[petsc-dev] Some warning messages.

Tue Jun 28 15:44:47 CDT 2011

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