Here it is:<br><br>#!/bin/bash<br># Nek5000 build config file<br># (c) 2008,2009,2010 UCHICAGO ARGONNE, LLC<br><br># source path <br>SOURCE_ROOT="$HOME/Codes/nek5_svn/trunk/nek" <br><br># Fortran compiler<br>F77="mpif77"<br>
<br># C compiler<br>CC="mpicc"<br><br># pre-processor symbol list <br># (set PPLIST=? to get a list of available symbols)<br>#PPLIST="?" <br><br># plug-in list<br>PLUGIN_LIST=""<br><br><br># OPTIONAL SETTINGS<br>
# -----------------<br><br># enable MPI (default true)<br>#IFMPI="false"<br><br># auxilliary files to compile<br># NOTE: source files have to located in the same directory as makenek<br># a makefile_usr.inc has to be provided containing the build rules <br>
#USR="foo.o"<br><br># linking flags<br>#USR_LFLAGS="-L/usr/lib -lfoo"<br><br># generic compiler flags<br>#G="-g"<br><br># optimization flags<br>#OPT_FLAGS_STD=""<br>#OPT_FLAGS_MAG=""<br>
<br># enable AMG coarse grid solver (default XXT)<br>#IFAMG="true"<br>#IFAMG_DUMP="true"<br><br># CVODE path<br>#CVODE_DIR=$HOME/cvode/lib<br> <br># MOAB/iMESH path<br>#MOAB_DIR="$HOME/moab"<br>
<br><br>###############################################################################<br># DONT'T TOUCH WHAT FOLLOWS !!!<br>###############################################################################<br># assign version tag<br>
mver=1<br># overwrite source path with optional 2nd argument<br>if [ -d $2 ] && [ $# -eq 2 ]; then<br> SOURCE_ROOT="$2"<br> echo "change source code directory to: ", $SOURCE_ROOT<br>fi<br># do some checks and create makefile<br>
source $SOURCE_ROOT/makenek.inc<br># compile<br>make -j4 -f makefile 2>&1 | tee compiler.out<br>exit 0<br><br><br><div class="gmail_quote">On 18 October 2011 19:13, <span dir="ltr"><<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Please post your makenek.<br>
-Stefan<br>
<br>
On 10/18/11, <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
<div><div></div><div class="h5"><<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>> wrote:<br>
> Hi,<br>
><br>
> Sorry for this very late response, it completely got out of my mind. Here<br>
> are the different outputs I get for these commands:<br>
><br>
> jean-christophe@dyf-corto:~/Calculs/Cavite2D/BaseFlow$ ulimit -a<br>
> core file size (blocks, -c) 0<br>
> data seg size (kbytes, -d) unlimited<br>
> scheduling priority (-e) 0<br>
> file size (blocks, -f) unlimited<br>
> pending signals (-i) 31533<br>
> max locked memory (kbytes, -l) 64<br>
> max memory size (kbytes, -m) unlimited<br>
> open files (-n) 1024<br>
> pipe size (512 bytes, -p) 8<br>
> POSIX message queues (bytes, -q) 819200<br>
> real-time priority (-r) 0<br>
> stack size (kbytes, -s) 8192<br>
> cpu time (seconds, -t) unlimited<br>
> max user processes (-u) 31533<br>
> virtual memory (kbytes, -v) unlimited<br>
> file locks (-x) unlimited<br>
><br>
> jean-christophe@dyf-corto:~/Calculs/Cavite2D/BaseFlow$ size nek5000<br>
> text data bss dec hex filename<br>
> 2232834 3484 185835044 188071362 b35bdc2 nek5000<br>
><br>
> jean-christophe@dyf-corto:~/Calculs/Cavite2D/BaseFlow$ cat SIZE<br>
> C Dimension file to be included<br>
> C<br>
> C HCUBE array dimensions<br>
> C<br>
> parameter (ldim=2)<br>
> parameter (lx1=11,ly1=lx1,lz1=1,lelt=225,lelv=lelt)<br>
> parameter (lxd=17,lyd=lxd,lzd=1)<br>
> parameter (lelx=20,lely=60,lelz=1)<br>
> c<br>
> parameter (lzl=3 + 2*(ldim-3))<br>
> c<br>
> parameter (lx2=lx1-2)<br>
> parameter (ly2=ly1-2)<br>
> parameter (lz2=1)<br>
> parameter (lx3=lx2)<br>
> parameter (ly3=ly2)<br>
> parameter (lz3=lz2)<br>
> c<br>
> c parameter (lpelv=lelv,lpelt=lelt,lpert=3) ! perturbation<br>
> c parameter (lpx1=lx1,lpy1=ly1,lpz1=lz1) ! array sizes<br>
> c parameter (lpx2=lx2,lpy2=ly2,lpz2=lz2)<br>
> c<br>
> parameter (lpelv=1,lpelt=1,lpert=1) ! perturbation<br>
> parameter (lpx1=1,lpy1=1,lpz1=1) ! array sizes<br>
> parameter (lpx2=1,lpy2=1,lpz2=1)<br>
> c<br>
> c<br>
> c parameter (lbelv=lelv,lbelt=lelt) ! MHD<br>
> c parameter (lbx1=lx1,lby1=ly1,lbz1=lz1) ! array sizes<br>
> c parameter (lbx2=lx2,lby2=ly2,lbz2=lz2)<br>
> c<br>
> parameter (lbelv=1,lbelt=1) ! MHD<br>
> parameter (lbx1=1,lby1=1,lbz1=1) ! array sizes<br>
> parameter (lbx2=1,lby2=1,lbz2=1)<br>
> c<br>
> C LX1M=LX1 when there are moving meshes; =1 otherwise<br>
> parameter (lx1m=lx1,ly1m=ly1,lz1m=lz1)<br>
> parameter (ldimt= 4) ! 3 passive scalars + T<br>
> parameter (ldimt1=ldimt+1)<br>
> parameter (ldimt3=ldimt+3)<br>
> parameter (lp = 8)<br>
> parameter (lelg = 300)<br>
> c<br>
> c Note: In the new code, LELGEC should be about sqrt(LELG)<br>
> c<br>
> PARAMETER (LELGEC = 1)<br>
> PARAMETER (LXYZ2 = 1)<br>
> PARAMETER (LXZ21 = 1)<br>
> c<br>
> PARAMETER (LMAXV=LX1*LY1*LZ1*LELV)<br>
> PARAMETER (LMAXT=LX1*LY1*LZ1*LELT)<br>
> PARAMETER (LMAXP=LX2*LY2*LZ2*LELV)<br>
> PARAMETER (LXZ=LX1*LZ1)<br>
> PARAMETER (LORDER=3)<br>
> PARAMETER (MAXOBJ=4,MAXMBR=LELT*6,lhis=100)<br>
> C<br>
> C Common Block Dimensions<br>
> C<br>
> PARAMETER (LCTMP0 =2*LX1*LY1*LZ1*LELT)<br>
> PARAMETER (LCTMP1 =4*LX1*LY1*LZ1*LELT)<br>
> C<br>
> C The parameter LVEC controls whether an additional 42 field arrays<br>
> C are required for Steady State Solutions. If you are not using<br>
> C Steady State, it is recommended that LVEC=1.<br>
> C<br>
> PARAMETER (LVEC=1)<br>
> C<br>
> C Uzawa projection array dimensions<br>
> C<br>
> parameter (mxprev = 80)<br>
> parameter (lgmres = 40)<br>
> C<br>
> C Split projection array dimensions<br>
> C<br>
> parameter(lmvec = 1)<br>
> parameter(lsvec = 1)<br>
> parameter(lstore=lmvec*lsvec)<br>
> c<br>
> c NONCONFORMING STUFF<br>
> c<br>
> parameter (maxmor = lelt)<br>
> C<br>
> C Array dimensions<br>
> C<br>
> COMMON/DIMN/NELV,NELT,NX1,NY1,NZ1,NX2,NY2,NZ2<br>
> $,NX3,NY3,NZ3,NDIM,NFIELD,NPERT,NID<br>
> $,NXD,NYD,NZD<br>
><br>
> c automatically added by makenek<br>
> parameter(lxo = lx1) ! max output grid size (lxo>=lx1)<br>
><br>
> c automatically added by makenek<br>
> parameter(lpart = 1 ) ! max number of particles<br>
><br>
> c automatically added by makenek<br>
> integer ax1,ay1,az1,ax2,ay2,az2<br>
> parameter (ax1=lx1,ay1=ly1,az1=lz1,ax2=lx2,ay2=ly2,az2=lz2) ! running<br>
> averages<br>
><br>
> c automatically added by makenek<br>
> parameter (lxs=1,lys=lxs,lzs=(lxs-1)*(ldim-2)+1) !New Pressure<br>
> Preconditioner<br>
><br>
> c automatically added by makenek<br>
> parameter (lfdm=0) ! == 1 for fast diagonalization method<br>
><br>
> Concerning Nek, yes I do get an output on the screen when lauching the<br>
> calculation. Attached is the logfile for one example (2D cavity, only with<br>
> 100 elements though but the problem is the same as I increase the number of<br>
> elements).<br>
><br>
> Cheers,<br>
><br>
> On 18 October 2011 18:03, Jean-Christophe Loiseau<br>
> <<a href="mailto:loiseau.jc@gmail.com">loiseau.jc@gmail.com</a>>wrote:<br>
><br>
>> Hi,<br>
>><br>
>> Sorry for this very late response, it completely got out of my mind. Here<br>
>> are the different outputs I get for these commands:<br>
>><br>
>> jean-christophe@dyf-corto:~/Calculs/Cavite2D/BaseFlow$ ulimit -a<br>
>> core file size (blocks, -c) 0<br>
>> data seg size (kbytes, -d) unlimited<br>
>> scheduling priority (-e) 0<br>
>> file size (blocks, -f) unlimited<br>
>> pending signals (-i) 31533<br>
>> max locked memory (kbytes, -l) 64<br>
>> max memory size (kbytes, -m) unlimited<br>
>> open files (-n) 1024<br>
>> pipe size (512 bytes, -p) 8<br>
>> POSIX message queues (bytes, -q) 819200<br>
>> real-time priority (-r) 0<br>
>> stack size (kbytes, -s) 8192<br>
>> cpu time (seconds, -t) unlimited<br>
>> max user processes (-u) 31533<br>
>> virtual memory (kbytes, -v) unlimited<br>
>> file locks (-x) unlimited<br>
>><br>
>> jean-christophe@dyf-corto:~/Calculs/Cavite2D/BaseFlow$ size nek5000<br>
>> text data bss dec hex filename<br>
>> 2232834 3484 185835044 188071362 b35bdc2 nek5000<br>
>><br>
>> jean-christophe@dyf-corto:~/Calculs/Cavite2D/BaseFlow$ cat SIZE<br>
>> C Dimension file to be included<br>
>> C<br>
>> C HCUBE array dimensions<br>
>> C<br>
>> parameter (ldim=2)<br>
>> parameter (lx1=11,ly1=lx1,lz1=1,lelt=225,lelv=lelt)<br>
>> parameter (lxd=17,lyd=lxd,lzd=1)<br>
>> parameter (lelx=20,lely=60,lelz=1)<br>
>> c<br>
>> parameter (lzl=3 + 2*(ldim-3))<br>
>> c<br>
>> parameter (lx2=lx1-2)<br>
>> parameter (ly2=ly1-2)<br>
>> parameter (lz2=1)<br>
>> parameter (lx3=lx2)<br>
>> parameter (ly3=ly2)<br>
>> parameter (lz3=lz2)<br>
>> c<br>
>> c parameter (lpelv=lelv,lpelt=lelt,lpert=3) ! perturbation<br>
>> c parameter (lpx1=lx1,lpy1=ly1,lpz1=lz1) ! array sizes<br>
>> c parameter (lpx2=lx2,lpy2=ly2,lpz2=lz2)<br>
>> c<br>
>> parameter (lpelv=1,lpelt=1,lpert=1) ! perturbation<br>
>> parameter (lpx1=1,lpy1=1,lpz1=1) ! array sizes<br>
>> parameter (lpx2=1,lpy2=1,lpz2=1)<br>
>> c<br>
>> c<br>
>> c parameter (lbelv=lelv,lbelt=lelt) ! MHD<br>
>> c parameter (lbx1=lx1,lby1=ly1,lbz1=lz1) ! array sizes<br>
>> c parameter (lbx2=lx2,lby2=ly2,lbz2=lz2)<br>
>> c<br>
>> parameter (lbelv=1,lbelt=1) ! MHD<br>
>> parameter (lbx1=1,lby1=1,lbz1=1) ! array sizes<br>
>> parameter (lbx2=1,lby2=1,lbz2=1)<br>
>> c<br>
>> C LX1M=LX1 when there are moving meshes; =1 otherwise<br>
>> parameter (lx1m=lx1,ly1m=ly1,lz1m=lz1)<br>
>> parameter (ldimt= 4) ! 3 passive scalars + T<br>
>> parameter (ldimt1=ldimt+1)<br>
>> parameter (ldimt3=ldimt+3)<br>
>> parameter (lp = 8)<br>
>> parameter (lelg = 300)<br>
>> c<br>
>> c Note: In the new code, LELGEC should be about sqrt(LELG)<br>
>> c<br>
>> PARAMETER (LELGEC = 1)<br>
>> PARAMETER (LXYZ2 = 1)<br>
>> PARAMETER (LXZ21 = 1)<br>
>> c<br>
>> PARAMETER (LMAXV=LX1*LY1*LZ1*LELV)<br>
>> PARAMETER (LMAXT=LX1*LY1*LZ1*LELT)<br>
>> PARAMETER (LMAXP=LX2*LY2*LZ2*LELV)<br>
>> PARAMETER (LXZ=LX1*LZ1)<br>
>> PARAMETER (LORDER=3)<br>
>> PARAMETER (MAXOBJ=4,MAXMBR=LELT*6,lhis=100)<br>
>> C<br>
>> C Common Block Dimensions<br>
>> C<br>
>> PARAMETER (LCTMP0 =2*LX1*LY1*LZ1*LELT)<br>
>> PARAMETER (LCTMP1 =4*LX1*LY1*LZ1*LELT)<br>
>> C<br>
>> C The parameter LVEC controls whether an additional 42 field arrays<br>
>> C are required for Steady State Solutions. If you are not using<br>
>> C Steady State, it is recommended that LVEC=1.<br>
>> C<br>
>> PARAMETER (LVEC=1)<br>
>> C<br>
>> C Uzawa projection array dimensions<br>
>> C<br>
>> parameter (mxprev = 80)<br>
>> parameter (lgmres = 40)<br>
>> C<br>
>> C Split projection array dimensions<br>
>> C<br>
>> parameter(lmvec = 1)<br>
>> parameter(lsvec = 1)<br>
>> parameter(lstore=lmvec*lsvec)<br>
>> c<br>
>> c NONCONFORMING STUFF<br>
>> c<br>
>> parameter (maxmor = lelt)<br>
>> C<br>
>> C Array dimensions<br>
>> C<br>
>> COMMON/DIMN/NELV,NELT,NX1,NY1,NZ1,NX2,NY2,NZ2<br>
>> $,NX3,NY3,NZ3,NDIM,NFIELD,NPERT,NID<br>
>> $,NXD,NYD,NZD<br>
>><br>
>> c automatically added by makenek<br>
>> parameter(lxo = lx1) ! max output grid size (lxo>=lx1)<br>
>><br>
>> c automatically added by makenek<br>
>> parameter(lpart = 1 ) ! max number of particles<br>
>><br>
>> c automatically added by makenek<br>
>> integer ax1,ay1,az1,ax2,ay2,az2<br>
>> parameter (ax1=lx1,ay1=ly1,az1=lz1,ax2=lx2,ay2=ly2,az2=lz2) !<br>
>> running<br>
>> averages<br>
>><br>
>> c automatically added by makenek<br>
>> parameter (lxs=1,lys=lxs,lzs=(lxs-1)*(ldim-2)+1) !New Pressure<br>
>> Preconditioner<br>
>><br>
>> c automatically added by makenek<br>
>> parameter (lfdm=0) ! == 1 for fast diagonalization method<br>
>><br>
>> Concerning Nek, yes I do get an output on the screen when lauching the<br>
>> calculation. Attached is the logfile for one example (2D cavity, only with<br>
>> 100 elements though but the problem is the same as I increase the number<br>
>> of<br>
>> elements).<br>
>><br>
>> Cheers,<br>
>><br>
>><br>
>> On 27 September 2011 17:40, <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>> wrote:<br>
>><br>
>>> Hi,<br>
>>><br>
>>> Do you get any output printed to the screen when you launch Nek?<br>
>>> Please provide the output of the following command:<br>
>>> ulimit -a (in case you are using bash)<br>
>>> size nek5000<br>
>>> cat SIZE<br>
>>><br>
>>> Can you post the command you are using to launch Nek in parallel?<br>
>>><br>
>>> Cheers,<br>
>>> Stefan<br>
>>><br>
>>><br>
>>><br>
>>> On 9/27/11, <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
>>> <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>> wrote:<br>
>>> > Hi Neks,<br>
>>> ><br>
>>> > I do get the same error when I try to run nek on my laptop. Did you<br>
>>> > find<br>
>>> any<br>
>>> > way to solve the problem John?<br>
>>> ><br>
>>> > Regards,<br>
>>> ><br>
>>> > On 11 May 2011 21:25, <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>> wrote:<br>
>>> ><br>
>>> >> Hi,<br>
>>> >><br>
>>> >> I have lp=512 in SIZE, and I did compile with IFMPI=true. I<br>
>>> >> recompiled<br>
>>> >> yesterday because I thought this may be the case, but I was still<br>
>>> getting<br>
>>> >> the same error. When I first start a simulation and run top, it shows<br>
>>> >> four<br>
>>> >> processors running nek5000, but this changes to one processor after a<br>
>>> few<br>
>>> >> seconds.<br>
>>> >><br>
>>> >> Thanks,<br>
>>> >><br>
>>> >> John<br>
>>> >><br>
>>> >> _______________________________________________<br>
>>> >> Nek5000-users mailing list<br>
>>> >> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
>>> >> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
>>> >><br>
>>> >><br>
>>> ><br>
>>> ><br>
>>> > --<br>
>>> > Jean-Christophe<br>
>>> ><br>
>>> _______________________________________________<br>
>>> Nek5000-users mailing list<br>
>>> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
>>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
>>><br>
>><br>
>><br>
>><br>
>> --<br>
>> Jean-Christophe<br>
>><br>
><br>
><br>
><br>
> --<br>
> Jean-Christophe<br>
><br>
_______________________________________________<br>
Nek5000-users mailing list<br>
<a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
<a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Jean-Christophe<br>