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

Mon Apr 30 11:49:09 CDT 2018

Hi again,

Thank you for your guidance! Increasing lpmin in SIZE fixed the problem. I
seem to have set up my case on a local workstation. It runs well and
preliminary results look fine.
On a different note, when I migrate on the computing cluster, the program
stops during/after "prereading mesh" (see attached log file). The
compilation is however reported successful.

Any ideas of this behaviour?

Cheers,
Vishal

---
*Vishal SAINI*
Master of Research,
University of Cambridge.
Master in Turbulence
EC Lille, ENSIP and ENSMA France.
Contact: vs434 at cam.ac.uk, vishal.saini.nitj at gmail.com
<vishal.saini.nitj at gmail.com>
               (+44) 7 459 186 139 (UK)
               (+33) 7 58 24 84 02  (France)

On Fri, Apr 27, 2018 at 8:00 AM, <nek5000-users at lists.mcs.anl.gov> wrote:

> See NekDoc FAQs
>
> On 26 Apr 2018, at 23:37, "nek5000-users at lists.mcs.anl.gov" <
> 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/hi
> ocfd/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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