<div dir="ltr">Paul, thanks for the answer<div>For param(12) I have in .rea</div><div><div> -0.00100E-00 p012 DT</div><div>So by putting</div><div> il_hptsout=-0.5/param(12)<br></div><div>in usrchk I wanted to ensure the output with timestep 0.5,</div><div>and I don't see problem here.</div><div><br></div><div>This simulation had been running for 52 hours on 1024 cores and ended with node falure</div><div>slurmd[node1-057-01]: *** JOB 1134244 CANCELLED AT 2015-10-17T06:56:44 DUE TO NODE FAILURE ***<br></div><div><br></div><div>So may be it was something wrong on cluster, but I don't understand why <span style="color:rgb(0,0,0);font-family:'Times New Roman';font-size:16px">gdt* files (through outpost in usrchk)</span></div><div><span style="color:rgb(0,0,0);font-family:'Times New Roman';font-size:16px">and hpts.out are OK.</span></div><div><span style="font-size:16px;color:rgb(0,0,0);font-family:'Times New Roman'">For me it is also annoying</span><span style="font-size:16px;color:rgb(0,0,0);font-family:'Times New Roman'"> since I wanted to continue this simulation, but I can only do so with unmodified field output.</span><br></div><div><font color="#000000" face="Times New Roman"><span style="font-size:16px">So I had to restart it from beginning.</span></font></div><div><br></div><div>Thank you, Ilias</div><div>P.S. Below is the beginning of .rea file<br></div><div><br></div><div><br></div><div><div> ****** PARAMETERS *****</div><div> 2.60999990 NEKTON VERSION</div><div> 2 DIMENSIONAL RUN</div><div> 120 PARAMETERS FOLLOW</div><div> 1.00000 p001 DENSITY</div><div> 0.103000E-01 p002 VISCOS</div><div> 0.00000 p003</div><div> -1.00000 p004 p04 Froude^2</div><div> 0.00000 p005</div><div> 0.00000 p006</div><div> 1.00000 p007 RHOCP</div><div> 0.144000E-04 p008 CONDUCT</div><div> 0.00000 p009</div><div> 9.00000E+03 p010 FINTIME</div><div> 0.100000E+10 p011 NSTEPS</div><div> -0.010000E-01 p012 DT</div><div> 0.00000 p013 IOCOMM</div><div> 0.50000 p014 IOTIME</div><div> 0000000 p015 IOSTEP</div><div> 0.00000 p016 PSSOLVER: 0=default</div><div> 0.00000 p017</div><div> 0.00000 p018 GRID < 0 --> # cells on screen</div><div> 0.00000 p019 INTYPE</div><div> 0.00000 p020 NORDER</div><div> 0.100000E-05 p021 DIVERGENCE</div><div> 0.100000E-08 p022 HELMHOLTZ</div><div> 0 p23 NPSCAL</div><div> 0.100000E-09 p024 TOLREL</div><div> 0.100000E-09 p025 TOLABS</div><div> 2.00000 p026 COURANT/NTAU</div><div> 2.00000 p027 TORDER</div><div> 0.00000 p028 TORDER: mesh velocity (0: p28=p27)</div><div> 0.00000 p029 = magnetic visc if > 0, = -1/Rm if < 0</div><div> 0.00000 p030 > 0 ==> properties set in uservp()</div><div> 0.00000 p031 NPERT: #perturbation modes</div><div> 0.00000 p032 #BCs in re2 file, if > 0</div><div> 0.00000 p033</div><div> 0.00000 p034</div><div> 0.00000 p035</div><div> 0.00000 p036</div><div> 0.00000 p037</div><div> 0.00000 p038</div><div> 0.00000 p039</div><div> 0.00000 p040</div><div> 0.00000 p041 1-->multiplicative SEMG</div><div> 0.00000 p042 0=gmres/1=pcg</div><div> 1.00000 p043 0=semg/1=schwarz</div><div> 0.00000 p044 0=E-based/1=A-based prec.</div><div> 0.00000 p045 Relaxation factor for DTFS</div><div> 0.00000 p046 reserved</div><div> 0.00000 p047 vnu: mesh matieral prop.</div><div> 0.00000 p048</div><div> 0.00000 p049</div><div> 0.00000 p050</div><div> 0.00000 p051</div><div> 0.00000 p052 IOHIS</div><div> 0.00000 p053</div><div> 0.00000 p054 fixed flow rate dir: |p54|=1,2,3=x,y,z</div><div> 0.00000 p055 vol.flow rate (p54>0) or Ubar (p54<0)</div><div> 0.00000 p056</div><div> 0.00000 p057</div><div> 0.00000 p058</div><div> 0.00000 p059 !=0 --> full Jac. eval. for each el.</div><div> 0.00000 p060 !=0 --> init. velocity to small nonzero</div><div> 0.00000 p061</div><div> 0.00000 p062 >0 --> force byte_swap for output</div><div> 0.00000 p063 =8 --> force 8-byte output</div><div> 0.00000 p064 =1 --> perturbation restart</div><div> 1.00000 p065 #iofiles (eg, 0 or 64); <0 --> sep. dirs</div><div> 6.00000 p066 output : <0=ascii, else binary</div><div> 6.00000 p067 restart: <0=ascii, else binary</div><div> 0.00000 p068 iastep: freq for avg_all (0=iostep)</div><div> 0.00000 p069</div><div> 0.00000 p070</div><div> 0.00000 p071</div><div> 0.00000 p072</div><div> 0.00000 p073</div><div> 0.00000 p074 verbose Helmholtz</div><div> 0.00000 p075</div><div> 0.00000 p076</div><div> 0.00000 p077</div><div> 0.00000 p078</div><div> 0.00000 p079</div><div> 0.00000 p080</div><div> 0.00000 p081</div><div> 0.00000 p082</div><div> 0.00000 p083</div><div> 0.00000 p084 !=0 --> sets initial timestep if p12>0</div><div> 0.00000 p085 dt ratio if p84 !=0, for timesteps>0</div><div> 0.00000 p086 reserved</div><div> 0.00000 p087</div><div> 0.00000 p088</div><div> 0.00000 p089 p89 reserved</div><div> 0.00000 p090</div><div> 0.00000 p091</div><div> 0.00000 p092</div><div> 50.0000 p093 Number of previous pressure solns saved</div><div> 5.00000 p094 start projecting velocity after p94 step</div><div> 5.00000 p095 start projecting pressure after p95 step</div><div> 0.00000 p096</div><div> 0.00000 p097</div><div> 0.00000 p098</div><div> 3.00000 p099 dealiasing: <0--> off/3--> old/4--> new</div><div> 0.00000 p100</div><div> 1.00000 p101 Number of additional modes to filter</div><div> 0.00000 p102 Dump out divergence at each time step</div><div> 0.05000 p103 weight of stabilizing filter (.01)</div><div> 0.00000 p104</div><div> 0.00000 p105</div><div> 0.00000 p106</div><div> 0.00000 p107 !=0 --> add to h2 array in hlmhotz eqn</div><div> 0.00000 p108</div><div> 0.00000 p109</div><div> 0.00000 p110</div><div> 0.00000 p111</div><div> 0.00000 p112</div></div><div><div> 0.00000 p113</div><div> 0.00000 p114</div><div> 0.00000 p115</div><div> 0.00000 p116 !=0: x elements for fast tensor product</div><div> 0.00000 p117 !=0: y elements for fast tensor product</div><div> 0.00000 p118 !=0: z elements for fast tensor product</div><div> 0.00000 p119 p119</div><div> 0.00000 p120 p120</div><div> 4 Lines of passive scalar data follows2 CONDUCT; 2RHOCP</div><div> 1.00000 1.00000 1.00000 1.00000 1.00000</div><div> 1.00000 1.00000 1.00000 1.00000</div><div> 1.00000 1.00000 1.00000 1.00000 1.00000</div><div> 1.00000 1.00000 1.00000 1.00000</div><div> 13 LOGICAL SWITCHES FOLLOW</div><div> T IFFLOW</div><div> T IFHEAT</div><div> T IFTRAN</div><div> T T F F F F F F F F F IFNAV & IFADVC (convection in P.S. fields)</div><div> F F T T T T T T T T T T IFTMSH (IF mesh for this field is T mesh)</div><div> F IFAXIS</div><div> F IFSTRS</div><div> F IFSPLIT</div><div> F IFMGRID</div><div> F IFMODEL</div><div> F IFKEPS</div><div> F IFMVBD</div><div> T IFCHAR</div><div> 100.000 100.000 -20.0000 -30.0000 XFAC,YFAC,XZERO,YZERO</div><div> **MESH DATA** 1st line is X of corner 1,2,3,4. 2nd line is Y.</div><div> 360000 2 360000 NEL,NDIM,NELV</div></div><div><br></div><div>...</div><div><br></div><div><div> 0 PRESOLVE/RESTART OPTIONS *****</div><div> 7 INITIAL CONDITIONS *****<br></div><div>C Default</div><div>C Default</div><div>C Default</div><div>C Default</div><div>C Default</div><div>C Default</div><div>C Default</div><div> ***** DRIVE FORCE DATA ***** BODY FORCE, FLOW, Q</div><div> 4 Lines of Drive force data follow</div><div>C</div><div>C</div><div>C</div><div>C</div><div> ***** Variable Property Data ***** Overrrides Parameter data.</div><div> 1 Lines follow.</div><div> 0 PACKETS OF DATA FOLLOW</div><div> ***** HISTORY AND INTEGRAL DATA *****</div><div> 0 POINTS. Hcode, I,J,H,IEL</div><div> ***** OUTPUT FIELD SPECIFICATION *****</div><div> 6 SPECIFICATIONS FOLLOW</div><div> F COORDINATES</div><div> T VELOCITY</div><div> F PRESSURE</div><div> T TEMPERATURE</div><div> F TEMPERATURE GRADIENT</div><div> 0 PASSIVE SCALARS</div><div> ***** OBJECT SPECIFICATION *****</div><div> 0 Surface Objects</div><div> 0 Volume Objects</div><div> 0 Edge Objects</div><div> 0 Point Objects</div><div> 3960173,8 Bot</div></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Oct 27, 2015 at 3:23 PM, <span dir="ltr"><<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-family:Tahoma;color:rgb(0,0,0);font-size:10pt">
<div><br>
</div>
There is an issue that you don't know for certain the sign of param(12)... so I would check
<div>to be sure to clean up your integer il_hptsout.</div>
<div><br>
</div>
<div>To me, however, it's not clear that that issue alone would be causing the problem.</div>
<div><br>
</div>
<div>Paul</div>
<div><br>
<div><br>
</div>
<div>
<div style="font-family:'Times New Roman';color:rgb(0,0,0);font-size:16px">
<hr>
<div style="direction:ltr"><font face="Tahoma" size="2" color="#000000"><b>From:</b> <a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov" target="_blank">nek5000-users-bounces@lists.mcs.anl.gov</a> [<a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov" target="_blank">nek5000-users-bounces@lists.mcs.anl.gov</a>] on behalf of <a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.gov</a> [<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.gov</a>]<br>
<b>Sent:</b> Tuesday, October 27, 2015 6:33 AM<br>
<b>To:</b> <a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.gov</a><br>
<b>Subject:</b> [Nek5000-users] output through .rea and through usrchk<br>
</font><br>
</div>
<div></div>
<div>
<div dir="ltr">Dear neks,
<div><br>
</div>
<div>Strange thing happend to a simulation where</div>
<div>I made "standart" output through .rea file,</div>
<div>i.e.</div>
<div>
<div> -0.010000E-01 p012 DT</div>
<div> 0.00000 p013 IOCOMM</div>
<div> 0.50000 p014 IOTIME</div>
<div>and at the same time I need scalar gradients, so I've put to usrchk:</div>
</div>
<div>
<div>
<div><br>
</div>
<div> il_hptsout=-0.5/param(12)</div>
</div>
<div><br>
</div>
<div> if ((istep.gt.0).and.(mod(istep,il_hptsout).eq.0)) then<br>
</div>
</div>
<div>
<div>
<div> call gradm1(dtdx,dtdy,dtdz,t)</div>
</div>
<div> call outpost(dtdx,dtdy,dtdz,pr,t,'gdt')<br>
</div>
</div>
<div>
<div> endif</div>
</div>
<div><br>
</div>
<div>The strange thing that gdt* (from usrchk) files are saved as should should be,</div>
<div>but "standart" CASE0.f* were saved onli partially, below is 'ls -rt' of the case directory.</div>
<div>Why whould that happen? may it be cluster issue? (file sizes are not small ~530mb)</div>
<div><br>
</div>
<div>
<div>-rw-rw-r-- 1 35K Oct 15 02:52 compiler.out</div>
<div>-rw-rw-r-- 1 99 Oct 15 02:55 <a href="http://SESSION.NAME" target="_blank">
SESSION.NAME</a></div>
<div>-rw-rw-r-- 1 52 Oct 15 02:55 lognekbmpi.txt</div>
<div>-rw-rw-r-- 1 353M Oct 15 03:54 gdtI0.f00001</div>
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