hifiles/hifiles-solver

High Fidelity Large Eddy Simulation Solver

hifiles-solver's Issues

Improving GPU utilization

When I run the Taylor Green vortex test case I find that only 21% of the GPU (Tesla C2050) is utilized.
[ejeyapau@r219i0n0 ~]$ nvidia-smi
Mon Jun 23 17:34:39 2014
+------------------------------------------------------+
| NVIDIA-SMI 3.295.41 Driver Version: 295.41 |
|-------------------------------+----------------------+----------------------+
| Nb. Name | Bus Id Disp. | Volatile ECC SB / DB |
| Fan Temp Power Usage /Cap | Memory Usage | GPU Util. Compute M. |
|===============================+======================+======================|
| 0. Tesla M2090 | 0000:02:00.0 Off | 0 0 |
| N/A N/A P0 137W / 225W | 7% 383MB / 5375MB | 21% Default |
|-------------------------------+----------------------+----------------------|
| Compute processes: GPU Memory |
| GPU PID Process name Usage |
|=============================================================================|
| 0. 78932 ../../../bin/HiFiLES 370MB |
+-----------------------------------------------------------------------------+

Does this mean that all of the 448 processing units are being utilized on the Tesla C2050 card? I am running this on a 12 core machine with 1 GPU card.
For better utilization, here are few options,
1.run multiple jobs on the same GPU
2.run a GPU job (uses 1 core) and a CPU job utilizing remaining 11 cores.
Are both good options?

Or rather, is there a way to estimate the optimal GPU requirements (memory & load) for a given problem.
Sorry, the question is not directly related to the code.
Thanks,
Elbert

ACCELERATE_BLAS & nvcc

The CUDA compiler (nvcc) doesn't recognize the -flax-vector-conversions compiler flag which is enabled by default when selecting the ACCELERATE_BLAS option.

Questions about Turbulence model

Hi:

The default value of turb_model = 0.
What does “0” mean here, RANS model or LES model or no model at all?
How to specify different turbulence model in HiFiLES?
There is LES options in the wiki. Could you give more introduction on RANS and Hybird LES?
If I would like to run DNS simulations?
What should I do?

Best regards!
Yue

Help for input file

Hi:
Could anyone help me?my question is what's the difference between the input file of cylinder case and the input file of 2D naca0012 case
Best regards!
chen

SA Model testcase

Hi,

I try the SA model on a flat plate but found the nu_tilde is pretty small. Do you have any testcase for RANS SA model to share? I noticed that there is a NACA0012 case on your paper, but could not find it in the source code.

Thank you.

help for "Subsonic inflow characteristic" boundary cond

Hi,
I've run a case (2D, Ma~0.1) in which the inflow boundary condition is "Subsonic inflow characteristic". And I got the u-velocity champ with value 0.4 !=1 (0.4 is just an example, what count is it < 1 ) far away from key zone of simulation (i.e., the zone where all variables vary smoothly). I think it could be the inflow boundary condition for my problem.
I've checked in the SU2 code (file solver_direct_tne2.cpp, line 4178), but I don't get any further information. Can, anyone, give me some references for this boundary condition?
Thanks in advance!
maxime LV

Update release

Hi:

Will you update HiFiLES to a new release?

Fans of HiFiLES

error when compile with MPI

./configure --with-BLAS=NO --with-MPI=mpicxx --with--MPI-include=/opt/openmpi-1.6.5/include
configure: WARNING: unrecognized options: --with--MPI-include
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
<<< Configuring library with Metis support >>>
./configure: line 3027: AX_TLS: command not found
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... configure: error: in /home/guang/git-fork/HiFiLES-solver': configure: error: cannot run C++ compiled programs. If you meant to cross compile, use--host'.
See `config.log' for more details

About time step in HiFiLES

Hi:
I am confused with Time Step in HiFiLES.
Here is Definitions on time step:
dt_type: Which type of time-advancement // Ok, I understand.

0 | Constant, user-supplied step size [default]  //OK, I understand.
1 | Global minimum CFL-based time step        //Ok,  I understand.
2 | Local CFL-based time stepping                   // What does this mean? What is "local"? What is the difference between 1 and 2? 

dt: Time step in non-dimensional units // Does HiFiLES use non-dimensional units in the whole system? May I put dt as seconds?
n_steps: Number of time steps [iterations] to perform //If I take unsteady simulations, does this mean iterations in each time step?
adv_type: Time integration method //Ok, I understand.

Best regards!
Yue

Questions about LES

Hi all,
I've some questions about the LES,

1. The filter process. I know the standard LES filter process is realized by a convolution. But I cannot understand what HiFiLES do. It works like: U_{filtered}=F_{filter matrix}*U_{origin}. I hope someone can give me some explications about this process and about the generation of the filter matrix. Or just give some reference papers and/or books.
2. In the code (method "CalcResidual" in solver.cpp), there are some comments before the call of the method "calc_sgs_terms" like "If at first RK step and using certain LES models, compute some model-related quantities". But I think the filter process is active in every RK step.
3. The balance between the order of approximate polynomial and the mesh size? It is better to use high order polynomial and coarse mesh or the opposite? Is there any suggestion about the polynomial order and the mesh size?

Thanks in advance!
Maxime

input file for [(3D) SD7003 wing section, 4° AoA, Re = 10,000] case?

Hi:

Could you share the input file for [(3D) SD7003 wing section, 4° AoA, Re = 10,000] case?
The wiki is not updated for quite a long time.

Best regards!
Yue Wang

compilation error

Dear support,

I try to install the HiFiLES on a RedHat cluster with mpich, but the installation failed with the error below.

the system is :
Red Hat Enterprise Linux Server release 6.4 (Santiago)
Linux tamnun 2.6.32-358.23.2.el6.x86_64 #1 SMP Sat Sep 14 05:32:37 EDT 2013 x86_64

Attached are the installation logs.
I appreciate your help.

make[1]: Entering directory /usr/local/HiFiLES-solver-master/obj' CXX ../src/___bin_HiFiLES-global.o g++: 1.0.0": No such file or directory <command-line>: warning: missing terminating " character make[1]: *** [../src/___bin_HiFiLES-global.o] Error 1 make[1]: Leaving directory/usr/local/HiFiLES-solver-master/obj'
make: *** [all-recursive] Error 1

The full installation log is below
Thanks,
Amihai

cat configure_run.sh

\file configure_run.sh

\brief Configuration script for HiFiLES

\author - Original code: SD++ developed by Patrice Castonguay, Antony Jameson,

Peter Vincent, David Williams (alphabetical by surname).

- Current development: Aerospace Computing Laboratory (ACL)

Aero/Astro Department. Stanford University.

\version 0.1.0

High Fidelity Large Eddy Simulation (HiFiLES) Code.

Copyright (C) 2014 Aerospace Computing Laboratory (ACL).

HiFiLES is free software: you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation, either version 3 of the License, or

(at your option) any later version.

HiFiLES is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

GNU General Public License for more details.

You should have received a copy of the GNU General Public License

along with HiFiLES. If not, see http://www.gnu.org/licenses/.

Standard (Helpful) Settings [Should not need to change these]

export HIFILES_HOME=$(pwd)

---------------------------------------------------------------

Basic User-Modifiable Build Settings [Change these as desired]

NODE="CPU" # CPU or GPU
CODE="RELEASE" # DEBUG or RELEASE
BLAS="ATLAS" # ATLAS, STANDARD, ACCLERATE, or NO
PARALLEL="YES" # YES or NO
TECIO="NO" # YES or NO
METIS="YES" # Build & link to the HiFiLES-supplied ParMETIS libraries? YES or NO

---------------------------------------------------------------

Compiler Selections [Change compilers or add full filepaths if needed]

CXX="g++" # C++ compiler - Typically g++ (default, GNU) or icpc (Intel)
NVCC="nvcc" # NVidia CUDA compiler
MPICC="mpicxx" # MPI C compiler

---------------------------------------------------------------

Library & Header File Locations [Change filepaths as needed]

BLAS_LIB="/usr/lib64/atlas"
BLAS_INCLUDE="/usr/include/atlas-x86_64-base"

TECIO_LIB="lib/tecio-2008/lib"
TECIO_INCLUDE="lib/tecio-2008/include"

CUDA_LIB="/usr/local/cuda/lib64"
CUDA_INCLUDE="/usr/local/cuda/include"

If building the supplied ParMETIS libraries, need the MPI header location

MPI_INCLUDE="/usr/include/mpich2-x86_64" # location of mpi.h

MPI_INCLUDE="/usr/include/openmpi-x86_64" # location of mpi.h

If NOT building the supplied ParMetis library, location of installed libraries

PARMETIS_LIB="/usr/local/lib" # location of libparmetis.a
PARMETIS_INCLUDE="/usr/local/include" # location of parmetis.h

METIS_LIB="/usr/local/lib" # location of libmetis.a
METIS_INCLUDE="/usr/local/include" # location of metis.h

---------------------------------------------------------------

Run configure using the chosen options [Should not change this]

if [[ "$NODE" == "GPU" ]]
then
_GPU=$NVCC
else
_GPU="NO"
fi
if [[ "$PARALLEL" == "YES" ]]
then
_MPI=$MPICC
else
_MPI="NO"
PARMETIS_LIB="NO"
PARMETIS_INCLUDE="NO"
fi
if [[ "$TECIO" == "NO" ]]
then
TECIO_LIB="NO"
TECIO_INCLUDE="NO"
fi
./configure --prefix=$HIFILES_RUN/..
--with-CXX=$CXX
--with-BLAS=$BLAS
--with-BLAS-lib=$BLAS_LIB
--with-BLAS-include=$BLAS_INCLUDE
--with-MPI=$_MPI
--with-MPI-include=$MPI_INCLUDE
--with-CUDA=$_GPU
--with-CUDA-lib=$CUDA_LIB
--with-CUDA-include=$CUDA_INCLUDE
--with-ParMetis-lib=$PARMETIS_LIB
--with-ParMetis-include=$PARMETIS_INCLUDE
--with-Metis-lib=$METIS_LIB
--with-Metis-include=$METIS_INCLUDE
--with-Tecio-lib=$TECIO_LIB
--with-Tecio-include=$TECIO_INCLUDE
--enable-metis=$METIS

[root@tamnun HiFiLES-solver-master]# ./configure_run.sh
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
<<< Configuring library with Metis support >>>
./configure: line 3027: AX_TLS: command not found
checking for /usr/lib64/atlas/libcblas.a... yes
checking for /usr/lib64/atlas/libatlas.a... yes
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether mpicxx accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of mpicxx... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking whether gcc and cc understand -c and -o together... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1966080
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @file support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... mpicxx -E
checking for ld used by mpicxx... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for mpicxx option to produce PIC... -fPIC -DPIC
checking if mpicxx PIC flag -fPIC -DPIC works... yes
checking if mpicxx static flag -static works... no
checking if mpicxx supports -c -o file.o... yes
checking if mpicxx supports -c -o file.o... (cached) yes
checking whether the mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
configure: creating ./config.status
config.status: creating lib/parmetis-4.0.2/Makefile
config.status: creating lib/parmetis-4.0.2/metis/Makefile
config.status: creating Makefile
config.status: creating lib/Makefile
config.status: creating obj/Makefile
config.status: executing depfiles commands
config.status: executing libtool commands

Build Configuration Summary:

Source code location: /usr/local/HiFiLES-solver-master
Install location:     /
Version:              1.0.0
Compiler:             mpicxx
Preprocessor flags:   
Compiler flags:        -D_MPI
Linker flags:         
BLAS support:         YES
MPI support:          YES
CUDA support:         NO
TecIO support:        NO

make

Making all in lib
make[1]: Entering directory /usr/local/HiFiLES-solver-master/lib' Making all in parmetis-4.0.2/ make[2]: Entering directory/usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2'
Making all in metis/
make[3]: Entering directory /usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2/metis' CC GKlib/libmetis_a-b64.o CC GKlib/libmetis_a-blas.o CC GKlib/libmetis_a-csr.o CC GKlib/libmetis_a-error.o CC GKlib/libmetis_a-evaluate.o CC GKlib/libmetis_a-fkvkselect.o CC GKlib/libmetis_a-fs.o CC GKlib/libmetis_a-getopt.o CC GKlib/libmetis_a-gkregex.o CC GKlib/libmetis_a-htable.o CC GKlib/libmetis_a-io.o CC GKlib/libmetis_a-itemsets.o CC GKlib/libmetis_a-mcore.o CC GKlib/libmetis_a-memory.o CC GKlib/libmetis_a-omp.o CC GKlib/libmetis_a-pdb.o CC GKlib/libmetis_a-pqueue.o CC GKlib/libmetis_a-random.o CC GKlib/libmetis_a-seq.o CC GKlib/libmetis_a-sort.o CC GKlib/libmetis_a-string.o GKlib/string.c: In function ‘gk_str2time’: GKlib/string.c:506: warning: comparison between pointer and integer CC GKlib/libmetis_a-timers.o CC GKlib/libmetis_a-tokenizer.o CC GKlib/libmetis_a-util.o CC libmetis/libmetis_a-auxapi.o CC libmetis/libmetis_a-balance.o CC libmetis/libmetis_a-bucketsort.o CC libmetis/libmetis_a-checkgraph.o CC libmetis/libmetis_a-coarsen.o CC libmetis/libmetis_a-compress.o CC libmetis/libmetis_a-contig.o CC libmetis/libmetis_a-debug.o CC libmetis/libmetis_a-fm.o CC libmetis/libmetis_a-fortran.o CC libmetis/libmetis_a-frename.o CC libmetis/libmetis_a-gklib.o CC libmetis/libmetis_a-graph.o CC libmetis/libmetis_a-initpart.o CC libmetis/libmetis_a-kmetis.o CC libmetis/libmetis_a-kwayfm.o CC libmetis/libmetis_a-kwayrefine.o CC libmetis/libmetis_a-mcutil.o CC libmetis/libmetis_a-mesh.o CC libmetis/libmetis_a-meshpart.o CC libmetis/libmetis_a-minconn.o CC libmetis/libmetis_a-mincover.o CC libmetis/libmetis_a-mmd.o CC libmetis/libmetis_a-ometis.o CC libmetis/libmetis_a-options.o CC libmetis/libmetis_a-parmetis.o CC libmetis/libmetis_a-pmetis.o CC libmetis/libmetis_a-refine.o CC libmetis/libmetis_a-separator.o CC libmetis/libmetis_a-sfm.o CC libmetis/libmetis_a-srefine.o CC libmetis/libmetis_a-stat.o CC libmetis/libmetis_a-timing.o CC libmetis/libmetis_a-util.o CC libmetis/libmetis_a-wspace.o AR libmetis.a make[3]: Leaving directory/usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2/metis'
make[3]: Entering directory /usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2' CC libparmetis/libparmetis_a-akwayfm.o CC libparmetis/libparmetis_a-ametis.o CC libparmetis/libparmetis_a-balancemylink.o CC libparmetis/libparmetis_a-comm.o CC libparmetis/libparmetis_a-csrmatch.o CC libparmetis/libparmetis_a-ctrl.o CC libparmetis/libparmetis_a-debug.o CC libparmetis/libparmetis_a-diffutil.o CC libparmetis/libparmetis_a-frename.o CC libparmetis/libparmetis_a-gkmetis.o CC libparmetis/libparmetis_a-gkmpi.o CC libparmetis/libparmetis_a-graph.o CC libparmetis/libparmetis_a-initbalance.o CC libparmetis/libparmetis_a-initmsection.o CC libparmetis/libparmetis_a-initpart.o CC libparmetis/libparmetis_a-kmetis.o CC libparmetis/libparmetis_a-kwayrefine.o CC libparmetis/libparmetis_a-match.o CC libparmetis/libparmetis_a-mdiffusion.o CC libparmetis/libparmetis_a-mesh.o CC libparmetis/libparmetis_a-mmetis.o CC libparmetis/libparmetis_a-move.o CC libparmetis/libparmetis_a-msetup.o CC libparmetis/libparmetis_a-node_refine.o CC libparmetis/libparmetis_a-ometis.o CC libparmetis/libparmetis_a-pspases.o CC libparmetis/libparmetis_a-redomylink.o CC libparmetis/libparmetis_a-remap.o CC libparmetis/libparmetis_a-renumber.o CC libparmetis/libparmetis_a-rmetis.o CC libparmetis/libparmetis_a-selectq.o CC libparmetis/libparmetis_a-serial.o CC libparmetis/libparmetis_a-stat.o CC libparmetis/libparmetis_a-timer.o CC libparmetis/libparmetis_a-util.o CC libparmetis/libparmetis_a-wave.o CC libparmetis/libparmetis_a-weird.o CC libparmetis/libparmetis_a-wspace.o CC libparmetis/libparmetis_a-xyzpart.o AR libparmetis.a make[3]: Leaving directory/usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2'
make[2]: Leaving directory /usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2' Making all in parmetis-4.0.2/metis make[2]: Entering directory/usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2/metis'
make[2]: Nothing to be done for all'. make[2]: Leaving directory/usr/local/HiFiLES-solver-master/lib/parmetis-4.0.2/metis'
make[2]: Entering directory /usr/local/HiFiLES-solver-master/lib' make[2]: Nothing to be done forall-am'.
make[2]: Leaving directory /usr/local/HiFiLES-solver-master/lib' make[1]: Leaving directory/usr/local/HiFiLES-solver-master/lib'
Making all in obj
make[1]: Entering directory /usr/local/HiFiLES-solver-master/obj' CXX ../src/___bin_HiFiLES-global.o g++: 1.0.0": No such file or directory <command-line>: warning: missing terminating " character make[1]: *** [../src/___bin_HiFiLES-global.o] Error 1 make[1]: Leaving directory/usr/local/HiFiLES-solver-master/obj'
make: *** [all-recursive] Error 1

Help for the boundary condition

could anyone help me?I have a question that I can not understand.in the cylinder testcase,The boundary conditions are "Sup_In "and"Sup_In ",why not "Sup_In "and"Sup_Out"?
And what is the differerence between"Sub_In_Simp"and"Sub_In_Char"
Sincerely
chen

Fatal error 'NaN residual encountered. Exiting' at ../src/output.cpp:1417

Hi:

When I run a 3D case of naca0012, I met a fata error : Fatal error 'NaN residual encountered. Exiting' at ../src/output.cpp:1417.
There is somgthing wrong with "norm_type not recognized".
I made the mesh by myself. It seems somt thing wrong when I extruded the 2D mesh.
I am using gmsh. The 2D case was OK to run except the smaller time step.

Best regards!
Yue

Diverging

Re-definition of pi Compilation Error in OS X (v10.10)

In file included from src/eles.cpp:59:
src/../include/global.h:34:15: error: redefinition of 'pi' with a different
      type: 'double' vs 'const double_t' (aka 'const double')
extern double pi;
              ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      previous definition is here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:593:18: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
        L_x = 2.*pi;
                 ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:594:15: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
        L_y = pi;
              ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:596:93: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
  ...pi*pos(2)/L_z);
     ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6006:30: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(0,0) = 1 + 0.2*pi*cos(pi*pos_fpts(in_fpt,in_ele,0)/10)*sin...
                             ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6006:37: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(0,0) = 1 + 0.2*pi*cos(pi*pos_fpts(in_fpt,in_ele,0)/10)*sin...
                                    ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6006:74: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
  ...= 1 + 0.2*pi*cos(pi*pos_fpts(in_fpt,in_ele,0)/10)*sin(pi*pos_fpts(in_fpt...
                                                           ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6006:113: warning: 'pi' is deprecated: first deprecated in OS X
      10.8 [-Wdeprecated-declarations]
  ...pi*run_input.rk_time/10);
     ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6007:26: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(0,1) = 0.2*pi*sin(pi*pos_fpts(in_fpt,in_ele,0)/10)*cos(pi*...
                         ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6007:33: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(0,1) = 0.2*pi*sin(pi*pos_fpts(in_fpt,in_ele,0)/10)*cos(pi*...
                                ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6007:70: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(0,1) = 0.2*pi*sin(pi*pos_fpts(in_fpt,in_ele,0)/10)*cos(pi*pos_...
                                                                     ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6007:109: warning: 'pi' is deprecated: first deprecated in OS X
      10.8 [-Wdeprecated-declarations]
  ...pi*run_input.rk_time/10);
     ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6008:26: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(1,0) = 0.2*pi*cos(pi*pos_fpts(in_fpt,in_ele,0)/10)*sin(pi*...
                         ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6008:33: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(1,0) = 0.2*pi*cos(pi*pos_fpts(in_fpt,in_ele,0)/10)*sin(pi*...
                                ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6008:70: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(1,0) = 0.2*pi*cos(pi*pos_fpts(in_fpt,in_ele,0)/10)*sin(pi*pos_...
                                                                     ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6008:109: warning: 'pi' is deprecated: first deprecated in OS X
      10.8 [-Wdeprecated-declarations]
  ...pi*run_input.rk_time/10);
     ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6009:30: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(1,1) = 1 + 0.2*pi*sin(pi*pos_fpts(in_fpt,in_ele,0)/10)*cos...
                             ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6009:37: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(1,1) = 1 + 0.2*pi*sin(pi*pos_fpts(in_fpt,in_ele,0)/10)*cos...
                                    ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6009:74: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
  ...= 1 + 0.2*pi*sin(pi*pos_fpts(in_fpt,in_ele,0)/10)*cos(pi*pos_fpts(in_fpt...
                                                           ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6009:113: warning: 'pi' is deprecated: first deprecated in OS X
      10.8 [-Wdeprecated-declarations]
  ...pi*run_input.rk_time/10);
     ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6051:30: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(0,0) = 1 + 0.2*pi*cos(pi*pos_upts(in_upt,in_ele,0)/10)*sin...
                             ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6051:37: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(0,0) = 1 + 0.2*pi*cos(pi*pos_upts(in_upt,in_ele,0)/10)*sin...
                                    ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6051:74: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
  ...= 1 + 0.2*pi*cos(pi*pos_upts(in_upt,in_ele,0)/10)*sin(pi*pos_upts(in_upt...
                                                           ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6051:113: warning: 'pi' is deprecated: first deprecated in OS X
      10.8 [-Wdeprecated-declarations]
  ...pi*run_input.rk_time/10);
     ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6052:26: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(0,1) = 0.2*pi*sin(pi*pos_upts(in_upt,in_ele,0)/10)*cos(pi*...
                         ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6052:33: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(0,1) = 0.2*pi*sin(pi*pos_upts(in_upt,in_ele,0)/10)*cos(pi*...
                                ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6052:70: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(0,1) = 0.2*pi*sin(pi*pos_upts(in_upt,in_ele,0)/10)*cos(pi*pos_...
                                                                     ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6052:109: warning: 'pi' is deprecated: first deprecated in OS X
      10.8 [-Wdeprecated-declarations]
  ...pi*run_input.rk_time/10);
     ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6053:26: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(1,0) = 0.2*pi*cos(pi*pos_upts(in_upt,in_ele,0)/10)*sin(pi*...
                         ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6053:33: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(1,0) = 0.2*pi*cos(pi*pos_upts(in_upt,in_ele,0)/10)*sin(pi*...
                                ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6053:70: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(1,0) = 0.2*pi*cos(pi*pos_upts(in_upt,in_ele,0)/10)*sin(pi*pos_...
                                                                     ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6053:109: warning: 'pi' is deprecated: first deprecated in OS X
      10.8 [-Wdeprecated-declarations]
  ...pi*run_input.rk_time/10);
     ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6054:30: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(1,1) = 1 + 0.2*pi*sin(pi*pos_upts(in_upt,in_ele,0)/10)*cos...
                             ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6054:37: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    out_d_pos(1,1) = 1 + 0.2*pi*sin(pi*pos_upts(in_upt,in_ele,0)/10)*cos...
                                    ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6054:74: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
  ...= 1 + 0.2*pi*sin(pi*pos_upts(in_upt,in_ele,0)/10)*cos(pi*pos_upts(in_upt...
                                                           ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6054:113: warning: 'pi' is deprecated: first deprecated in OS X
      10.8 [-Wdeprecated-declarations]
  ...pi*run_input.rk_time/10);
     ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6571:14: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    lenx = 2*pi;
             ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
src/eles.cpp:6572:16: warning: 'pi' is deprecated: first deprecated in OS X 10.8
      [-Wdeprecated-declarations]
    areayz = 2*pi;
               ^
/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/fp.h:1191:23: note: 
      'pi' has been explicitly marked deprecated here
extern const double_t pi                                             __O...
                      ^
37 warnings and 1 error generated.
make: *** [obj/eles.o] Error 1

Supersonic NACA0012 case diverged!

Hello,

I have checked out the feature-shock branch and tested the supersonic NACA0012 case. Unfortunately, it is diverged after 207457 iterations. I didn't modify the input file and let it run with the original dt and the artificial viscosity settings. The mesh is Naca_0012_4K.neu. Any suggestions?

Also, the convergence is too too slow using a RK45, do you guys really use an explicit scheme to run steady state problems?

How about RANS, i find out that there is a SA branch. But, can not find a RANS testcase.

Thank you!

Fatal error '$PhysicalNames tag not found!' at ../src/geometry.cpp:1884

Hi:

 I made a 2d C-grid (s809.msh) with ICEM. Only two boundary conditions: pressure-far-field and wall. 
I copied input_cylinder_visc as input and change the mesh name.
Then I got the Fatal error above.
What is wrong with the settings?
Could you kindly have a look with my mesh file and input file itions (I could send them by email to you)?
Could you kindly change it and tell me how to set boundary conditions?

Best regards!
Yue Wang

Could you share the case of SD7003 airfoil

Hi:

Thank you for sharing your code.
Could you share the case of Transitional Flow over SD7003 airfoil?

With my best regards！
Yue

OS X Configure Issue

On OS X (v10.9.3), after running configure and then make, make returns:

make: *** No targets.  Stop.

This appears to result from the fact that configure is writing the contents of what should be the makefile.in file to both makefile.in and Makefile. Currently the workaround is to copy the Makefile from $HiFiLES_HOME/makefiles to $HiFiLES_HOME and change settings manually.

Mapping from existing solution to high-order scheme

Hi,

I am going to test a backward facing step flow with LES. I thought it may be helpful to use an existing RANS result as the initial condition. However, I found the RANS result is solved by the finite volume mesh and does not fit the solution points for CPR scheme. (The RANS model in your code only support 2D) Do you have any ideas how to perform the mapping? Is simply linear interpolation decrease the accuracy? Thank you.

Sherry

documentation and testcases

Hi, Thank you for sharing the code. But the documentation is not very sufficient.
Can you guys provide some documentations about the Code structure and important classes and processes of the Code?
Besides, Can you provide more 3D testcases? (such as sphere, SD7003 etc)
Than you very much!

parallel installation and run my own case

hi:
when I run ./configure_run.sh.there is problem here:err ParMETIS requested but library file not found.I do not kown how to fix it .is it need install the necessary libraries?
if i want to run my own case ,can you tell me the process?

Best regards!
Shibin Zhu

Installation Issue

I've been trying to compile HiFiLES for a couple of hours now, but I keep running into an interesting problem. I was originally trying to compile with MPI, ParMETIS, and TecIO on a Linux cluster (running CentOS), but wasn't successful. I tried the most simple installation possible, no options besides --prefix, but the problem persists. So, I tried to compile on my local machine (Fedora 20). I encountered the exact same problem. Running ./configure seems fine, but when I run make, I get the following:

make
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /home/james/codes/HiFiLES-solver/missing --run aclocal-1.11  -I m4
/home/james/codes/HiFiLES-solver/missing: line 52: aclocal-1.11: command not found
WARNING: `aclocal-1.11' is missing on your system.  You should only need it if
         you modified `acinclude.m4' or `configure.ac'.  You might want
         to install the `Automake' and `Perl' packages.  Grab them from
         any GNU archive site.
 cd . && /bin/sh /home/james/codes/HiFiLES-solver/missing --run automake-1.11 --foreign
/home/james/codes/HiFiLES-solver/missing: line 52: automake-1.11: command not found
WARNING: `automake-1.11' is missing on your system.  You should only need it if
         you modified `Makefile.am', `acinclude.m4' or `configure.ac'.
         You might want to install the `Automake' and `Perl' packages.
         Grab them from any GNU archive site.
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /home/james/codes/HiFiLES-solver/missing --run autoconf
configure.ac:30: error: possibly undefined macro: AM_INIT_AUTOMAKE
      If this token and others are legitimate, please use m4_pattern_allow.
      See the Autoconf documentation.
configure.ac:122: error: possibly undefined macro: AM_CONDITIONAL
configure.ac:413: error: possibly undefined macro: AM_PROG_CC_C_O
configure.ac:414: error: possibly undefined macro: AM_PROG_LIBTOOL
make: *** [configure] Error 1
[james@feynman HiFiLES-solver]$ 

The first thing I see is this:
You might want to install the Automake' and Perl' packages.
Automake and Perl are both up-to-date. I also see a warning that aclocal is missing, which also seems to be wrong:

[james@feynman HiFiLES-solver]$ aclocal --version
aclocal (GNU automake) 1.13.4
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv2+: GNU GPL version 2 or later <http://gnu.org/licenses/gpl-2.0.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Tom Tromey <[email protected]>
       and Alexandre Duret-Lutz <[email protected]>.

I see a lot of notes about "You should only need this if you modified ...", but I didn't touch any of the files.

Any ideas what I'm doing wrong here?

Thanks,

James

channel flow

Hi,
I'm just wondering are there any limitations to run the channel flow? I try to run this case with different parameters, which always gave me NaN residual. And for the updated version of the code, it seems that the body force term is designed for the periodic hill. Is that also valid for the channel flow case?

Thank you.

A "strange" phenomenon troubled me

Hi all,
I recently use HiFiLES (DNS) to simulate a 2D external flow. It stop at a certain time step for NaN error called by "calc_diagnostic_fields_ppts" (eles.cpp, in fact, it's "u" who should be attributed to). I then halve the timestep about 5 times, but they are all stop at the same ITERATION step! Both euler and RK advance methods have been tried.
It just conflict with my understanding. Can anyone help me out?
Thanks in advance!
Maxime

3D mesh

I'm trying to run my first 3D mesh in the solver but am getting the error "Some mpi_faces were not matched." I recall getting this error in a 2D case I ran previously and it was associated with boundary conditions. I've played with various boundary conditions for this model but am still unable to get past the mismatched faces issue. Can anyone shed light on what I may be doing wrong? I'm exporting a neutral format mesh using Gambit. I've defined the object (cylinder of aspect ratio 1) face as "Isotherm_Fix" whereas the boundaries have been set to "Sup_In" or a combination of "Sub_In_Simp" and "Sub_Out_Simp." Thank you kindly!

A Critical Problem in Memory Scalability

I tried it with BLAS=NO and parmetis=YES and OpenMPI.
In Cylinder test case It took ~7M of memory for serial but in Parallel each processor took near to 10M of memory (It is supposed 7M must be divided to number of processor) and it exactly opposite of memory scalaibility.

how to make test

I type make test
make: *** No rule to make target `test'. Stop.

So, how to run all the testcases?
Or, how to run a one own build case?
cp the cylinder directory to HiFiLES_HOME
in the HiFiLES_HOME directory, I type /bin/HiFiLES cylinder, it seems that the code runs by one in serial. So how to run it in parallel? Could you write a short readme for this. Thank you!

compilation issue

Configuration is ok.

Build Configuration Summary:

Source code location: /home/gao/Codes/HiFiLES-solver
Install location:     /
Version:              1.0.0
Compiler:             mpicxx
Preprocessor flags:   
Compiler flags:        -D_MPI
Linker flags:         
BLAS support:         
MPI support:          YES
CUDA support:         NO
TecIO support:        NO

But compilation turns out some erros shown below. What should I do?

make[3]: Leaving directory /home/gao/Codes/HiFiLES-solver/lib/parmetis-4.0.2/metis' make[3]: Entering directory/home/gao/Codes/HiFiLES-solver/lib/parmetis-4.0.2'
CC libparmetis/libparmetis_a-akwayfm.o
In file included from ./libparmetis/parmetislib.h:21:0,
from libparmetis/akwayfm.c:14:
./include/parmetis.h:18:19: fatal error: metis.h: No such file or directory
compilation terminated.
make[3]: *** [libparmetis/libparmetis_a-akwayfm.o] Error 1
make[3]: Leaving directory /home/gao/Codes/HiFiLES-solver/lib/parmetis-4.0.2' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory/home/gao/Codes/HiFiLES-solver/lib/parmetis-4.0.2'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/gao/Codes/HiFiLES-solver/lib'
make: *** [all-recursive] Error 1

How to set boundary conditions?

Hi:

I tried to made a mesh for HiFiLES by Gambit.
Do I need to set boundary conditions in Gambit?
However, when I chose generic solver in Gambit (the solver can export .neu mesh), there is no types for the boundary settings, like wall, inlet or other boundary types for HiFiLES.
What kind of software should I use for the pre-processing of HiFiLES?

Best regards!
Yue Wang

versioned makefiles

When I configure, several versioned files are modified, causing me a dilemma when I want to commit changes to the remote branch. The files are:

modified: Makefile

modified: Makefile.in

modified: aclocal.m4

modified: autom4te.cache/output.1

modified: autom4te.cache/requests

modified: autom4te.cache/traces.1

modified: config.status

modified: configure

modified: lib/Makefile.in

modified: lib/parmetis-4.0.2/Makefile

modified: lib/parmetis-4.0.2/Makefile.in

modified: lib/parmetis-4.0.2/metis/Makefile.in

modified: libtool

modified: obj/Makefile.in

Should any of these be version-controlled?

Time averaging

Hi all,

It seems the code cannot do time averaging?

Is there anyone working on that please?

Jack

Could you share any 3D case with gmsh mesh?

Hi:

Could you share any 3D simulation with gmsh mesh?
Could you please share the .geo file and the input file?
If it is a LES simulation, it would be better.

Best regards!
Yue

volume_cub_order

Anyone knows what does volume_cub_order do please?

BTW, inters_cub_order seems to do with LES? Might be better in 'LES option'?

Thanks,
Jack

Roe Flux for 3D

Hi,

Roe flux has already been coded for both 2D and 3D calculation, but it is only allowed for 2D calculation. Anyone knows why please?

Thanks,
Jack

GMSH reader does not work for quads

Discovered today that, although the Gmsh reader works properly for triangles, it does not appear to be functioning for quads (variable "xv" appears to be scrambled after reading mesh - proper number of nodes, but nodes out of order, and duplicates). Will attempt to fix over the weekend.

For reference, here is a simple 3x3 cartesian mesh that HiFiLES fails to read:

$MeshFormat
2.2 0 8
$EndMeshFormat
$PhysicalNames
5
1 1 "Sup_Out"
1 2 "Sup_In"
1 3 "Sup_In"
1 4 "Sup_Out"
1 5 "FLUID"
$EndPhysicalNames
$Nodes
16
1 -10.000000 -10.000000 0.000000
2 -3.333333 -10.000000 0.000000
3 3.333333 -10.000000 0.000000
4 10.000000 -10.000000 0.000000
5 -10.000000 -3.333333 0.000000
6 -3.333333 -3.333333 0.000000
7 3.333333 -3.333333 0.000000
8 10.000000 -3.333333 0.000000
9 -10.000000 3.333333 0.000000
10 -3.333333 3.333333 0.000000
11 3.333333 3.333333 0.000000
12 10.000000 3.333333 0.000000
13 -10.000000 10.000000 0.000000
14 -3.333333 10.000000 0.000000
15 3.333333 10.000000 0.000000
16 10.000000 10.000000 0.000000
$EndNodes
$Elements
21
1 3 2 5 5 1 2 6 5
2 3 2 5 5 2 3 7 6
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4 3 2 5 5 5 6 10 9
5 3 2 5 5 6 7 11 10
6 3 2 5 5 7 8 12 11
7 3 2 5 5 9 10 14 13
8 3 2 5 5 10 11 15 14
9 3 2 5 5 11 12 16 15
10 1 2 1 1 13 14
11 1 2 1 1 14 15
12 1 2 1 1 15 16
13 1 2 2 2 1 2
14 1 2 2 2 2 3
15 1 2 2 2 3 4
16 1 2 3 3 1 5
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20 1 2 4 4 8 12
21 1 2 4 4 12 16
$EndElements

Cloud scalability

This may be a bit off the wall, but I've been looking into Amazon's High Performance Computing cloud services. Does anyone have any experience or suggestions with regards to the utilization of HiFiLES through this framework?

input file

Hi:

Could you send me an input file for an unsteady simulation?
For example, the input file for [(3D) SD7003 wing section, 4° AoA, Re = 10,000] case?
My email is [email protected]

Best regards!
Yue Wang

Cylinder Case Error

Hi,

I have installed HiFiLES code according to the instruction in the page "https://github.com/HiFiLES/HiFiLES-solver/wiki/Installation" without any problem (including running 'configure' and 'make' commands).
And the compiled executable was created in "./bin/HiFiLES" folder.
After that I was intended to run the cylinder example and used this command in the terminal:
'HiFiLES input_cylinder_visc'
But I faced the following error.

---------------------- Non-dimensionalization ---------------------
uvw_ref: 69.4256
rho_free_stream: 5.38898e-06
rho_c_ic=1
u_c_ic=1
v_c_ic=0
w_c_ic=0
mu_c_ic=0.05

----------------------- Mesh Preprocessing ------------------------
reading connectivity ...
done reading connectivity
reading vertices
vrtlist: 714, 27, 4, 40
done reading vertices
Setting up mesh connectivity
Done setting up mesh connectivity
reading boundary conditions
Gambit mesh specs from header: , 1468, 714, 1, 3, 2
GROUP: 1 ELEMENTS: 714 MATERIAL: 2 NFLAGS: 1
fluid.1
done reading boundary conditions

---------------- Flux Reconstruction Preprocessing ----------------
initializing elements
tris
Initializing tris
Fatal error 'environment variable HIFILES_HOME is undefined' at ../src/cubature_1d.cpp:74

Would you mind helping me to fix this problem?
Thank you.

Bijan

nondimensionalization

Hi,
it can be found that a non-dimensional NS equation is solved in the solver. there should be a term (1/Re) or (Ma/Re) in the viscous term, for the equation is non-dimensionalized by free stream velocity here, there should be 1/Re in the viscous term, but i can not found it in viscFlux function. where can i find the 1/Re in the viscous term?

Best Regards,
Jiamin

Runing problem using excutable compiled from handwritten makefile

Hi,

I managed to use both configure script and handwritten Makefile to compile the code successfully. Using the executable compiled from configure script to run testcases is also fine. But, when I run testcase using the executable compiled from handwritten makefile, flow filed and output residual maintain zero. I cannot figure out what the problem is.

My local linux system is opensuse 11.4. I have tried different clusters and it gives me the same problem.

Handwritten Makefile is copied from makefiles folder and makefile.in is:

NODE= CPU
CODE= DEBUG
BLAS= NO
COMP= GCC
PARALLEL= NO
TECIO= NO
ATLAS= NO

BLAS_DIR= /usr/local/cblas

PARMETIS_DIR = /usr/local/parmetis-4.0.3

PARMETIS_BUILD_DIR = /usr/local/parmetis-4.0.3/build/Darwin-x86_64

TECIO_DIR = /usr/local/tecio-2013

CUDA_DIR = /usr/local/cuda-5.0

MPI_DIR = /usr/mpi/gcc/mvapich-1.2.0

Your help is very much appreciated.

Best wishes,
Jack

Is the any sequence to read the code?

Hi:

There are many files with *.cpp.
If I want to read the code, what should I do?

Best regards!
Yue

Negative Jacobian at solution points

Hi,

Anyone encountered this error?

I used GMSH to generate a triangle 2D mesh around an airfoile.

Best wishes,
Jack

how hifiles treat inner surfaces

May I define two "Cyclic" surfaces in a mesh?
I used "Extrude" in Gmsh to change 2D naca0012_structured mesh to 3D.
Two surfaces should be defined as "Cyclic" as I think. Question is should I define them in one Physical surface with a "Cyclic", or I could define them separately with the same name "Cyclic".

Another question: In extruded 3D naca0012 structured mesh, there are surfaces between different blocks. Is there any effect with the inner surfaces? (The outer surfaces has been defined as Boundary conditions). Will HiFiLES treat them as "real" surfaces (then it is wrong)?

Best regards!
Yue

Channel flow test case

Hi,

I'm trying to run a channel flow test case using HiFiLES. It seems that HiFi has a built-in channel flow. I have several issues about that. First, I think there might be a typo in the perturbation equation (the position of the '-' sign, line 596, eles.cpp). And could you provide me with some references of the theoretical basis of this perturbation form? I believe it's adding perturbation by using the wall normal injection, but I've never seen this before. Second, I always got a NaN body force. Do you have any suggestions on that?

Thank you.

Yongkai

Could you help me?

Hi
I have made a neu for HiFiLES by Gambit.
but I failed to set the boundary conditions after many times trial
Could you send me an neu.file and the input file for the case (2D) NACA 0012 0° AoA?
my email is [email protected]
Thank you very much!

Best regards!
chen

What is the maximum of mesh cells?

Hi,

I am wondering what is the largest mesh file you have used up to now? I am running a case with 1GB gambit mesh file and it runs out the memory of 16 processors. Thank you.

Sherry

Trouble making

Hello, I'm trying to get the solver running to perform a serial solution at this time. I'm not concerned with MPI, BLAS, etc. However, after I configure, I run the make command and get the following error on Ubuntu 14.04:

Making all in obj
make[1]: Entering directory /home/aero/CFD/HiFiLES-solver-master/obj' CXXLD ../bin/HiFiLES ../src/___bin_HiFiLES-eles.o: In functioneles::calc_src_upts_SA(int)':
/home/aero/CFD/HiFiLES-solver-master/obj/../src/eles.cpp:2753: undefined reference to calc_source_SA_3d(array<double>&, array<double>&, double&, double&)' /home/aero/CFD/HiFiLES-solver-master/obj/../src/eles.cpp:2751: undefined reference tocalc_source_SA_2d(array&, array&, double&, double&)'
collect2: error: ld returned 1 exit status
make[1]: *** [../bin/HiFiLES] Error 1
make[1]: Leaving directory `/home/aero/CFD/HiFiLES-solver-master/obj'
make: *** [all-recursive] Error 1

I have noticed it is associated with eles.cpp which seems to be one of the most recently updated files. Could there perhaps be an error with the latest update? Any help would be greatly appreciated.

Anyone manage to compile and run GPU version?

Hi,

I am struggling to use GPU version. It compiles fine but always gives me an error of invalid device function.

If you manage to use GPU version, could you please tell me which compiler and machine are you using? Could you also tell me how did you compile parmetis-4.0.2/ in the package if you use handwritten Makefile?

Your help is much appreciated.

Best wishes,
jack