Users August 2011

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17 participants
39 discussions

Problems with mpich2
by jhar131＠cct.lsu.edu 18 Dec '11

18 Dec '11

When attempting to build a simulation (in fedora), I encounter an undefined reference error pertaining to MPI. I have installed mpich2 and mpich2-devel both automatically with yum -y as suggested in the notation; as well as manually after this error. Any suggestions? Creating cactus_Test in /home/joshua/Cactus/exe from CactusBase/Boundary CactusBase/CartGrid3D CactusBase/CoordBase CactusConnect/HTTPD CactusConnect/HTTPDExtra CactusWave/IDScalarWaveC CactusBase/IOASCII CactusBase/IOBasic CactusIO/IOJpeg CactusBase/IOUtil CactusPUGHIO/IsoSurfacer CactusBase/LocalReduce CactusPUGH/PUGH CactusPUGH/PUGHReduce CactusPUGH/PUGHSlab CactusConnect/Socket CactusBase/SymBase CactusBase/Time CactusWave/WaveBinarySource CactusWave/WaveToyC ExternalLibraries/libjpeg /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_trid' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_trvalid' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_env2int' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_trrealloc' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_trspace' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_trDebugLevel' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_TrSetMaxMem' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_trlevel' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_trmalloc' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_env2bool' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_env2range' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_trcalloc' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_trfree' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_env2str' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_trstrdup' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_trdump' /usr/lib64/mpich2/lib/libmpich.so: undefined reference to `MPL_trinit' collect2: ld returned 1 exit status

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Problem with CarpetRegrid2/AMR
by Hal Finkel 15 Dec '11

15 Dec '11

I am trying to setup a simple simulation using CarpetRegrid2's AMR capability. As Erik has already pointed out to me (off list), the adaptive-refinement triggering code is still under development. Nevertheless, I would really like to get it working. In my current test case, I am using Kranc to solve a Klein-Gordon equation (with a non-linear potential). With the provided initial conditions, the system has an expanding bubble. This works well when refinement is turned off. To be clear, the evolution equation is: evolCalc = { Name -> "SFBubble_Evolve", Schedule -> {"in MoL_CalcRHS"}, Where -> Interior, Shorthands -> {}, Equations -> { dot[chi] -> chiM, dot[chiM] -> PD[chi,li,lj] Euc[ui,uj] - Vchi[chi] } }; where Vchi[chi_] := V'[chi] (V is the potential). The AMR level_mask is set by: lvlmskSet = { Name -> "SFBubble_SetLevelMask", Schedule -> {"AT preregrid"}, Where -> Interior, Shorthands -> { adchix, adchiy, adchiz }, Equations -> { adchix -> fabs[dx PD[chi,1]], adchiy -> fabs[dy PD[chi,2]], adchiz -> fabs[dz PD[chi,3]], "level_mask" -> ( Max[ adchix, adchiy, adchiz ]/dchimax ) /. Max[a_, b_, c_] -> fmax[a, fmax[b, c]] } }; (in words: the value of chi should not change by more than dchimax over the length of one grid cell) I am using the Periodic thorn to provide periodic boundary conditions. I've attached six pictures. They are at t = 0, the first level 1 intermediate time step, and the first coarse time step. The first three pictures are the value of chi on a slice through the middle of the box. The second three pictures are the value of level_mask. As can be seen in the second chi image, the interpolation into the refined region seems to be incorrect. The "boundary" seems to have appeared in the middle of the block. I have also attached the block descriptions. Is there something I could be doing incorrectly which would cause this? Otherwise, does anyone have any ideas on where to look for the problem? I am using the trunk version as of this morning. Thank you in advance, Hal -- Hal Finkel Postdoctoral Appointee Leadership Computing Facility Argonne National Laboratory

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new CarpetIOASCII/src/util/Carpet2ygraph.pl
by Bruno Giacomazzo 09 Oct '11

09 Oct '11

Hi, I was trying to use the script CarpetIOASCII/src/util/Carpet2ygraph.pl (it is the same both in the git and hg versions of Carpet), but it was not working. I modified it in order to be able again to produce different output for the different refinement levels and now it can also work with more than 9 refinement levels. I have attached my version and the diff with the version in the repository. The only problem is that it still doesn't know how to remove ghost points, so the output files may contain duplicated points. Im my parfile I'm using CarpetIOASCII::out3D_ghosts = "no" and consequently I don't have any problem. But if you have ghostpoints in your .asc files, you may see duplicated points in the output produced by the script. Any suggestion is appreciated. Cheers, Bruno Dr. Bruno Giacomazzo Department of Astronomy University of Maryland College Park MD 20742-2421 USA Tel. : +1 301 405 0676 Fax : +1 301 314 9067 Tel. : +1 301 286 3809 (NASA/GSFC) Fax : +1 301 286 7230 (NASA/GSFC) email : bgiacoma(a)astro.umd.edu web: http://www.brunogiacomazzo.org ---------------------------------------------------------------------- There are only 10 types of people in the world: Those who understand binary, and those who don't ----------------------------------------------------------------------

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trac.einsteintoolkit.org not reachable?
by Erik Schnetter 31 Aug '11

31 Aug '11

I can't reach trac.einsteintoolkit.org. Could someone check whether this is a server problem? -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 28 Aug '11

28 Aug '11

Hi Please consider joining the weekly Einstein Toolkit phone call at 10 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ I short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. My agenda will contain: - Status of CCE tests - Fall workshop: - announcement on users mailing lists - infos on wiki page [1] - please let me know if you plan to come so that we have an idea how many rooms to book - svn/trac servers are currently not reacting - maybe by the time of the call we know why and can tell you. - Meeting next week (Labor day in the US) Frank Loeffler [1] https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Fall_2011#Fall_Einstei…

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Einstein Toolkit / Cactus fall 2011 workshops
by Frank Loeffler 28 Aug '11

28 Aug '11

Dear Cactus and Einstein Toolkit users The numerical relativity and the frameworks groups at the Center for Computation and Technology at LSU invite you to join them for either the Cactus or the Einstein Toolkit fall workshop 2011, or both. Both events target existing users and developers and will happen at the same time, and in parts also the same place. However, their focus will be different. While the Einstein Toolkit workshop will concentrate on issues directly connected to numerical relativity, the focus of the Cactus workshop will be on general Cactus infrastructure improvements. In particular, users of the Einstein Toolkit have expressed interest in resistive MHD development, and possibly issues with different kinds of equations of state. The Cactus workshop on the other hand, will likely focus on GPGPU support in Cactus, and the long-planned overhaul of the Cactus scheduler. Both events are scheduled for Mon, Oct 31st, noon - Thu Nov 3rd, noon, at the Center for Computation and Technology at LSU, Baton Rouge, Louisiana. Please use the ET wiki [1] for the latest information about the workshops. Please either register by sending an email to Frank Loeffler <knarf(a)cct.lsu.edu>, or by entering your name into the mentioned wiki page [1]. Frank Loeffler [1] https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Fall_2011#Fall_Einstei…

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Einstein Toolkit bibtex file clean-up
by Erik Schnetter 26 Aug '11

26 Aug '11

I just cleaned up the Einstein Toolkit bibtex file. The most prominent changes were (a) using consisten entry names if the entry is not in Spires; I followed the existing convention of inventing a Spires-like name in this case instead of choosing different format for the entry name. I also (b) ensured that the eprint entries show up correctly; Spires splits up eprint entries into eprint, archivePrefix, and primaryClass, which are unfortunately ignored by most bibtex styles. I realise in hindsight that this is a substantial change; if you disagree, I will revert this change, and we can then discuss it. -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/

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easy question
by Steven R. Brandt 24 Aug '11

24 Aug '11

Is there an easy way to initialize all variables to zero (including _p _pp)? Cheers, Steve

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update new user guide for non-TeraGrid/XSEDE users?
by Friesen, Brian 24 Aug '11

24 Aug '11

Hi. I'm new to Cactus, the Einstein Toolkit, and mailing lists in general. Hope this works... Are there plans at some point to update/append the Tutorial for New Users to make it more general than just for TeraGrid/XSEDE users? At the UC-HIPACC school at LBL Erik showed us how to build/run on Hopper at NERSC (I'm a regular NERSC user so this was very helpfu), and the steps were considerably different. Unfortunately I didn't write down what we did and so am now a bit stuck. So Erik, if you're reading this, could you look through your shell history and maybe dig up the commands you used? :-P I'm trying to figure out how to do it again right now, and if I have any success would be more than happy to contribute to the tutorial. -- Brian C. Friesen Graduate Research Assistant University of Oklahoma friesen(a)ou.edu http://www.nhn.ou.edu/~friesen

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simfactory: memory request?
by Scott Hawley 23 Aug '11

23 Aug '11

Does simfactory automatically know how much memory I'm going to request from the host machine? I've looked in the Tutorial (perl) and the Advanced Tutorial, and haven't found such an option to set. Thanks. -- Scott H. Hawley, Ph.D. Asst. Prof. of Physics Chemistry & Physics Dept Office: Hitch 100D Belmont University Tel: +1-615-460-6206 Nashville, TN 37212 USA Fax: +1-615-460-5458 PGP Key at http://sks-keyservers.net

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Users August 2011