[petsc-dev] Some warning messages.

[Satish Balay]

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
> 
> 
> 
> 
> 
>