[Nek5000-users] turbJet compiling problem

nek5000-users at lists.mcs.anl.gov nek5000-users at lists.mcs.anl.gov
Fri Oct 18 10:58:36 CDT 2013 

PS -- sorry; I was looking at turbChan, not turbJet.

Katie is right -- turbJet is larger still.

My suggestions below however would still apply.

Paul


On Fri, 18 Oct 2013, nek5000-users at lists.mcs.anl.gov wrote:

>
> My guess is simply the amount of memory required, which is 1.3 GB
> per node (as set up in the example; one can easily lower this by
> a factor of P when running on P processors; just set
> lelt and lelv to be ~ 512 / P).
>
> Note that this example compiles here at ANL with 4 different
> compilers, both in parallel an in serial, as do all the other
> examples, so somehow it must have something to do with your
> local environment settings.
>
> I just tried it on my workstation - no issues.
>
> What type of platform are you compiling on, etc.
>
> Paul
>
>
> On Fri, 18 Oct 2013, 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
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>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
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>>> 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
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