The next thing to try is removing '-mp'. The next step is adding '-g'. But this is really a compiler issue - so perhaps the NERSC admins can help with figuring this out..
Satish On Tue, 28 Jun 2011, Rebecca Xuefei Yuan wrote: > Hello Satish, > > I am sorry that I misunderstand that... > > I did remove -fast and past the rest to rerun it, however, it still halts... > > I do not have problem making this code with petsc/3.1. > > Thanks very much! > > Best, > > Rebecca > > > > > Quoting Satish Balay <balay at mcs.anl.gov>: > > > I meant copy/paste/modify what you see on screen: > > > > i.e You see: > > > > cc -o pcmhd1qsd3.o -c -fast -mp > > -I/global/u2/x/xyuan/Software_HOPPER/petsc-dev/include > > -I/global/u2/x/xyuan/Software_HOPPER/petsc-dev/arch-cray-xt6-pkgs-opt/include > > -I/opt/cray/udreg/2.2-1.0301.2966.16.2.gem/include > > -I/opt/cray/ugni/2.1-1.0301.2967.10.23.gem/include > > -I/opt/cray/pmi/2.1.1-1.0000.8296.10.8.gem/include > > -I/opt/cray/dmapp/3.0-1.0301.2968.22.24.gem/include > > -I/opt/cray/xpmem/0.1-2.0301.25333.20.2.gem/include > > -I/opt/cray/mpt/5.2.1/xt/gemini/mpich2-pgi/include > > -I/opt/cray/mpt/5.2.1/xt/gemini/sma/include > > -I/opt/xt-libsci/10.5.01/pgi/include -I/usr/include/alps > > -I/opt/pgi/11.2.0/linux86-64/11.2/include > > -I/opt/cray/xe-sysroot/3.1.61.securitypatch.20110308/usr/include > > -D__INSDIR__= > > pcmhd1qsd3.c > > > > > > So you would copy/paste this on to bash - and modify as follows - and run > > it.. > > [instead of running make] > > > > cc -o pcmhd1qsd3.o -c -mp > > -I/global/u2/x/xyuan/Software_HOPPER/petsc-dev/include > > -I/global/u2/x/xyuan/Software_HOPPER/petsc-dev/arch-cray-xt6-pkgs-opt/include > > -I/opt/cray/udreg/2.2-1.0301.2966.16.2.gem/include > > -I/opt/cray/ugni/2.1-1.0301.2967.10.23.gem/include > > -I/opt/cray/pmi/2.1.1-1.0000.8296.10.8.gem/include > > -I/opt/cray/dmapp/3.0-1.0301.2968.22.24.gem/include > > -I/opt/cray/xpmem/0.1-2.0301.25333.20.2.gem/include > > -I/opt/cray/mpt/5.2.1/xt/gemini/mpich2-pgi/include > > -I/opt/cray/mpt/5.2.1/xt/gemini/sma/include > > -I/opt/xt-libsci/10.5.01/pgi/include -I/usr/include/alps > > -I/opt/pgi/11.2.0/linux86-64/11.2/include > > -I/opt/cray/xe-sysroot/3.1.61.securitypatch.20110308/usr/include > > -D__INSDIR__= > > pcmhd1qsd3.c > > > > This is just to debug the reason for the hang you are encountering > > when compling this sourcefile. > > > > Satish > > > > On Tue, 28 Jun 2011, Rebecca Xuefei Yuan wrote: > > > > > Dear Satish, > > > > > > Thanks very much for your kind reply. > > > > > > I have my makefile : > > > > > > ------------------------------------------- > > > PETSC_ARCH = arch-cray-xt6-pkgs-opt > > > include ${PETSC_DIR}/conf/variables > > > include ${PETSC_DIR}/conf/rules > > > include ${PETSC_DIR}/conf/test > > > > > > CLINKER = cc > > > > > > pcmhd1qsd3: pcmhd1qsd3.o chkopts > > > -${CLINKER} -v -o pcmhd1qsd3.exe pcmhd1qsd3.o ${PETSC_SNES_LIB} > > > -lpgf90rtl > > > > > > ------------------------------------------- > > > > > > Which option indicates for -fast? > > > > > > I am not sure I understand the way this makefile do. > > > > > > For example, if I have "module load petsc" on Hopper, I only need to do > > > > > > cc -o hello.exe hello.c > > > > > > to complete the make, but as I would like to use local petsc-dev, I use > > > the > > > above makefile. Is this a right way to do so? > > > > > > Thanks very much! > > > > > > Rebecca > > > > > > > > > > > > Quoting Satish Balay <balay at mcs.anl.gov>: > > > > > > > On Tue, 28 Jun 2011, Rebecca Xuefei Yuan wrote: > > > > > > > > > Hello all, > > > > > > > > > > I have installed petsc-dev on Hopper, and when I try to run examples, > > > > I > > > > > found > > > > > there are some warning messages during make, shall I ignore them? > > > > > > > > > > newcouple/trunk> make ex19 > > > > > cc -o ex19.o -c -fast -mp > > > > > -I/global/u2/x/xyuan/Software_HOPPER/petsc-dev/include > > > > > > > > > -I/global/u2/x/xyuan/Software_HOPPER/petsc-dev/arch-cray-xt6-pkgs-opt/include > > > > > -I/opt/cray/udreg/2.2-1.0301.2966.16.2.gem/include > > > > > -I/opt/cray/ugni/2.1-1.0301.2967.10.23.gem/include > > > > > -I/opt/cray/pmi/2.1.1-1.0000.8296.10.8.gem/include > > > > > -I/opt/cray/dmapp/3.0-1.0301.2968.22.24.gem/include > > > > > -I/opt/cray/xpmem/0.1-2.0301.25333.20.2.gem/include > > > > > -I/opt/cray/mpt/5.2.1/xt/gemini/mpich2-pgi/include > > > > > -I/opt/cray/mpt/5.2.1/xt/gemini/sma/include > > > > > -I/opt/xt-libsci/10.5.01/pgi/include -I/usr/include/alps > > > > > -I/opt/pgi/11.2.0/linux86-64/11.2/include > > > > > -I/opt/cray/xe-sysroot/3.1.61.securitypatch.20110308/usr/include > > > > > -D__INSDIR__= > > > > > ex19.c > > > > > cc -v -o ex19.exe ex19.o > > > > > > > > > -L/global/u2/x/xyuan/Software_HOPPER/petsc-dev/arch-cray-xt6-pkgs-opt/lib > > > > > -lpetsc > > > > > > > > > -Wl,-rpath,/global/u2/x/xyuan/Software_HOPPER/petsc-dev/arch-cray-xt6-pkgs-opt/lib > > > > > -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord > > > > > -lsuperlu_dist_2.5 > > > > > -lparmetis -lmetis -L/opt/acml/4.4.0/pgi64/lib -lacml -lacml_mv -ldl > > > > > /opt/cray/xt-asyncpe/4.9/bin/cc: INFO: Compiling for compute nodes > > > > running > > > > > CLE. > > > > > > > > > > /usr/bin/ld /usr/lib64/crt1.o /usr/lib64/crti.o > > > > > /opt/pgi/11.2.0/linux86-64/11.2/lib/trace_init.o > > > > > /usr/lib64/gcc/x86_64-suse-linux/4.3/crtbeginT.o > > > > > /opt/pgi/11.2.0/linux86-64/11.2/lib/initmp.o -m elf_x86_64 > > > > -dynamic-linker > > > > > /lib64/ld-linux-x86-64.so.2 /opt/pgi/11.2.0/linux86-64/11.2/lib/pgi.ld > > > > > > > > > -L/global/u2/x/xyuan/Software_HOPPER/petsc-dev/arch-cray-xt6-pkgs-opt/lib > > > > > -L/opt/acml/4.4.0/pgi64/lib > > > > > -L/opt/cray/udreg/2.2-1.0301.2966.16.2.gem/lib64 > > > > > -L/opt/cray/ugni/2.1-1.0301.2967.10.23.gem/lib64 > > > > > -L/opt/cray/pmi/2.1.1-1.0000.8296.10.8.gem/lib64 > > > > > -L/opt/cray/dmapp/3.0-1.0301.2968.22.24.gem/lib64 > > > > > -L/opt/cray/xpmem/0.1-2.0301.25333.20.2.gem/lib64 > > > > > -L/opt/cray/mpt/5.2.1/xt/gemini/mpich2-pgi/lib > > > > > -L/opt/cray/mpt/5.2.1/xt/gemini/sma/lib64 > > > > -L/opt/xt-libsci/10.5.01/pgi/lib > > > > > -L/opt/cray/portals/default/lib64 > > > > > -L/opt/cray/xe-sysroot/3.1.61.securitypatch.20110308/usr/lib64 > > > > > -L/opt/cray/xe-sysroot/3.1.61.securitypatch.20110308/lib64 > > > > > -L/opt/cray/xe-sysroot/3.1.61.securitypatch.20110308/usr/lib/alps > > > > > -L/usr/lib/alps -L/opt/pgi/11.2.0/linux86-64/11.2/lib -L/usr/lib64 > > > > > -L/usr/lib64/gcc/x86_64-suse-linux/4.3 -Bstatic ex19.o -lpetsc -rpath > > > > > > > > > /global/u2/x/xyuan/Software_HOPPER/petsc-dev/arch-cray-xt6-pkgs-opt/lib > > > > > -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord > > > > > -lsuperlu_dist_2.5 > > > > > -lparmetis -lmetis -lacml -lacml_mv -ldl > > > > > -rpath=/opt/cray/udreg/2.2-1.0301.2966.16.2.gem/lib64 > > > > > -rpath=/opt/cray/ugni/2.1-1.0301.2967.10.23.gem/lib64 > > > > > -rpath=/opt/cray/pmi/2.1.1-1.0000.8296.10.8.gem/lib64 > > > > > -rpath=/opt/cray/dmapp/3.0-1.0301.2968.22.24.gem/lib64 > > > > > -rpath=/opt/cray/xpmem/0.1-2.0301.25333.20.2.gem/lib64 > > > > > /opt/cray/atp/1.1.2/lib/atpSigHandler.o > > > > --undefined=__atpHandlerInstall > > > > > -rpath=/opt/cray/mpt/5.2.1/xt/gemini/mpich2-pgi/lib > > > > > -rpath=/opt/cray/mpt/5.2.1/xt/gemini/sma/lib64 > > > > > -rpath=/opt/xt-libsci/10.5.01/pgi/lib > > > > > -rpath=/opt/xt-libsci/default/pgi/lib > > > > > -rpath=/opt/cray/portals/default/lib64 -rpath=/usr/lib/alps > > > > --start-group > > > > > -lscicpp -lstdc++ -lsci_mc12_mp -lmpich -lmpl -lsma -lxpmem -ldmapp > > > > -lugni > > > > > -lpmi -lalpslli -lalpsutil -ludreg -lpthread --end-group -rpath > > > > > /opt/pgi/11.2.0/linux86-64/11.2/lib -o ex19.exe > > > > > /opt/pgi/11.2.0/linux86-64/11.2/lib/nonuma.o -lpgmp -Bdynamic -Bstatic > > > > > -lpthread -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc > > > > > -lpgc > > > > > -lrt -lpthread -lm -lgcc -lgcc_eh -lc -lgcc -lgcc_eh -lc > > > > > /usr/lib64/gcc/x86_64-suse-linux/4.3/crtend.o /usr/lib64/crtn.o > > > > > > > > > /global/u2/x/xyuan/Software_HOPPER/petsc-dev/arch-cray-xt6-pkgs-opt/lib/libpetsc.a(fuser.o): > > > > > In function `PetscGetUserName': > > > > > > > > > /global/u2/x/xyuan/Software_HOPPER/petsc-dev/src/sys/utils/./fuser.c:61: > > > > > warning: Using 'getpwuid' in statically linked applications requires > > > > at > > > > > runtime the shared libraries from the glibc version used for linking > > > > > > > > > /global/u2/x/xyuan/Software_HOPPER/petsc-dev/arch-cray-xt6-pkgs-opt/lib/libpetsc.a(send.o): > > > > > In function `PetscOpenSocket': > > > > > > > > > /global/u2/x/xyuan/Software_HOPPER/petsc-dev/src/sys/viewer/impls/socket/./send.c:98: > > > > > warning: Using 'gethostbyname' in statically linked applications > > > > requires > > > > > at > > > > > runtime the shared libraries from the glibc version used for linking > > > > > > > > yes you can ignore these message. > > > > > > > > > > > > > > > > > > > Moreover, when I try to make my new code (on Hopper), it halts > > > > without any > > > > > messages, like the screen freeze as > > > > > > > > > > newcouple/trunk> make pcmhd1qsd3 > > > > > cc -o pcmhd1qsd3.o -c -fast -mp > > > > > -I/global/u2/x/xyuan/Software_HOPPER/petsc-dev/include > > > > > > > > > -I/global/u2/x/xyuan/Software_HOPPER/petsc-dev/arch-cray-xt6-pkgs-opt/include > > > > > -I/opt/cray/udreg/2.2-1.0301.2966.16.2.gem/include > > > > > -I/opt/cray/ugni/2.1-1.0301.2967.10.23.gem/include > > > > > -I/opt/cray/pmi/2.1.1-1.0000.8296.10.8.gem/include > > > > > -I/opt/cray/dmapp/3.0-1.0301.2968.22.24.gem/include > > > > > -I/opt/cray/xpmem/0.1-2.0301.25333.20.2.gem/include > > > > > -I/opt/cray/mpt/5.2.1/xt/gemini/mpich2-pgi/include > > > > > -I/opt/cray/mpt/5.2.1/xt/gemini/sma/include > > > > > -I/opt/xt-libsci/10.5.01/pgi/include -I/usr/include/alps > > > > > -I/opt/pgi/11.2.0/linux86-64/11.2/include > > > > > -I/opt/cray/xe-sysroot/3.1.61.securitypatch.20110308/usr/include > > > > > -D__INSDIR__= > > > > > pcmhd1qsd3.c > > > > > > > > > > > > > > > Any suggestions why this happens? > > > > > > > > I guess the optimizer is taking forever. You can try compiling this > > > > code without -fast and see if it completes. i.e manually copy/paste > > > > the compile command and modify.. > > > > > > > > Satish > > > > > > > > > > > > > > Thanks very much! > > > > > > > > > > Rebecca > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Rebecca Xuefei YUAN > > > Department of Applied Physics and Applied Mathematics > > > Columbia University > > > Tel:917-399-8032 > > > www.columbia.edu/~xy2102 > > > > > > > > > > > > > Rebecca Xuefei YUAN > Department of Applied Physics and Applied Mathematics > Columbia University > Tel:917-399-8032 > www.columbia.edu/~xy2102 >