[petsc-dev] Some warning messages.

Tue Jun 28 16:09:30 CDT 2011

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
> 