[Nek5000-users] turbJet compiling problem

Fri Oct 18 10:43:03 CDT 2013

Hi,

the turbJet example is one of the larger examples included, with 9372
elements.  The SIZE file is set to just under 1200 elements per processor,
to be run on 8 processes in total.

The "relocation truncated to fit: R_X86_64_PC32" errors all point to there
not being enough memory available to allocate for the executable.

You can try lowering the SIZE parameter, lelt.  This is the number of
elements per process, so be sure that you increase the number of mpi
processes you run on accordingly.

Katie

On Fri, Oct 18, 2013 at 10:00 AM, <nek5000-users at lists.mcs.anl.gov> wrote:

> Hi,
>
> What's inherently different with this example turbJet and most of the
> other's (they compiled correctly)?.
>
> Anyways, that's what I got after turning off MPI (IFMPI="false"):
>
> cc -c -Ktrap=fp -mcmodel=medium -O2 -DPTRSIZE8 -DLONGINT8 -DUNDERSCORE
> -DGLOBAL_LONG_LONG  -DPREFIX=jl_ /work/alexf/nek5_svn/trunk/nek/jl/xxt.c -o
> obj/jl_xxt.o
> cc -c -Ktrap=fp -mcmodel=medium -O2 -DPTRSIZE8 -DLONGINT8 -DUNDERSCORE
> -DGLOBAL_LONG_LONG  -DPREFIX=jl_ /work/alexf/nek5_svn/trunk/nek/jl/fcrs.c
> -o obj/jl_fcrs.o
> ftn -c -Ktrap=fp -mcmodel=medium -O2 -r8 -Mpreprocess -DPTRSIZE8
> -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG
> -I/work/alexf/nek_examples/turbJet -I/work/alexf/nek5_svn/trunk/nek -I./
> /work/alexf/nek_examples/turbJet/jet.f    -o obj/jet.o
> ftn -o nek5000 -Ktrap=fp -mcmodel=medium obj/jet.o obj/drive.o
> obj/drive1.o obj/drive2.o obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o
> obj/connect1.o obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o
> obj/gauss.o obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o
> obj/navier2.o obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o
> obj/map2.o obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o
> obj/math.o obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o
> obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o
> obj/hsmg.o obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o
> obj/navier6.o obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o
> obj/calcz.o obj/byte.o obj/chelpers.o obj/byte_mpi.o obj/postpro.o
> obj/cvode_driver.o obj/nek_comm.o obj/init_plugin.o obj/setprop.o
> obj/qthermal.o obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o
> obj/dsygv.o obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/comm_mpi.o
> obj/mpi_dummy.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o
> obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o
> obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o
> obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o
> obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o
> obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o
> /usr/lib64/libpthread.a(ptw-close.o): In function `close':
> /usr/src/packages/BUILD/glibc-2.11.1/nptl/../sysdeps/unix/syscall-template.S:82:
> relocation truncated to fit: R_X86_64_PC32 against symbol
> `__pthread_multiple_threads' defined in COMMON section in
> /usr/lib64/libpthread.a(vars.o)
> /usr/lib64/libpthread.a(ptw-open.o): In function `open64':
> /usr/src/packages/BUILD/glibc-2.11.1/nptl/../sysdeps/unix/syscall-template.S:82:
> relocation truncated to fit: R_X86_64_PC32 against symbol
> `__pthread_multiple_threads' defined in COMMON section in
> /usr/lib64/libpthread.a(vars.o)
> /usr/lib64/libpthread.a(pthread_create.o): In function `__nptl_setxid':
> /usr/src/packages/BUILD/glibc-2.11.1/nptl/allocatestack.c:1066: relocation
> truncated to fit: R_X86_64_PC32 against symbol `__xidcmd' defined in COMMON
> section in /usr/lib64/libpthread.a(nptl-init.o)
> /usr/lib64/libpthread.a(pthread_create.o): In function `allocate_stack':
> /usr/src/packages/BUILD/glibc-2.11.1/nptl/allocatestack.c:462: relocation
> truncated to fit: R_X86_64_PC32 against symbol `__static_tls_align_m1'
> defined in COMMON section in /usr/lib64/libpthread.a(nptl-init.o)
> /usr/src/packages/BUILD/glibc-2.11.1/nptl/allocatestack.c:468: relocation
> truncated to fit: R_X86_64_PC32 against symbol `__static_tls_size' defined
> in COMMON section in /usr/lib64/libpthread.a(nptl-init.o)
> /usr/src/packages/BUILD/glibc-2.11.1/nptl/allocatestack.c:549: relocation
> truncated to fit: R_X86_64_PC32 against symbol
> `__libc_multiple_threads_ptr' defined in COMMON section in
> /usr/lib64/libpthread.a(pthread_create.o)
> /usr/src/packages/BUILD/glibc-2.11.1/nptl/allocatestack.c:549: relocation
> truncated to fit: R_X86_64_PC32 against symbol `__pthread_multiple_threads'
> defined in COMMON section in /usr/lib64/libpthread.a(vars.o)
> /usr/src/packages/BUILD/glibc-2.11.1/nptl/allocatestack.c:715: relocation
> truncated to fit: R_X86_64_PC32 against symbol `__static_tls_size' defined
> in COMMON section in /usr/lib64/libpthread.a(nptl-init.o)
> /usr/src/packages/BUILD/glibc-2.11.1/nptl/allocatestack.c:362: relocation
> truncated to fit: R_X86_64_PC32 against symbol `__static_tls_size' defined
> in COMMON section in /usr/lib64/libpthread.a(nptl-init.o)
> /usr/src/packages/BUILD/glibc-2.11.1/nptl/allocatestack.c:368: relocation
> truncated to fit: R_X86_64_PC32 against symbol `__static_tls_align_m1'
> defined in COMMON section in /usr/lib64/libpthread.a(nptl-init.o)
> /usr/src/packages/BUILD/glibc-2.11.1/nptl/allocatestack.c:407: additional
> relocation overflows omitted from the output
> make: *** [nek5000] Error 2
>
> And this is the relevant part of my makenek file:
>
> nk/nek/mpi_dummy.f -o obj/mpi_dummy.o
> ftn -c -Ktrap=fp -mcmodel=medium -O2 -r8 -Mpreprocess -DPTRSIZE8
> -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG
> -I/work/alexf/nek_examples/turbJet -I/work/alexf/nek5_svn/trunk/nek -I./
> /work/alexf/nek5_svn/trunk/nek/singlmesh.f -o obj/singlmesh.o
> #!/bin/bash
> # Nek5000 build config file
> # (c) 2008,2009,2010 UCHICAGO ARGONNE, LLC
>
> # source path
> SOURCE_ROOT="/work/alexf/nek5_svn/trunk/nek"
>
> # Fortran compiler
> F77="ftn"
>
> # C compiler
> CC="cc"
>
> # pre-processor symbol list
> # (set PPLIST=? to get a list of available symbols)
> #PPLIST="?"
>
> # plug-in list
> PLUGIN_LIST=""
>
>
> # OPTIONAL SETTINGS
> # -----------------
>
> # enable MPI (default true)
> IFMPI="false"
>
> # auxilliary files to compile
> # NOTE: source files have to located in the same directory as makenek
> #       a makefile_usr.inc has to be provided containing the build rules
> #USR="foo.o"
>
> # linking flags
> #USR_LFLAGS="-L/usr/lib -lfoo"
>
>
> # generic compiler flags
> G="-Ktrap=fp -mcmodel=medium"
>
>
> On Oct 18, 2013, at 10:37 AM, <nek5000-users at lists.mcs.anl.gov>
>  wrote:
>
> >
> > Do you know what compiler was used for the mpi build ?
> >
> > You might try turning off mpi in the makenek script.
> >
> > Also, are you not using mpif77 / mpicc ?  (Obviously
> > if you set IFMPI to false then you don't want these
> > compilers.)
> >
> > Paul
> >
> >
> > ----- Original Message -----
> > From: nek5000-users at lists.mcs.anl.gov
> > To: "<nek5000-users at lists.mcs.anl.gov>" <nek5000-users at lists.mcs.anl.gov
> >
> > Sent: Friday, October 18, 2013 9:22:23 AM
> > Subject: Re: [Nek5000-users] turbJet compiling problem
> >
> > After adding G= -Ktrap=fp -mcmodel=medium, the compilation completed
> correctly for gfortran but for PGI I got a new error:
> >
> > /opt/cray/mpt/5.5.4/gni/mpich2-pgi/119/lib/libmpich_pgi.a(gni_poll.o):
> In function `MPID_nem_gni_process_remote_data_ack':
> > gni_poll.c:(.text+0x15b): relocation truncated to fit: R_X86_64_32S
> against symbol `MPID_nem_gni_send_recv_bufs' defined in COMMON section in
> /opt/cray/mpt/5.5.4/gni/mpich2-pgi/119/lib/libmpich_pgi.a(gni_init.o)
> > gni_poll.c:(.text+0x216): relocation truncated to fit: R_X86_64_32S
> against symbol `MPID_nem_gni_send_bufs' defined in COMMON section in
> /opt/cray/mpt/5.5.4/gni/mpich2-pgi/119/lib/libmpich_pgi.a(gni_init.o)
> > /opt/cray/mpt/5.5.4/gni/mpich2-pgi/119/lib/libmpich_pgi.a(gni_poll.o):
> In function `MPID_nem_gni_progress_localCQ':
> > gni_poll.c:(.text+0xdde): relocation truncated to fit: R_X86_64_PC32
> against symbol `MPID_nem_gni_local_nic_addrs' defined in COMMON section in
> /opt/cray/mpt/5.5.4/gni/mpich2-pgi/119/lib/libmpich_pgi.a(gni_init.o)
> > gni_poll.c:(.text+0xe5b): relocation truncated to fit: R_X86_64_PC32
> against symbol `MPID_nem_gni_local_nic_addrs' defined in COMMON section in
> /opt/cray/mpt/5.5.4/gni/mpich2-pgi/119/lib/libmpich_pgi.a(gni_init.o)
> > gni_poll.c:(.text+0xe75): relocation truncated to fit: R_X86_64_PC32
> against symbol `MPID_nem_gni_nic_hndls' defined in COMMON section in
> /opt/cray/mpt/5.5.4/gni/mpich2-pgi/119/lib/libmpich_pgi.a(gni_init.o)
> > /opt/cray/mpt/5.5.4/gni/mpich2-pgi/119/lib/libmpich_pgi.a(gni_poll.o):
> In function `MPID_nem_gni_check_localCQ':
> > gni_poll.c:(.text+0xf63): relocation truncated to fit: R_X86_64_PC32
> against symbol `MPID_nem_gni_local_nic_addrs' defined in COMMON section in
> /opt/cray/mpt/5.5.4/gni/mpich2-pgi/119/lib/libmpich_pgi.a(gni_init.o)
> > gni_poll.c:(.text+0xf8e): relocation truncated to fit: R_X86_64_PC32
> against symbol `MPID_nem_gni_nic_hndls' defined in COMMON section in
> /opt/cray/mpt/5.5.4/gni/mpich2-pgi/119/lib/libmpich_pgi.a(gni_init.o)
> > gni_poll.c:(.text+0x127f): relocation truncated to fit: R_X86_64_32S
> against symbol `MPID_nem_gni_queue_work_head' defined in COMMON section in
> /opt/cray/mpt/5.5.4/gni/mpich2-pgi/119/lib/libmpich_pgi.a(gni_init.o)
> > gni_poll.c:(.text+0x1299): relocation truncated to fit: R_X86_64_PC32
> against symbol `MPID_nem_gni_queue_work_head' defined in COMMON section in
> /opt/cray/mpt/5.5.4/gni/mpich2-pgi/119/lib/libmpich_pgi.a(gni_init.o)
> > gni_poll.c:(.text+0x12a4): relocation truncated to fit: R_X86_64_PC32
> against symbol `MPID_nem_gni_queue_work_head' defined in COMMON section in
> /opt/cray/mpt/5.5.4/gni/mpich2-pgi/119/lib/libmpich_pgi.a(gni_init.o)
> > gni_poll.c:(.text+0x1478): additional relocation overflows omitted from
> the output
> > make: *** [nek5000] Error 2
> >
> >
> > On Oct 17, 2013, at 12:31 PM, nek5000-users at lists.mcs.anl.gov wrote:
> >
> >>
> >> Try modifying makenek to have the line:
> >>
> >> G= -Ktrap=fp -mcmodel=medium
> >>
> >> (the G= is there but is commented out)
> >>
> >> Then:
> >>
> >> makenek clean
> >>
> >> and remake...
> >>
> >> Paul
> >>
> >>
> >> On Thu, 17 Oct 2013, nek5000-users at lists.mcs.anl.gov wrote:
> >>
> >>> Hi neks,
> >>>
> >>> I am trying to compile the out-of-the-box turbojet case in the
> examples.
> >>>
> >>> This is the output I got for PGI:
> >>>
> >>> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o): In function
> `__hpf_myprocnum':
> >>> initpar.c:(.text+0x6): relocation truncated to fit: R_X86_64_PC32
> against symbol `__hpf_lcpu' defined in COMMON section in
> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o)
> >>> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o): In function
> `__hpf_ncpus':
> >>> initpar.c:(.text+0x16): relocation truncated to fit: R_X86_64_PC32
> against symbol `__hpf_tcpus' defined in COMMON section in
> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o)
> >>> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o): In function
> `__hpf_getioproc':
> >>> initpar.c:(.text+0x26): relocation truncated to fit: R_X86_64_PC32
> against symbol `__hpf_ioproc' defined in COMMON section in
> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o)
> >>> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o): In function
> `__hpf_is_ioproc':
> >>> initpar.c:(.text+0x36): relocation truncated to fit: R_X86_64_PC32
> against symbol `__hpf_lcpu' defined in COMMON section in
> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o)
> >>> initpar.c:(.text+0x3e): relocation truncated to fit: R_X86_64_PC32
> against symbol `__hpf_ioproc' defined in COMMON section in
> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o)
> >>> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o): In function
> `__hpf_abort':
> >>> initpar.c:(.text+0x7a): relocation truncated to fit: R_X86_64_PC32
> against symbol `__hpf_lcpu' defined in COMMON section in
> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o)
> >>> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o): In function
> `__hpf_abortp':
> >>> initpar.c:(.text+0xe0): relocation truncated to fit: R_X86_64_PC32
> against symbol `__hpf_lcpu' defined in COMMON section in
> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o)
> >>> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o): In function
> `__hpf_passargs':
> >>> initpar.c:(.text+0x4c2): relocation truncated to fit: R_X86_64_PC32
> against symbol `__hpf_lcpu' defined in COMMON section in
> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o)
> >>> initpar.c:(.text+0x616): relocation truncated to fit: R_X86_64_PC32
> against symbol `__hpf_lcpu' defined in COMMON section in
> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o)
> >>> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o): In function
> `pghpf_init':
> >>> initpar.c:(.text+0x7d8): relocation truncated to fit: R_X86_64_PC32
> against symbol `__hpf_np2' defined in COMMON section in
> /opt/pgi/12.8.0/linux86-64/12.8/lib/libpgf90.a(initpar.o)
> >>> initpar.c:(.text+0x7e2): additional relocation overflows omitted from
> the output
> >>> make: *** [nek5000] Error 2
> >>>
> >>> and this is for gfortran
> >>>
> >>> obj/postpro.o: In function `intpts_':
> >>> postpro.f:(.text+0x1818): relocation truncated to fit: R_X86_64_32S
> against symbol `intp_r_' defined in COMMON section in obj/postpro.o
> >>> postpro.f:(.text+0x1831): relocation truncated to fit: R_X86_64_32S
> against symbol `intp_r_' defined in COMMON section in obj/postpro.o
> >>> postpro.f:(.text+0x1878): relocation truncated to fit: R_X86_64_32S
> against symbol `intp_i_' defined in COMMON section in obj/postpro.o
> >>> postpro.f:(.text+0x1915): relocation truncated to fit: R_X86_64_32S
> against symbol `intp_r_' defined in COMMON section in obj/postpro.o
> >>> postpro.f:(.text+0x1927): relocation truncated to fit: R_X86_64_32S
> against symbol `intp_i_' defined in COMMON section in obj/postpro.o
> >>> postpro.f:(.text+0x1c7d): relocation truncated to fit: R_X86_64_32S
> against symbol `intp_r_' defined in COMMON section in obj/postpro.o
> >>> postpro.f:(.text+0x1dc4): relocation truncated to fit: R_X86_64_32S
> against symbol `intp_r_' defined in COMMON section in obj/postpro.o
> >>> obj/postpro.o: In function `tens3d1_':
> >>> postpro.f:(.text+0x1ef0): relocation truncated to fit: R_X86_64_32S
> against symbol `ctensor_' defined in COMMON section in obj/postpro.o
> >>> postpro.f:(.text+0x1ef8): relocation truncated to fit: R_X86_64_32S
> against symbol `ctensor_' defined in COMMON section in obj/postpro.o
> >>> obj/postpro.o: In function `build_1d_filt_':
> >>> postpro.f:(.text+0x2124): relocation truncated to fit: R_X86_64_32S
> against symbol `cfiltr_' defined in COMMON section in obj/postpro.o
> >>> postpro.f:(.text+0x2136): additional relocation overflows omitted from
> the output
> >>> collect2: ld returned 1 exit status
> >>> make: *** [nek5000] Error 1
> >>>
> >>>
> >>> Any help?. Thanks
> >>>
> >>> ________________________________
> >>>
> >>> CSI has been ranked one of America’s Best Colleges 2014<
> http://colleges.usnews.rankingsandreviews.com/best-colleges/rankings/regional-universities-north/top-public/spp+50/page+2>
> (North East Public) by US News and World Report.
> >>> _______________________________________________
> >> Nek5000-users mailing list
> >> Nek5000-users at lists.mcs.anl.gov
> >>
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users_______________________________________________
> >> Nek5000-users mailing list
> >> Nek5000-users at lists.mcs.anl.gov
> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >
> >
> > ________________________________
> >
> > CSI has been ranked one of America’s Best Colleges 2014<
> http://colleges.usnews.rankingsandreviews.com/best-colleges/rankings/regional-universities-north/top-public/spp+50/page+2>
> (North East Public) by US News and World Report.
> > _______________________________________________
> > Nek5000-users mailing list
> > Nek5000-users at lists.mcs.anl.gov
> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> > _______________________________________________
> > Nek5000-users mailing list
> > Nek5000-users at lists.mcs.anl.gov
> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>
>
> ________________________________
>
> CSI has been ranked one of America’s Best Colleges 2014<
> http://colleges.usnews.rankingsandreviews.com/best-colleges/rankings/regional-universities-north/top-public/spp+50/page+2>
> (North East Public) by US News and World Report.
> _______________________________________________
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