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    <div class="moz-cite-prefix">Hi<br>
      <br>
      No, not this way. First of all you have to setup linear
      simulation. For this you need to modify SIZE to let all the
      perturbation variables to be used. You should have following
      section setting correct array sizes:<br>
            parameter (lpelv=lelv,lpelt=lelt,lpert=1) ! perturbation<br>
            parameter (lpx1=lx1,lpy1=ly1,lpz1=lz1)     ! array sizes<br>
            parameter (lpx2=lx2,lpy2=ly2,lpz2=lz2)<br>
      <br>
      Next you have to set p031 = -1 to have evolution of the single
      perturbation with constant base flow. Base flow has to be
      specified in and ###.rea file as a restart option; e.g.<br>
         1 PRESOLVE/RESTART OPTIONS  *****<br>
      baseflow.bsf<br>
         7         INITIAL CONDITIONS *****<br>
      <br>
      Setting p108 = 0 you simply turn off Arnoldi, so only dns is
      performed.<br>
      Regards<br>
      Adam<br>
      <br>
      <br>
      On 2016-03-30 14:25, <a class="moz-txt-link-abbreviated" href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a> wrote:<br>
    </div>
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cite="mid:mailman.18472.1459340753.24727.nek5000-users@lists.mcs.anl.gov"
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                        <div>Hi Adam, <br>
                          <br>
                        </div>
                        Thanks for your response. Here is what I
                        understand the steps I should follow to run the
                        'ext_cyl' example, from <a
                          moz-do-not-send="true"
                          href="https://nek5000.mcs.anl.gov/toolboxes/"
                          target="_blank"><a class="moz-txt-link-freetext" href="https://nek5000.mcs.anl.gov/toolboxes/">https://nek5000.mcs.anl.gov/toolboxes/</a></a>:<br>
                        <br>
                      </div>
                      Base flow run: Compile with the following
                      parameter setting:<br>
                    </div>
                    <br>
                    p031 = 0<br>
                  </div>
                  p069 = 0<br>
                  <br>
                </div>
                and I think I should also set p108 = 0 (without setting
                p108 = 0, I get an error saying "ERROR: arnoldi has to
                be run in perturbation mode")<br>
                <br>
              </div>
              Hence, I do a base flow run with p031=0, p069=0 and p108 =
              0. Am I correct here?<br>
              <br>
            </div>
            If I do the base flow run with p031=0, p069=0 and p108 = 0,
            I see lot of error in ext_cyl.log file as:<br>
            <br>
            Step   1826, t= 9.1300000E+00, DT= 5.0000000E-03, C=  0.000
            3.5844E+02 1.9493E-01<br>
             Solving for fluid F T T<br>
              1826   100 **ERROR**: Failed in HMHOLTZ: VELX         
            NaN          NaN   1.0000E-10<br>
              1826   100 **ERROR**: Failed in HMHOLTZ: VELY         
            NaN          NaN   1.0000E-10<br>
            <br>
          </div>
          Nevertheless, I do see a file 'ext_cyl0.f00001' written after
          some simulation time, however, I do not see the restart files,
          'ARVext_cy0.f00001' and 'ARPext_cy0.f00001', written at the
          same time. I will continue to run the base flow simulation for
          longer duration, in the meantime, I wanted to confirm if I am
          on the right path so far?<br>
          <br>
        </div>
        <div>Regards, <br>
        </div>
        <div>Ravi<br>
          <br>
        </div>
        <br>
        <div>
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            <div>
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      <div class="gmail_extra"><br>
        <div class="gmail_quote">On Wed, Mar 30, 2016 at 6:52 AM, <span
            dir="ltr"><<a moz-do-not-send="true"
              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:0 0 0
            .8ex;border-left:1px #ccc solid;padding-left:1ex">
            <div text="#000000" bgcolor="#FFFFFF">
              <div>Hi Ravi<br>
                <br>
                The first error means you have no restart files, which
                is obvious for the first run. Restart files are (ARP###
                and ARV###) are generated at the end of the run if the
                tolerance is not reached. You control it by parameter 69
                in ###.rea. Simply set it to 0 for the first run. In
                addition parameters 71 and 72 set the checkpoint number
                for reading and writing (to avoid overwriting). Number
                of files depends on the other parameters and
                preprocessing flags used.<br>
                Regards<br>
                Adam
                <div>
                  <div class="h5"><br>
                    <br>
                    On 2016-03-27 04:45, <a moz-do-not-send="true"
                      href="mailto:nek5000-users@lists.mcs.anl.gov"
                      target="_blank">nek5000-users@lists.mcs.anl.gov</a>
                    wrote:<br>
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              <div>
                <div class="h5">
                  <blockquote type="cite">
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                            <div>Hi Adam, <br>
                              <br>
                            </div>
                            I am guessing I am using your code for
                            stability tools in NEK. I have downloaded
                            the code from <a moz-do-not-send="true"
                              href="https://nek5000.mcs.anl.gov/toolboxes/"
                              target="_blank">https://nek5000.mcs.anl.gov/toolboxes/</a>.<br>
                            <br>
                          </div>
                          I am trying to reproduce the ext_cyl example,
                          as is, to get some familiarity. <br>
                          <br>
                        </div>
                        I have been able to compile the code (after some
                        modifications to compile on the platform I
                        intent to run my analysis). I have the base flow
                        file "ext_cyl0.f00005" in the simulation folder.
                        When I run the ext_cyl, I get the following
                        error:<br>
                        <br>
                        <br>
******************************************************************************************************************<br>
                        call userchk<br>
                         ARNOLDI:<br>
                         Reading checkpoint<br>
                               0       0 OPEN: ARPext_cyl0.f00005<br>
                        ARPext_cyl0.f00005<br>
                        byte_read() :: fopen failure2!<br>
                         ERROR: mfi_arnp, wrong header; abort.<br>
                        <br>
                        call exitt: dying ...<br>
******************************************************************************************************************<br>
                      </div>
                      <br>
                      <div><br>
                        <div>I have also pasted below  the parameters
                          printed in the log file for your reference.  <br>
                        </div>
                        <div><br>
******************************************************************************************************************<br>
                        </div>
                        122   Parameters from <a moz-do-not-send="true">file:/global/u2/r/rtumkur/eig_Setup/ARNOLDI/ext_cyl.rea</a><br>
                           1      1.00000     p001 DENSITY<br>
                           2     -50.0000     p002 VISCOS<br>
                           7      1.00000     p007 RHOCP<br>
                           8      1.00000     p008 CONDUCT<br>
                          11      50003.0     p011 NSTEPS<br>
                          12    -5.000000E-03 p012 DT<br>
                          15      2500.00     p015 IOSTEP<br>
                          17      1.00000     p017<br>
                          18     0.500000E-01 p018 GRID < 0 --> #
                        cells on screen<br>
                          19     -1.00000     p019 INTYPE<br>
                          20      7.00000     p020 NORDER<br>
                          21     0.100000E-09 p021 DIVERGENCE<br>
                          22     0.100000E-09 p022 HELMHOLTZ<br>
                          24     0.100000E-09 p024 TOLREL<br>
                          25     0.100000E-04 p025 TOLABS<br>
                          26      1.00000     p026 COURANT/NTAU<br>
                          27      3.00000     p027 TORDER<br>
                          28      0.00000     p028 TORDER: mesh velocity
                        (0: p28=p27)<br>
                          31      -1.00000     p031 NPERT: #perturbation
                        modes<br>
                          59      0.00000     p059 !=0 --> full Jac.
                        eval. for each el.<br>
                          65      1.00000     p065 #iofiles (eg, 0 or
                        64); <0 --> sep. dirs<br>
                          66      4.00000     p066 output : <0=ascii,
                        else binary<br>
                          67      4.00000     p067 restart: <0=ascii,
                        else binary<br>
                          69      1.00000     p069 : PROPER RESTART: 0 -
                        do not use my_full_restart; 1- use it<br>
                          71      5.00000     p071 : ARNOLDI: checkpoint
                        file number for restart (reading)<br>
                          72      6.00000     p072 : ARNOLDI: checkpoint
                        file number for saving data<br>
                          99      3.00000     p099 dealiasing:
                        <0--> off/3--> old/4--> new<br>
                         102      1.00000     p102 Dump out divergence
                        at each time step<br>
                         108      1.00000     p108 : ARNOLDI: 0 if no
                        arnoldi<br>
                         109      40.0000     p109 : ARNOLDI: frequency
                        of calling arn_solve<br>
                         110      4.00000     p110 : ARNOLDI: maximal
                        number of arnoldi cycles<br>
                         111      90.0000     p111 : ARNOLDI: size of
                        Krylov space<br>
                         112      30.0000     p112 : ARNOLDI: number of
                        eigenvectors<br>
                         113      1.00000E-06 p113 : ARNOLDI: arpack
                        tolerance<br>
                         119      1.00000     p119 : SPONGE STRENGTH<br>
                         120      25.0000     p120 : SPONGE TOTAL WIDTH<br>
                         121      3.00000     p121 : SPONGE DROP WIDTH
                        (INFLOW)<br>
                         122      5.00000     p122 : SPONGE RISE WIDTH
                        (OUTFLOW)<br>
******************************************************************************************************************<br>
                        <br>
                      </div>
                      <div>I'd appreciate if you can let me what am I
                        missing in the set up which might be leading to
                        this issue? Please let me know if you need any
                        other information to understand this issue.<br>
                        <br>
                        <br>
                      </div>
                      <div>Regards, <br>
                      </div>
                      <div>Ravi<br>
                        <br>
                      </div>
                      <div>
                        <div>
                          <div><br>
                          </div>
                        </div>
                      </div>
                    </div>
                    <div class="gmail_extra"><br>
                      <div class="gmail_quote">On Tue, Mar 15, 2016 at
                        4:06 AM, <span dir="ltr"><<a
                            moz-do-not-send="true"
                            href="mailto:nek5000-users@lists.mcs.anl.gov"
                            target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a></a>></span>
                        wrote:<br>
                        <blockquote class="gmail_quote" style="margin:0
                          0 0 .8ex;border-left:1px #ccc
                          solid;padding-left:1ex">Hi<br>
                          <br>
                          To force base flow to be constant you have to
                          set negative param(31) in your ###.rea file.
                          Something like<br>
                             -1.00000     p031 NPERT: #perturbation
                          modes<br>
                          Of course you need the base flow as well. It
                          could be analytical one set in useric, or just
                          a field read during initialisation.<br>
                          Regards<br>
                          Adam
                          <div>
                            <div><br>
                              <br>
                              <br>
                              On 2016-03-15 08:49, <a
                                moz-do-not-send="true"
                                href="mailto:nek5000-users@lists.mcs.anl.gov"
                                target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a></a>
                              wrote:<br>
                              <blockquote class="gmail_quote"
                                style="margin:0 0 0 .8ex;border-left:1px
                                #ccc solid;padding-left:1ex"> Hi Neks,<br>
                                <br>
                                I'm trying to use the linear stability
                                tool of Nek5000.<br>
                                <br>
                                To start with, I am trying to run the
                                ext_cyl example. However, I have found
                                the following problem:<br>
                                <br>
                                ERROR: arnoldi assumes constant base
                                flow.<br>
                                <br>
                                I have found on the README tutorial that
                                the base flow has to be specified on the
                                .rea file. I have included a file in the
                                PRESOLVE/RESTART option, however I still
                                have the same error.<br>
                                <br>
                                What should I modify?<br>
                                <br>
                                Finally, I have also used a subroutine
                                defined in the .usr file that reads the
                                file containing the base flow. However,
                                the error persist...<br>
                                <br>
                                Could you help me, please?<br>
                                <br>
                                Cheers<br>
                                SL<br>
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                      <br>
                      -- <br>
                      <div>
                        <div dir="ltr"><span style="font-family:arial
                            narrow,sans-serif"><font size="4">Ravi Kumar
                              R. Tumkur</font>,<b> </b><font size="4">PhD.</font><br>
                            Phone: <a moz-do-not-send="true"
                              value="+12177787538">217 778 7538</a></span></div>
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        <br>
        -- <br>
        <div class="gmail_signature">
          <div dir="ltr"><span style="font-family:arial
              narrow,sans-serif"><font size="4">Ravi Kumar R. Tumkur</font>,<b>
              </b><font size="4">PhD.</font><br>
              Phone: <a moz-do-not-send="true" value="+12177787538">217
                778 7538</a></span></div>
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