[petsc-dev] Some warning messages.

Rebecca Xuefei Yuan xy2102 at columbia.edu
Tue Jun 28 16:06:03 CDT 2011 

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

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