<div dir="ltr"><div><div><div><div><div>Hi again,<br><br></div>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.<br></div>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.<br><br></div>Any ideas of this behaviour?<br><br></div>Cheers,<br></div>Vishal<br><div><div><br><br></div></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><font size="1"><span style="color:rgb(7,55,99)"><font style="background-color:rgb(255,255,255)" face="trebuchet ms, sans-serif">---<b><br>Vishal SAINI</b></font><br></span></font></div><font size="1"><span style="color:rgb(7,55,99)"><font face="garamond, serif">Master of Research,<br>University of Cambridge.<br>Master in Turbulence</font></span></font><font size="1"><span style="color:rgb(7,55,99)"><font style="background-color:rgb(255,255,255)" face="garamond, serif"><br>EC Lille, ENSIP and ENSMA </font></span></font><span><font size="1"><span style="color:rgb(7,55,99)"><span style="background-color:rgb(255,255,255)"><font face="garamond, serif">France.</font></span></span></font></span><div><div><font size="1"><span style="color:rgb(7,55,99)"><span style="background-color:rgb(255,255,255)"><font face="garamond, serif">Contact: <a href="mailto:vishal.saini.nitj@gmail.com" target="_blank">vs434@cam.ac.uk, vishal.saini.nitj@gmail.com</a><br></font></span></span></font></div><div><font size="1"><span style="color:rgb(7,55,99)"><span style="background-color:rgb(255,255,255)"><font face="garamond, serif"> (+44) 7 459 186 139 (UK)<br></font></span></span></font></div><div><font size="1"><span style="color:rgb(7,55,99)"><span style="background-color:rgb(255,255,255)"><font face="garamond, serif"> (+33) 7 58 24 84 02 (France)<br></font></span></span></font></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Fri, Apr 27, 2018 at 8:00 AM, <span dir="ltr"><<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto"><div></div><div>See NekDoc FAQs</div><div><div class="h5"><div><br>On 26 Apr 2018, at 23:37, "<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.<wbr>gov</a>" <<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.<wbr>gov</a>> wrote:<br><br></div></div></div><blockquote type="cite"><div><div><div class="h5"><div dir="ltr"><div class="gmail_quote"><div dir="ltr"><div>Hi all,<br><br></div>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 <a href="https://www.grc.nasa.gov/hiocfd/wp-content/uploads/sites/22/C3.3_Twente.pdf" target="_blank">https://www.grc.nasa.gov/hi<wbr>ocfd/wp-content/uploads/sites/<wbr>22/C3.3_Twente.pdf</a>) 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:<br><br>"""<br>makenek - automatic build tool for Nek5000<br>generating makefile ...<br>build 3rd-party software ...<br>‘tgv.usr’ -> ‘tgv.f’<br>mpif77 -c -O2 -fdefault-real-8 -fdefault-double-8 -cpp -DMPI -DUNDERSCORE -DTIMER -I/gpfs/home/lboro/ttvs3/Nek50<wbr>00/run/tgv -I/gpfs/home/lboro/ttvs3/Nek50<wbr>00/core -I./ /gpfs/home/lboro/ttvs3/Nek5000<wbr>/run/tgv/tgv.f -o obj/tgv.o <br>mpif77 -O2 -fdefault-real-8 -fdefault-double-8 -cpp -DMPI -DUNDERSCORE -DTIMER -I/gpfs/home/lboro/ttvs3/Nek50<wbr>00/run/tgv -I/gpfs/home/lboro/ttvs3/Nek50<wbr>00/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/Nek50<wbr>00/3rd_party/gslib/lib -lgs -L/trinity/shared/apps/local/b<wbr>zip2/1.0.6/1/lib -I/trinity/shared/apps/local/t<wbr>k/8.5.13/1/lib -I/trinity/shared/apps/local/t<wbr>cl/8.5.13/1/lib -L/trinity/shared/apps/local/z<wbr>lib/1.2.11/1/lib<br>obj/drive2.o: In function `dofcnt_':<br>drive2.f:(.text+0x8d50): relocation truncated to fit: R_X86_64_PC32 against symbol `scrns_' defined in COMMON section in obj/convect.o<br>obj/plan5.o: In function `midstep_':<br>plan5.f:(.text+0x186): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o<br>plan5.f:(.text+0x379): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o<br>plan5.f:(.text+0x391): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o<br>plan5.f:(.text+0x3c9): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o<br>obj/plan4.o: In function `crespsp_':<br>plan4.f:(.text+0x9db): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o<br>plan4.f:(.text+0xb1a): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o<br>plan4.f:(.text+0xc79): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o<br>plan4.f:(.text+0xd7a): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o<br>plan4.f:(.text+0xd90): relocation truncated to fit: R_X86_64_32S against symbol `scrns_' defined in COMMON section in obj/convect.o<br>plan4.f:(.text+0xda3): additional relocation overflows omitted from the output<br>collect2: error: ld returned 1 exit status<br>make: *** [nek5000] Error 1<br>"""<br><div><br></div><div>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.<br><br></div><div>Any input is highly appreciated.</div><div><br></div><div>PS- Thanks Prof. Fischer for your reply. Hope this one is more clear.<br><br></div><div>Cheers,<br></div><div>Vishal<br></div><div><br></div></div>
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