From nek5000-users at lists.mcs.anl.gov Thu Apr 5 11:10:35 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 05 Apr 2012 18:10:35 +0200 Subject: [Nek5000-users] Transfer data from an nelx*nely*nelz array of Nth-order to an n*n*n array for FFT analysis Message-ID: <4F7DC3FB.3020605@onera.fr> Hi neks ! For a given velocity field (vx(1:lx1,1:ly1,1:lz1,1:lelv),vy(1:lx1,1:ly1,1:lz1,1:lelv),vz(1:lx1,1:ly1,1:lz1,1:lelv)) i would like to calculate the energy spectrum, this implies FFT transformation on regular arrays vx(1:n,1:n,1:n),vy(1:n,1:n,1:n),vz(1:n,1:n,1:n) (need deltax=deltay=deltaz=cst). On the emailing-list it has been said : "We do have off-line serial routines that can transfer data from an nelx x nely x nelz array of Nth-order elements to an nxnxn array - this allows for analysis by FFTs etc" Can you please tell me more about this ? What are these routines ?? B.regards Can From nek5000-users at lists.mcs.anl.gov Fri Apr 13 01:04:57 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 13 Apr 2012 08:04:57 +0200 Subject: [Nek5000-users] Transfer data from an nelx*nely*nelz array of Nth-order to an n*n*n array for FFT analysis In-Reply-To: <4F7DC3FB.3020605@onera.fr> References: <4F7DC3FB.3020605@onera.fr> Message-ID: Hi Neks, Hi Can, I too would be very interested in getting more information about these routines. regards Jan Am 5. April 2012 18:10 schrieb : > Hi neks ! > > For a given velocity field > (vx(1:lx1,1:ly1,1:lz1,1:lelv),vy(1:lx1,1:ly1,1:lz1,1:lelv),vz(1:lx1,1:ly1,1:lz1,1:lelv)) > i would like to calculate the energy spectrum, this implies FFT > transformation on regular arrays > vx(1:n,1:n,1:n),vy(1:n,1:n,1:n),vz(1:n,1:n,1:n) (need > deltax=deltay=deltaz=cst). > On the emailing-list it has been said : > "We do have off-line serial routines > that can transfer data from an nelx x nely x nelz array of Nth-order > elements to an nxnxn array - this allows for analysis by FFTs etc" > > > Can you please tell me more about this ? What are these routines ?? > B.regards > Can > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Apr 20 07:50:12 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 20 Apr 2012 14:50:12 +0200 Subject: [Nek5000-users] Forcing nek to read useric routine with PRESOLVE/RESTART OPTIONS set to 1 ?? Message-ID: <4F915B84.9000502@onera.fr> Hi neks, I would like to load a field (blah.f00001) and (before the first time step occur) set the velocity of some region of the domain to 0. (I want to introduce a columnar vortex in a turbulent field) For this i need nek to read the useric subroutine after it loads my blah.f00001 but by default if PRESOLVE/RESTART OPTIONS is set to 1 it doesn't read the useric subroutine. Is there a way to force it to do this ?? B.regards Can From nek5000-users at lists.mcs.anl.gov Fri Apr 20 08:39:33 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 20 Apr 2012 08:39:33 -0500 (CDT) Subject: [Nek5000-users] Forcing nek to read useric routine with PRESOLVE/RESTART OPTIONS set to 1 ?? In-Reply-To: <4F915B84.9000502@onera.fr> References: <4F915B84.9000502@onera.fr> Message-ID: Hi Can, I would read the blah.f00001 file as you are currently doing, then, in userchk() add something like: n = nx1*ny1*nz1*nelv if (istep.eq.0) then do i=1,n x = xm1(i,1,1,1) y = ym1(i,1,1,1) z = zm1(i,1,1,1) vx(i,1,1,1) = function ux of ( x , y, z ) vy(i,1,1,1) = function uy of ( x , y, z ) vz(i,1,1,1) = function uz of ( x , y, z ) enddo endif for whatever vx,vy,vz functions you want. Paul On Fri, 20 Apr 2012, nek5000-users at lists.mcs.anl.gov wrote: > Hi neks, > I would like to load a field (blah.f00001) and (before the first time step > occur) set the velocity of some region of the domain to 0. > (I want to introduce a columnar vortex in a turbulent field) > For this i need nek to read the useric subroutine after it loads my > blah.f00001 but by default if PRESOLVE/RESTART OPTIONS is set to 1 it doesn't > read the useric subroutine. > Is there a way to force it to do this ?? > > B.regards > Can > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Mon Apr 23 09:57:21 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 23 Apr 2012 16:57:21 +0200 Subject: [Nek5000-users] Problem with restart option Message-ID: <4F956DD1.1010009@googlemail.com> Hi neks, I'm having some problems with the restart feature in the version 803 of Nek5000. When I want to restart from a field-file, I get a warning saying "WARNING: reading depreacted header!" and my program crashes because of a division by zero. The file I use for my restart is from the same version of Nek5000 and the header looks like "#std 4 8 8 8 29016 29016 0.2500539468005E+02 2554 0 1 UPT " followed by bytes. Nek5000 has been compiled with Intel compilers (version 12.1.3) and OpenMPI (version 1.5.3). Is there something I'm missing? Best regards Alex -------------- next part -------------- A non-text attachment was scrubbed... Name: nek5000.log Type: text/x-log Size: 56215 bytes Desc: not available URL: -------------- next part -------------- ****** PARAMETERS ***** 2.610000 NEKTON VERSION 3 DIMENSIONAL RUN 118 PARAMETERS FOLLOW 1.00000 p001 DENSITY -2800.0 p002 VISCOS 0.00000 p003 0.00000 p004 0.00000 p005 0.00000 p006 1.00000 p007 RHOCP 0.100000 p008 CONDUCT 0.00000 p009 200.00000 p010 FINTIME 0.0000 p011 NSTEPS 0.01 p012 DT 0.00000 p013 IOCOMM 5.00000 p014 IOTIME 0.000 p015 IOSTEP 0.00000 p016 PSSOLVER: 0=default 0.00000 p017 0.500000E-01 p018 GRID < 0 --> # cells on screen -1.00000 p019 INTYPE 4.00000 p020 NORDER 1.000E-05 p021 DIVERGENCE 1.0000E-08 p022 HELMHOLTZ 0 p23 NPSCAL 0.100000E-01 p024 TOLREL 0.100000E-01 p025 TOLABS 2.00000 p026 COURANT/NTAU 3.00000 p027 TORDER 0.00000 p028 TORDER: mesh velocity (0: p28=p27) 0.00000 p029 = magnetic visc if > 0, = -1/Rm if < 0 0.00000 p030 > 0 ==> properties set in uservp() 0.00000 p031 NPERT: #perturbation modes 0.00000 p032 #BCs in re2 file, if > 0 0.00000 p033 0.00000 p034 0.00000 p035 0.00000 p036 0.00000 p037 0.00000 p038 0.00000 p039 0.00000 p040 0.00000 p041 1-->multiplicative SEMG 0.00000 p042 0=gmres/1=pcg 0.00000 p043 0=semg/1=schwarz 0.00000 p044 0=E-based/1=A-based prec. 0.00000 p045 Relaxation factor for DTFS 0.00000 p046 reserved 0.00000 p047 vnu: mesh matieral prop. 0.00000 p048 0.00000 p049 0.00000 p050 0.00000 p051 0.00000 p052 IOHIS 0.00000 p053 1.00000 p054 fixed flow rate dir: |p54|=1,2,3=x,y,z 12.56637E+00 p055 vol.flow rate (p54>0) or Ubar (p54<0) 0.00000 p056 0.00000 p057 0.00000 p058 0.00000 p059 !=0 --> full Jac. eval. for each el. 0.00000 p060 !=0 --> init. velocity to small nonzero 0.00000 p061 0.00000 p062 >0 --> force byte_swap for output 0.00000 p063 =8 --> force 8-byte output 0.00000 p064 =1 --> perturbation restart 0.00000 p065 #iofiles (eg, 0 or 64); <0 --> sep. dirs 0.00000 p066 output : <0=ascii, else binary 6.00000 p067 restart: <0=ascii, else binary 100.00000 p068 iastep: freq for avg_all (0=iostep) 0.00000 p069 0.00000 p070 0.00000 p071 0.00000 p072 0.00000 p073 0.00000 p074 verbose Helmholtz 0.00000 p075 0.00000 p076 0.00000 p077 0.00000 p078 0.00000 p079 0.00000 p080 0.00000 p081 0.00000 p082 0.00000 p083 0.00000 p084 !=0 --> sets initial timestep if p12>0 0.00000 p085 dt ratio if p84 !=0, for timesteps>0 0.00000 p086 reserved 0.00000 p087 0.00000 p088 0.00000 p089 0.00000 p090 0.00000 p091 0.00000 p092 20.0000 p093 Number of previous pressure solns saved 0.00000 p094 start projecting velocity after p94 step 5.00000 p095 start projecting pressure after p95 step 0.00000 p096 0.00000 p097 0.00000 p098 4.00000 p099 dealiasing: <0--> off/3--> old/4--> new 0.00000 p100 0.00000 p101 Number of additional modes to filter 1.00000 p102 Dump out divergence at each time step 0.05 p103 weight of stabilizing filter (.01) 0.00000 p104 0.00000 p105 0.00000 p106 0.00000 p107 !=0 --> add to h2 array in hlmhotz eqn 0.00000 p108 0.00000 p109 0.00000 p110 0.00000 p111 0.00000 p112 0.00000 p113 0.00000 p114 0.00000 p115 0.00000 p116 !=0: x elements for fast tensor product 0.00000 p117 !=0: y elements for fast tensor product 0.00000 p118 !=0: z elements for fast tensor product 4 Lines of passive scalar data follows2 CONDUCT; 2RHOCP 1.00000 1.00000 1.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 1.00000 1.00000 1.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 13 LOGICAL SWITCHES FOLLOW T IFFLOW T IFHEAT T IFTRAN T T T T T T T T T T T IFNAV & IFADVC (convection in P.S. fields) F F T T T T T T T T T T IFTMSH (IF mesh for this field is T mesh) F IFAXIS F IFSTRS F IFSPLIT F IFMGRID F IFMODEL F IFKEPS F IFMVBD T IFCHAR 8.00000 8.00000 -0.500000 -4.00000 XFAC,YFAC,XZERO,YZERO **MESH DATA** 6 lines are X,Y,Z;X,Y,Z. Columns corners 1-4;5-8 -29016 3 29016 NEL,NDIM,NELV 1 PRESOLVE/RESTART OPTIONS ***** restart0005.fld U P 7 INITIAL CONDITIONS ***** C Default C Default C Default C Default C Default C Default C Default ***** DRIVE FORCE DATA ***** BODY FORCE, FLOW, Q 4 Lines of Drive force data follow C C C C ***** Variable Property Data ***** Overrrides Parameter data. 1 Lines follow. 0 PACKETS OF DATA FOLLOW ***** HISTORY AND INTEGRAL DATA ***** 0 POINTS. Hcode, I,J,H,IEL ***** OUTPUT FIELD SPECIFICATION ***** 6 SPECIFICATIONS FOLLOW F COORDINATES T VELOCITY T PRESSURE T TEMPERATURE F TEMPERATURE GRADIENT 0 PASSIVE SCALARS ***** OBJECT SPECIFICATION ***** 0 Surface Objects 0 Volume Objects 0 Edge Objects 0 Point Objects From nek5000-users at lists.mcs.anl.gov Mon Apr 23 10:18:26 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 23 Apr 2012 17:18:26 +0200 Subject: [Nek5000-users] Problem with restart option In-Reply-To: <4F956DD1.1010009@googlemail.com> References: <4F956DD1.1010009@googlemail.com> Message-ID: <4F9572C2.6040605@itv.rwth-aachen.de> Dear Jens and Alex, try to use "mpif90" instead of "mpif77". The "mpif77" configuration on rz cluster is broken... Kind regards, Fabian On 04/23/2012 04:57 PM, nek5000-users at lists.mcs.anl.gov wrote: > Hi neks, > > I'm having some problems with the restart feature in the version 803 > of Nek5000. When I want to restart from a field-file, I get a warning > saying "WARNING: reading depreacted header!" and my program crashes > because of a division by zero. The file I use for my restart is from > the same version of Nek5000 and the header looks like > "#std 4 8 8 8 29016 29016 0.2500539468005E+02 > 2554 0 1 UPT " > followed by bytes. Nek5000 has been compiled with Intel compilers > (version 12.1.3) and OpenMPI (version 1.5.3). Is there something I'm > missing? > > Best regards > Alex > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Apr 23 10:41:59 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 23 Apr 2012 17:41:59 +0200 Subject: [Nek5000-users] Problem with restart option In-Reply-To: <4F9572C2.6040605@itv.rwth-aachen.de> References: <4F956DD1.1010009@googlemail.com> <4F9572C2.6040605@itv.rwth-aachen.de> Message-ID: Hi Alex, Not sure if this is a compiler related problem as stated by Fabian. That question to answer is the following: It looks like the read statement at 2255 at ic.f fails, that's why we jump into the parser of the old header (by mistake). This results in mess the code expects a different format of the header. That's why you get the integer division by ZERO. Cheers, -Stefan. On 4/23/12, nek5000-users at lists.mcs.anl.gov wrote: > Dear Jens and Alex, > > try to use "mpif90" instead of "mpif77". The "mpif77" configuration on > rz cluster is broken... > > Kind regards, > Fabian > > On 04/23/2012 04:57 PM, nek5000-users at lists.mcs.anl.gov wrote: >> Hi neks, >> >> I'm having some problems with the restart feature in the version 803 >> of Nek5000. When I want to restart from a field-file, I get a warning >> saying "WARNING: reading depreacted header!" and my program crashes >> because of a division by zero. The file I use for my restart is from >> the same version of Nek5000 and the header looks like >> "#std 4 8 8 8 29016 29016 0.2500539468005E+02 >> 2554 0 1 UPT " >> followed by bytes. Nek5000 has been compiled with Intel compilers >> (version 12.1.3) and OpenMPI (version 1.5.3). Is there something I'm >> missing? >> >> Best regards >> Alex >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > From nek5000-users at lists.mcs.anl.gov Mon Apr 23 10:44:42 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 23 Apr 2012 17:44:42 +0200 Subject: [Nek5000-users] Problem with restart option In-Reply-To: References: <4F956DD1.1010009@googlemail.com> <4F9572C2.6040605@itv.rwth-aachen.de> Message-ID: <4F9578EA.5050009@googlemail.com> Thanks guys, using the mpif90-wrapper solved the problem. Best wishes, Alex On 23.04.2012 17:41, nek5000-users at lists.mcs.anl.gov wrote: > Hi Alex, > > Not sure if this is a compiler related problem as stated by Fabian. > That question to answer is the following: > It looks like the read statement at 2255 at ic.f fails, that's why we > jump into the parser of the old header (by mistake). This results in > mess the code expects a different format of the header. That's why you > get the integer division by ZERO. > > Cheers, > -Stefan. > > > > > > On 4/23/12, nek5000-users at lists.mcs.anl.gov > wrote: >> Dear Jens and Alex, >> >> try to use "mpif90" instead of "mpif77". The "mpif77" configuration on >> rz cluster is broken... >> >> Kind regards, >> Fabian >> >> On 04/23/2012 04:57 PM, nek5000-users at lists.mcs.anl.gov wrote: >>> Hi neks, >>> >>> I'm having some problems with the restart feature in the version 803 >>> of Nek5000. When I want to restart from a field-file, I get a warning >>> saying "WARNING: reading depreacted header!" and my program crashes >>> because of a division by zero. The file I use for my restart is from >>> the same version of Nek5000 and the header looks like >>> "#std 4 8 8 8 29016 29016 0.2500539468005E+02 >>> 2554 0 1 UPT " >>> followed by bytes. Nek5000 has been compiled with Intel compilers >>> (version 12.1.3) and OpenMPI (version 1.5.3). Is there something I'm >>> missing? >>> >>> Best regards >>> Alex >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Mon Apr 30 16:00:14 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 30 Apr 2012 16:00:14 -0500 Subject: [Nek5000-users] Good input dataset for NEK5000 runs In-Reply-To: References: Message-ID: Hi, I am looking for a suitable input set for using NEK to compare some platforms (with diff interconnects). What is a good input set to do experiments up to 256 cores ? One from examples ? I came across papers where people have used G6a but I am unable to find that. Thanks, Abhishek On Mon, Apr 30, 2012 at 3:55 PM, Abhishek Gupta wrote: > Hi, > > I am looking for a suitable input set for using NEK to compare some > platforms (with diff interconnects). What is a good input set to do > experiments up to 256 cores ? One from examples ? I came across papers > where people have used G6a but I am unable to find that. > > Thanks, > Abhishek > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Apr 30 15:55:31 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 30 Apr 2012 15:55:31 -0500 Subject: [Nek5000-users] Good input dataset for NEK5000 runs Message-ID: Hi, I am looking for a suitable input set for using NEK to compare some platforms (with diff interconnects). What is a good input set to do experiments up to 256 cores ? One from examples ? I came across papers where people have used G6a but I am unable to find that. Thanks, Abhishek -------------- next part -------------- An HTML attachment was scrubbed... URL: