[Nek5000-users] Fwd: 3D Taylor-Green vortex - error

Fri Apr 27 02:00:18 CDT 2018

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On 26 Apr 2018, at 23:37, "nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov> " <nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov> > wrote:

Hi all,

This is my second day with Nek5000. Day one was to go through the process of setting up the simulations with example eddy case and periodic hill case running fine on a single core of local workstation. I was hoping to run the 3D Taylor-Green vortex case (described in https://www.grc.nasa.gov/hiocfd/wp-content/uploads/sites/22/C3.3_Twente.pdf) very quickly to compare the CPU wall clock time with OpenFOAM. Ideally I'd like to run a 16^3 elements cubical box [-pi,pi] with polynomial order 4 providing 64^3 degrees of freedom. I'm targeting 28-84 cores. The boundary conditions of the case are triply periodic and initial conditions are defined as trigonometric expressions of space. I didn't know how to write expressions such as sin(x)cos(y)sin(z) in Nek5000. So, I tried with initial condition uy=uz=0 and ux=1. I keep getting the following error with my set up:

"""
makenek - automatic build tool for Nek5000
generating makefile ...
build 3rd-party software ...
‘tgv.usr’ -> ‘tgv.f’
mpif77 -c  -O2 -fdefault-real-8 -fdefault-double-8 -cpp -DMPI -DUNDERSCORE -DTIMER -I/gpfs/home/lboro/ttvs3/Nek5000/run/tgv -I/gpfs/home/lboro/ttvs3/Nek5000/core -I./ /gpfs/home/lboro/ttvs3/Nek5000/run/tgv/tgv.f  -o obj/tgv.o 
mpif77  -O2 -fdefault-real-8 -fdefault-double-8 -cpp -DMPI -DUNDERSCORE -DTIMER -I/gpfs/home/lboro/ttvs3/Nek5000/run/tgv -I/gpfs/home/lboro/ttvs3/Nek5000/core -I./ -o nek5000 obj/tgv.o obj/drive.o obj/drive1.o obj/drive2.o obj/plan5.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/mvmesh.o obj/ic.o obj/gfldr.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/intp_usr.o obj/cvode_driver.o obj/nek_comm.o obj/vprops.o obj/makeq_aux.o obj/papi.o obj/nek_in_situ.o obj/reader_rea.o obj/reader_par.o obj/reader_re2.o obj/finiparser.o obj/iniparser.o obj/dictionary.o obj/hpf.o obj/mxm_std.o obj/comm_mpi.o obj/singlmesh.o obj/blas.o obj/dsygv.o -L/gpfs/home/lboro/ttvs3/Nek5000/3rd_party/gslib/lib -lgs -L/trinity/shared/apps/local/bzip2/1.0.6/1/lib -I/trinity/shared/apps/local/tk/8.5.13/1/lib -I/trinity/shared/apps/local/tcl/8.5.13/1/lib -L/trinity/shared/apps/local/zlib/1.2.11/1/lib
obj/drive2.o: In function `dofcnt_':
drive2.f:(.text+0x8d50): relocation truncated to fit: R_X86_64_PC32 against symbol `scrns_' defined in COMMON section in obj/convect.o
obj/plan5.o: In function `midstep_':
plan5.f:(.text+0x186): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o
plan5.f:(.text+0x379): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o
plan5.f:(.text+0x391): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o
plan5.f:(.text+0x3c9): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o
obj/plan4.o: In function `crespsp_':
plan4.f:(.text+0x9db): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o
plan4.f:(.text+0xb1a): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o
plan4.f:(.text+0xc79): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o
plan4.f:(.text+0xd7a): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o
plan4.f:(.text+0xd90): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o
plan4.f:(.text+0xda3): additional relocation overflows omitted from the output
collect2: error: ld returned 1 exit status
make: *** [nek5000] Error 1
"""

In your experience, the error is related to my compiler/mpi or the set up files? If latter, can anyone be kind enough to check out my set up files please? If you want to save time and have done this case before, you can share those files from the past.

Any input is highly appreciated.

PS- Thanks Prof. Fischer for your reply. Hope this one is more clear.

Cheers,
Vishal

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