot run >>> executables created with the C compiler. >>> >>> This problem seems to be persistent across a number of PETSc versions. I >>> need to use 3.4.5 for compatibility reasons, but I’ve attempted the same >>> build with 3.5, 3.3 and 3.0 with the exact same results. >>> >>> Would really appreciate it if anyone can offer guidance on how to force >>> PETSc to build its shared library. The configure log from the above options >>> is provided in the attachment. >> >> Shared libraries with IBM compilers is something I've not tired. If its just >> a matter >> of using '-qmkshrobj' - you could try to build it manually - and see if it >> works. >> >> [when I try it I get errors.] >> >> Satish >> >> ---------- >> >> [balay@vestalac1 ~]$ cd petsc/arch-xl-opt-nopkg/lib/ >> [balay@vestalac1 lib]$ ar x libpetsc.a >> [balay@vestalac1 lib]$ mpixlc -qmkshrobj -o libpetsc.so *.o >> [balay@vestalac1 lib]$ file libpetsc.so >> libpetsc.so: ELF 64-bit MSB shared object, 64-bit PowerPC or cisco 7500, >> version 1 (SYSV), dynamically linked, not stripped >> [balay@vestalac1 lib]$ mv libpetsc.a libpetsc-bkp.a >> [balay@vestalac1 lib]$ cd $PETSC_DIR >> [balay@vestalac1 petsc]$ cd src/ksp/ksp/examples/tutorials/ >> [balay@vestalac1 tutorials]$ make ex2 >> mpixlc_r -o ex2.o -c -qpic -O3 -qhot=level=0 -qsimd=auto -qmaxmem=-1 >> -qstrict -qstrict_induction -I/home/balay/petsc/include >> -I/home/balay/petsc/arch-xl-opt-nopkg/include >> -I/bgsys/drivers/V1R2M1/ppc64/comm/include >> -I/bgsys/drivers/V1R2M1/ppc64/comm/lib/gnu -I/bgsys/drivers/V1R2M1/ppc64 >> -I/bgsys/drivers/V1R2M1/ppc64/comm/sys/include >> -I/bgsys/drivers/V1R2M1/ppc64/spi/include >> -I/bgsys/drivers/V1R2M1/ppc64/spi/include/kernel/cnk `pwd`/ex2.c >> mpixlc_r -qpic -O3 -qhot=level=0 -qsimd=auto -qmaxmem=-1 -qstrict >> -qstrict_induction -o ex2 ex2.o -L/home/balay/petsc/arch-xl-opt-nopkg/lib >> -lpetsc -L/soft/libraries/alcf/current/xl/LAPACK/lib -llapack >> -L/soft/libraries/alcf/current/xl/BLAS/lib -lblas -lpthread >> -L/bgsys/drivers/V1R2M1/ppc64/comm/lib >> -L/bgsys/drivers/V1R2M1/ppc64/comm/lib64 >> -L/bgsys/drivers/V1R2M1/ppc64/spi/lib >> -L/bgsys/drivers/V1R2M1/ppc64/comm/sys/lib >> -L/soft/compilers/ibmcmp-may2014/xlsmp/bg/3.1/bglib64 >> -L/soft/compilers/ibmcmp-may2014/xlmass/bg/7.3/bglib64 >> -L/soft/compilers/ibmcmp-may2014/vac/bg/12.1/bglib64 >> -L/soft/compilers/ibmcmp-may2014/vacpp/bg/12.1/bglib64 >> -L/bgsys/drivers/toolchain/V1R2M1_base-efix033/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6 >> -L/bgsys/drivers/toolchain/V1R2M1_base-efix033/gnu-linux/lib/gcc >> -L/bgsys/drivers/toolchain/V1R2M1_base-efix033/gnu-linux/powerpc64-bgq-linux/lib >> -L/soft/compilers/ibmcmp-may2014/xlf/bg/14.1/bglib64 >> -Wl,-rpath,/soft/compilers/ibmcmp-may2014/lib64/bg/bglib64 -lmpichf90-gcc >> -lxlf90_r -lxlomp_ser -lxlfmath -lm -lmpichcxx-gcc -libmc++ -ldl -lmpich-gcc >> -lopa-gcc -lmpl-gcc -lpami-gcc -lSPI -lSPI_cnk -lrt -lpthread -lstdc++ >> -lxlopt -lxl -lnss_files -lnss_dns -lresolv -lgcc_eh -ldl >> /bgsys/drivers/ppcfloor/gnu-linux/powerpc64-bgq-linux/bin/ld: cannot find >> -lpetsc >> make: [ex2] Error 1 (ignored) >> /bin/rm -f ex2.o >> [balay@vestalac1 tutorials]$
