Fwd: 3D Taylor-Green vortex - error
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
Vishal, This is answered in the FAQ https://nek5000.github.io/NekDoc/faq.html -Dillon From: Nek5000-users [mailto:[email protected]] On Behalf Of [email protected] Sent: Thursday, April 26, 2018 3:19 PM To: [email protected] Subject: [Nek5000-users] Fwd: 3D Taylor-Green vortex - error 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
Hi Vishal, You could try reducing lelt in SIZE file. If you are planning to use 32 MPI ranks, lelt can be as small as 16^3/32 = 128. Regards, Li ________________________________ From: Nek5000-users [[email protected]] on behalf of [email protected] [[email protected]] Sent: Thursday, April 26, 2018 15:19 To: [email protected] Subject: [Nek5000-users] Fwd: 3D Taylor-Green vortex - error 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<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.grc.nasa.gov_hiocfd_wp-2Dcontent_uploads_sites_22_C3.3-5FTwente.pdf&d=DwMFaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=S9SjAAlS_BJoPCNyzHr0oyFG2zUTUvTfH4rJs7HSwok&m=GYfc8AwoXqUSjzspQgBFKsocM8KjgkXLBhULAr3DXFs&s=KXzsV2w3DrPQcfovYX4y6MUwxtH-f2__WrUjKagT7XY&e=>) 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
See NekDoc FAQs On 26 Apr 2018, at 23:37, "[email protected] <mailto:[email protected]> " <[email protected] <mailto:[email protected]> > 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 _______________________________________________ Nek5000-users mailing list [email protected] <mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
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: [email protected], [email protected] <[email protected]> (+44) 7 459 186 139 (UK) (+33) 7 58 24 84 02 (France) On Fri, Apr 27, 2018 at 8:00 AM, <[email protected]> wrote:
See NekDoc FAQs
On 26 Apr 2018, at 23:37, "[email protected]" < [email protected]> 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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Hmm ... this looks odd. Can you please send me your case. You'll find my email address on the Nek5000 webpage. Cheers, Steffan -----Original message-----
From:[email protected] <[email protected]> Sent: Monday 30th April 2018 18:53 To: [email protected] Subject: Re: [Nek5000-users] Fwd: 3D Taylor-Green vortex - error
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
<br clear="all" />--- Vishal SAINI Master of Research, University of Cambridge. Master in Turbulence EC Lille, ENSIP and ENSMA France. Contact: [email protected], [email protected] <mailto:[email protected]> (+44) 7 459 186 139 (UK) (+33) 7 58 24 84 02 (France)
On Fri, Apr 27, 2018 at 8:00 AM, <[email protected] <mailto:[email protected]>> wrote: See NekDoc FAQs
On 26 Apr 2018, at 23:37, "[email protected] <mailto:[email protected]>" <[email protected] <mailto:[email protected]>> 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 <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 Id like to run a 16^3 elements cubical box [-pi,pi] with polynomial order 4 providing 64^3 degrees of freedom. Im targeting 28-84 cores. The boundary conditions of the case are triply periodic and initial conditions are defined as trigonometric expressions of space. I didnt 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 o bj/nek_i n_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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