[Nek5000-users] turbulent 3d box

Mon Dec 16 02:31:46 CST 2013

    Hi Paul,
    It seems that many more things are missing. Here is the compilation errors:

    mpicc -c  -O2 -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE
-DGLOBAL_LONG_LONG  -DPREFIX=jl_
/home/galanti/COMPUTING/NEK5000/nek5_svn/trunk/nek/jl/xxt.c -o obj/jl_xxt.o
    mpicc -c  -O2 -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE
-DGLOBAL_LONG_LONG  -DPREFIX=jl_
/home/galanti/COMPUTING/NEK5000/nek5_svn/trunk/nek/jl/fcrs.c -o
obj/jl_fcrs.o
    mpif77 -c  -O2 -fdefault-real-8 -fdefault-double-8 -x f77-cpp-input
-DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG
-I/home/galanti/COMPUTING/NEK5000/nek5_svn/TEST-examples/turbBox
-I/home/galanti/COMPUTING/NEK5000/nek5_svn/trunk/nek -I./
/home/galanti/COMPUTING/NEK5000/nek5_svn/TEST-examples/turbBox/turbBox.f    -o
obj/turbBox.o
    mpif77 -o nek5000  obj/turbBox.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/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
    obj/drive1.o: In function `nek_init_':
    drive1.f:(.text+0x48b): undefined reference to `usrdat_'
    drive1.f:(.text+0x578): undefined reference to `usrdat3_'
    drive1.f:(.text+0x5b5): undefined reference to `userchk_'
    obj/drive1.o: In function `nek_solve_':
    drive1.f:(.text+0xc7e): undefined reference to `userchk_'
    drive1.f:(.text+0xcf7): undefined reference to `userchk_'
    obj/bdry.o: In function `faceiv_':
    bdry.f:(.text+0x2a5f): undefined reference to `userbc_'
    bdry.f:(.text+0x2e74): undefined reference to `userbc_'
    bdry.f:(.text+0x2f53): undefined reference to `userbc_'
    bdry.f:(.text+0x309f): undefined reference to `userbc_'
    bdry.f:(.text+0x31d9): undefined reference to `userbc_'
    obj/bdry.o:bdry.f:(.text+0x3352): more undefined references to
`userbc_' follow
    obj/conduct.o: In function `nekuq_':
    conduct.f:(.text+0xdcf): undefined reference to `userq_'
    obj/ic.o: In function `nekuic_':
    ic.f:(.text+0x6a6): undefined reference to `useric_'
    ic.f:(.text+0x980): undefined reference to `useric_'
    ic.f:(.text+0xad0): undefined reference to `useric_'
    obj/ssolv.o: In function `gostep_':
    ssolv.f:(.text+0x1954): undefined reference to `userchk_'
    obj/ssolv.o: In function `go1step_':
    ssolv.f:(.text+0x2424): undefined reference to `userchk_'
    obj/subs1.o: In function `nekuvp_':
    subs1.f:(.text+0x90c): undefined reference to `uservp_'
    collect2: error: ld returned 1 exit status
    make: *** [nek5000] Error 1

    Attached the .usr and .box files which I used. What about the turBox.f
file ?
    All the best,
    Barak

    Quoting nek5000-users at lists.mcs.anl.gov:
> Hi Barak,
>
>   Just take the box file from turbChannel
>   and set nelx nely nelz to (say) -8 -8 -8
>   with periodic BCs  P  ,P  ,P  ,P  ,P  ,
>
>   Then, use a blank .usr file and set ffx fry ffz to be the
>   formulas you have below in userf() in the .usr file.
>
>   Finally, add the following to usrdat2()
>
>        a=0
>        b=2*pi
>        call rescale_x(xm1,a,b)
>        call rescale_x(ym1,a,b)
>        call rescale_x(zm1,a,b)
>
>   which will put your box on [0,2pi]^3.
>
>   Paul
>
>
>   ----- Original Message -----
>   From: nek5000-users at lists.mcs.anl.gov
>   To: nek5000-users at lists.mcs.anl.gov
>   Sent: Sunday, December 15, 2013 4:14:22 PM
>   Subject: [Nek5000-users] turbulent 3d box
>
>   Dear nek's,
>   I would like to run the following problem:
>   a 3D periodic box, small viscosity and the following forcing:
>
>   fx=cos(y)+sin(z)
>   fy=cos(z)+sin(x)
>   fz=cos(x)+sin(y)
>
>   Do you have a similar example?
>
>   Many thanks,
>   Barak
>
>
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