Users May 2012

users@lists.einsteintoolkit.org

21 participants
44 discussions

ETK vs. ET
by Steven R. Brandt 24 May '12

24 May '12

This may seem like a fussy point, but what is the correct abbreviation for Einstein Toolkit? Is it ET or ETK? I've seen both used (and I'm partial to ETK myself). Cheers, Steve

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Re: [Users] MPI problem on Mac OS X
by Babiuc-Hamilton, Maria 24 May '12

24 May '12

Hi Bernard, It's a game of trial and learning from errors. Scott gave very good instructions, but no computer behaves identically. Here is what it worked for me: 1) First, install VisIt 2.4.2. Go to: http://portal.nersc.gov/svn/visit/trunk/releases/2.4.2/ Download visit-install2_4_2 and visit2_4_2.darwin-x86_64.tar.gz (Ctrl-Click, Save files as) $ sudo ./visit-install2_4_2.sh 2.4.2 darwin-x86_64 /opt/local/ Password: Choose a system configuration file…… Enter (1-14): 1 (compiling) . . find: /opt/local//2.4.2+/.visit/bin: No such file or directory find: /opt/local//2.4.2+/.visit/bin: No such file or directory visit-install done 2) Now, it's time to prepare your paths: $ vi ~/.profile Add to your path: /opt/local/2.4.2/darwin-x86_64/bin $ source ~/.profile $ echo $PATH /opt/local/bin:/opt/local/sbin:/opt/local/2.4.2/darwin-x86_64/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/X11/bin $ source ~/.profile $ sudo ln -s /opt/local/lib/libmpi_cxx.dylib /usr/lib/ $ sudo ln -s /opt/local/lib/libmpi.dylib /usr/lib/ $ sudo ln -s /opt/local/lib/libopen-rte.dylib /usr/lib/ $ sudo ln -s /opt/local/lib/libopen-pal.dylib /usr/lib/ 3) Now, build the Carpet plugin. $ svn co https://svn.cactuscode.org/VizTools/CarpetHDF5/trunk/ CarpetHDF5 $ sudo ./install CMake: CXXFLAGS = -I/opt/local/2.4.2/darwin-x86_64/include/ -I/opt/local/2.4.2/darwin-x86_64/include/hdf5/include LDFLAGS = -L/opt/local/2.4.2/darwin-x86_64/lib -L/opt/local/lib Save, and close .(compiling) . . [100%] Built target MCarpetHDF5Database 4) Finally, take heart and open visit $ sudo visit -noconfig Let me know fi it's working for you. best, Maria ________________________________________ From: Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] [bernard.j.kelly(a)nasa.gov] Sent: Wednesday, May 23, 2012 9:25 PM To: Babiuc-Hamilton, Maria Subject: Re: [Users] MPI problem on Mac OS X Hi Maria. Thanks; I'm using Barry's modern Lion config successfully to compile on Snow Leopard with all the MacPorts stuff he suggests. However this doesn't help me with VisIt. I'm still getting the same old error we've both seen before: "The metadata server running on host localhost has exited abnormally. VisIt is trying to restart it. Shortly thereafter, the following occured... VisIt was unable to open "/Users/bjkelly1/Projects/CODES/Cactus/exe/ML_BSSN_Kerr/ml_bssn::ml_lapse.h 5". Each attempt to open it caused VisIt's metadata server to crash. This can occur when the file is corrupted, or when the underlying file format has changed and VisIt's readers have not been updated yet, or when the reader VisIt is using for your file format is not robust. Please check whether the file is corrupted and, if not, contact a VisIt developer. " Are you telling me you've got past this to a successful data read-in? Bernard On 5/23/12 4:55 PM, "Babiuc-Hamilton, Maria" <babiuc(a)marshall.edu> wrote: >Hi, > >I fixed the problem. Yes, the config file for Snow-Leopard uses ithe >system's own mpi from /usr/include. On one laptop, this was fine, but on >the other one, after I linked the libraries, it got messed up. Panicked, >I did some hacking in /usr/local, /usr/bin and /usr/include of which I am >not proud, but now it works! >I might have not needed to do this, but I wanted to clean any residue of >openmpi that was there. > >Barry, wow, I'm succesfully using your lion configuration on the Snow >Leopard! > >Bernard, it is safe to use the lion configuration on the Snow Leopard, >after you do the macport installs specified in the header, and this will >greatly simply your problem with VisIt. > > >Thanks, >Maria > >From: Barry Wardell ><barry.wardell(a)gmail.com<mailto:barry.wardell@gmail.com>> >Date: Wednesday, May 23, 2012 10:35 AM >To: Ian Hinder <ian.hinder(a)aei.mpg.de<mailto:ian.hinder@aei.mpg.de>> >Cc: "users(a)einsteintoolkit.org<mailto:users@einsteintoolkit.org>" ><users(a)einsteintoolkit.org<mailto:users@einsteintoolkit.org>>, Maria >Babiuc <babiuc(a)marshall.edu<mailto:babiuc@marshall.edu>> >Subject: Re: [Users] MPI problem on Mac OS X > > >On May 23, 2012 3:20 AM, "Ian Hinder" ><ian.hinder(a)aei.mpg.de<mailto:ian.hinder@aei.mpg.de>> wrote: >> I notice in Barry's Lion optionlist he uses MacPorts for OpenMPI, >>whereas in Snow Leopard we both use the system version. It might be >>that the system version doesn't work for us in Lion. > >I think the problem was that OpenMPI isn't included in OSX as of Lion. > >Barry >_______________________________________________ >Users mailing list >Users(a)einsteintoolkit.org >http://lists.einsteintoolkit.org/mailman/listinfo/users

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Re: [Users] carpetmercurial password?
by Scott Hawley 24 May '12

24 May '12

The publically-downloadable einsteintoolkit.th file includes the lines # Carpet, the AMR driver !TARGET = $ARR !TYPE = hg !AUTH_URL = ssh://carpetmercurial@carpetcode.org/carpet !URL = http://www.carpetcode.org/hg/carpet # For the git version of Carpet, comment the previous three lines and uncomment # the next three #!TYPE = git #!AUTH_URL = carpetgit@carpetcode.org:carpet #!URL = git://carpetcode.org/carpet !CHECKOUT = Carpet/doc Carpet/Carpet ..etc Is there a reason why the public thornlist configured so that many users get asked for an ssh password they / we don't have? Whenever I try to perform a fresh checkout with GetComponents, I have to bypass the Carpet part and grab it manually.. How about, instead, something like: !TYPE = hg !AUTH_URL = http://www.carpetcode.org/hg/carpet !URL = http://www.carpetcode.org/hg/carpet It would be great if this could be the default for the version of einsteintool.th on the Download Page. Cheers, Scott On 4/2/12 3:46 PM, "Erik Schnetter" <eschnetter(a)perimeterinstitute.ca> wrote: >Scott > >If you use GetComponents from the Einstein Toolkit, then you don't >need to do anything manually. > >In your case, it seems that the instructions are slightly wrong. There >should be a directory named "carpet" instead of "carpetcode"; can you >make the respective replacement in the "ln" command? > >-erik > >On Mon, Apr 2, 2012 at 4:20 PM, Scott Hawley <scott.hawley(a)belmont.edu> >wrote: >> Thanks. I did the "hg clone" method for read-only access.. >> What it does is give me this structure: >> >> hedges:~> cd Cactus >> hedges:~/Cactus> cd carpet/ >> hedges:~/Cactus/carpet> ls >> Carpet/ CarpetAttic/ CarpetDev/ CarpetExtra/ Doxyfile README >> test-carpet >> >> >> if I then do (following http://www.carpetcode.org/get-carpet.html) >> >> >> cd arrangements >> ln -s ../carpetcode/Carpet* . >> >> >> There no "carpetcode" directory so the link fails. >> >> >> So now I'm trying gitŠ That seems to work. >> >> >> I'm just using the Maxwell einsteintoolkit.th file. So that file >>assumes >> that your new users already have exchanged SHH keys? >> -Scott >> >> >> >> >> On 4/2/12 3:14 PM, "Erik Schnetter" <eschnetter(a)perimeterinstitute.ca> >> wrote: >> >>>Scott >>> >>>Access is enabled via ssh keys; if you send me a public ssh key, I >>>will give you access. Passwords as such don't work. >>> >>>For read-only access, you can also use "hg clone >>>http://www.carpetcode.org/hg/carpet", which does not require a >>>password either. >>> >>>-erik >>> >>>On Mon, Apr 2, 2012 at 4:06 PM, Scott Hawley <scott.hawley(a)belmont.edu> >>>wrote: >>>> Hi Erik, >>>> I'm being prompted for a password. I've tried "anonymous" and >>>>"anon". I >>>> can't find it on the carpetcode.org server. >>>> What do I need to do? >>>> Thanks, >>>> Scott >>>> >>>> >>>> % ./GetComponents einsteintoolkit.th >>>> Š >>>> ----------------------------------------------------------------- >>>> Checking out module: Carpet/doc >>>> from repository: ssh://carpetmercurial@carpetcode.org/carpet >>>> into: Cactus/arrangements >>>> carpetmercurial(a)carpetcode.org's password: >>>> carpetmercurial(a)carpetcode.org's password: >>>> >>> >>>-- >>>Erik Schnetter <eschnetter(a)perimeterinstitute.ca> >>>http://www.perimeterinstitute.ca/personal/eschnetter/ >>>AIM: eschnett247, Skype: eschnett, Google Talk: schnetter(a)gmail.com >>> >> >> > > > >-- >Erik Schnetter <eschnetter(a)perimeterinstitute.ca> >http://www.perimeterinstitute.ca/personal/eschnetter/ >AIM: eschnett247, Skype: eschnett, Google Talk: schnetter(a)gmail.com >

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MPI problem on Mac OS X
by Babiuc-Hamilton, Maria 23 May '12

23 May '12

Hello, I reinstalled openmpi on Mac OSX because of a broken dyld link, I was able to configure cactus, but at the end of compilation I get: ndefined symbols for architecture x86_64: "MPI::Win::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Win in libthorn_Carpet.a(helpers.cc.o) vtable for MPI::Win in libthorn_Carpet.a(ScheduleWrapper.cc.o) vtable for MPI::Win in libthorn_CarpetIOHDF5.a(CarpetIOHDF5.cc.o) vtable for MPI::Win in libthorn_CarpetInterp.a(interp.cc.o) vtable for MPI::Win in libthorn_CarpetInterp2.a(interp2.cc.o) vtable for MPI::Win in libthorn_CarpetRegrid.a(regrid.cc.o) vtable for MPI::Win in libthorn_CarpetRegrid2.a(regrid.cc.o) ... ld: symbol(s) not found for architecture x86_64 collect2: ld returned 1 exit status I think this is an easy fix, but I don't remember what do I have to do? My MPI related config log is: Setting MPI to 'OpenMPI' Setting OPENMPI_DIR to '/usr/local' Setting MPI_LIBS to 'mpi' ........................................ Configuring with MPI OpenMPI selected Using " /usr/local/include/openmpi/" as OpenMPI include path Using no explicit OpenMPI library path thanks, Maria

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Re: [Users] ETK Maxwell checkout failing for McLachlan, KrancNumericalTools
by Ian Hinder 23 May '12

23 May '12

On 23 May 2012, at 13:56, Ian Hinder wrote: > > On 23 May 2012, at 13:25, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote: > >> Hi Ian. >> >> Yes, I should have explained that this was an additional checkout after >> most of ETK was already checked out (hence the number 12 instead of 175 or >> so). But the original checkout was also Maxwell, and was performed only a >> day or two earlier, with the same GetComponents and thornlist. >> >> I just moved that whole Cactus aside and redid from scratch. Identical >> failure (but this time saying 175). Almost everything checks out fine; >> just not McLachlan and KrancNumericalTools, and GetComponents itself, >> apparently (?). >> >> I've redone the checkout (again after the main checkout) with the >> "--verbose" option. Result after main text. The option "--verbose 2" >> fails, so presumably the correct syntax is slightly different; I didn't >> hang around to check. >> >> BTW, I don't really think the issue has anything to do with my OS X >> version, though I suppose my MacPorts git might have some funny settings. > > Hi Bernard, > > Can we move this back to the list? Others might have suggestions and will benefit in future from the discussion. I have done this: > > MacBook-2:temp $ git clone --depth 1 git://carpetcode.org/McLachlan > Cloning into McLachlan... > remote: Counting objects: 3878, done. > remote: Compressing objects: 100% (2222/2222), done. > remote: Total 3878 (delta 3229), reused 2050 (delta 1638) > Receiving objects: 100% (3878/3878), 2.38 MiB | 838 KiB/s, done. > Resolving deltas: 100% (3229/3229), done. > MacBook-2:temp $ cd McLachlan/ > MacBook-2:McLachlan (master) $ git checkout --track -b ET_2011_10 origin/ET_2011_10 > Branch ET_2011_10 set up to track remote branch ET_2011_10 from origin. > Switched to a new branch 'ET_2011_10' > MacBook-2:McLachlan (ET_2011_10) $ git --version > git version 1.7.5.4 > > Those are the commands that GetComponents claims to be using. Can you try these commands on their own and see what happens? It might be something to do with old versions of Git, or maybe GetComponents is doing something different than the commands it outputs. > > Have a look at http://stackoverflow.com/questions/499316/git-plugin-for-hudson-checkout-pr…, and other google hits for the checkout error message. It's looking like it might be a problem with an old version of git. > > -- > Ian Hinder > http://numrel.aei.mpg.de/people/hinder > -- Ian Hinder http://numrel.aei.mpg.de/people/hinder

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ETK Maxwell checkout failing for McLachlan, KrancNumericalTools
by Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] 23 May '12

23 May '12

Hi. I decided to check out ETK Maxwell on a different Mac, this time one running Lion. I'm having trouble with the checkout of McLachlan and KrancNumericalTools. I haven't seen this GetComponents error message before; has something changed with these repositories, possibly related to the next release? Thanks, Bernard ----------------------------------------- 12 components checked out. 0 components updated. Unable to process KrancNumericalTools/GenericFD: symlinks may be broken Unable to process McLachlan/doc: symlinks may be broken Unable to process GetComponents: symlinks may be broken Summary of Warnings: Could not checkout KrancNumericalTools/GenericFD, unable to switch to branch ET_2011_10. Any existing symlinks to KrancNumericalTools/GenericFD will be broken Could not checkout McLachlan/doc, unable to switch to branch ET_2011_10. Any existing symlinks to McLachlan/doc will be broken Could not checkout GetComponents, unable to switch to branch ET_2011_10. Any existing symlinks to GetComponents will be broken Time Elapsed: 0 minutes, 39 seconds ----------------------------------------- --------------------------------------------------------------------------- -- Bernard Kelly -- CRESST Research Associate, NASA/GSFC Phone: +1 (301) 286-7243 E-Mail: bernard.j.kelly(a)nasa.gov Web: http://science.gsfc.nasa.gov/sed/index.cfm?fuseAction=people.jumpBio&iphone bookid=13052 --------------------------------------------------------------------------- --

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Re: [Users] [Einstein Toolkit] #919: simfactory fails for standard thornlist copied using sync
by Frank Loeffler 22 May '12

22 May '12

On Tue, May 22, 2012 at 05:02:36PM -0000, Einstein Toolkit wrote: > Since we seem to be accumulating Trac issues with simfactory faster than > for > any other component (right now: 93 open simfactory tickets vs. 62 for > Cactus > which is the next biggest chunk), I'd like to suggest the following (this > was > originally prepared within <RANT>...</RANT> tags so hopefully I > sufficiently > defused the wording when copying it in): > > We do not currently seem to have anyone in the project who is the official > maintainer of simfactory (since Michael Thomas left LSU), yes? At least no > one > who feels confident enough and actually has time to fix bugs as they are > reported? I admit that I am not very good at fixing bugs in simfactory > since I > most often find the code hard to understand and too deeply nested. Given > that > we consider simfactory one of our core components should we at one point > schedule an EVO/Skype/Email/IM simfactory bug sqashing session to try and > reduce the number and more maintainers become familarized enough with the > internals? ... taking this to the users list ... I think that this is in general a good idea. It will be a challenge to find time for it though. Frank

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meeting minutes
by Frank Löffler 21 May '12

21 May '12

Present were: Frank, Philipp, Ian, Erik, Tanja, Peter, Steve, Dennis, Eloisa I (Roland) missed the meeting so these notes are essentially made up from what I was told was discussed. ET release: * checkpoint/recovery failures in Carpet when more time levels than required by prolongation_order_time are activated (see ticket https://trac.einsteintoolkit.org/ticket/626) * Cactus Users Guide and Reference Manual share appendix -> leads to non-existent reference * remaining tasks until the release * please all run all testsuites * Until the release, the ET is frozen as of this evening: - except for documentation, two maintainers are required for commits Roland

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param.ccl: accessing non-restricted variables of another thorn?
by Scott Hawley 21 May '12

21 May '12

Hi, in my thorn I want to "share" variables from thorn ADMMass, e.g. ADMMass::ADMMass_number. I already have INHERITS: ADMMass in my interface.ccl file. I've been reading http://einsteintoolkit.org/documentation/UsersGuide/UsersGuidech12.html and Cactus/arrangements/EinsteinInitialData/GRHydro_InitData/*.ccl Šbut am still having trouble implementing this: In param.ccl, I've tried "SHARES: ADMMass", but then I get an error CST error 1: -> Thorn "TexMEx" attempted to EXTEND or USE non-restricted parameter "ADMMass_number" from implementation "ADMMASS" If I take out the USES, then I get /Users/shawley/Cactus/configs/texmex/bindings/Parameters/TexMEx_Parameters. c:19:41: fatal error: ParameterCRestrictedADMMASS.h: No such file or directory If I take out the SHARES, and just try to reference ADMMass::ADMMass_number in my initital.cc code, e.g., fprintf(log_file," ADMMass_number = %d\n", ADMMass::ADMMass_number); , then I get the error: /Users/shawley/Cactus/arrangements/texmex/TexMEx/src/initial.cc /Users/shawley/Cactus/configs/texmex/build/TexMEx/initial.cc: In function 'void TexMEx_initial(cGH*)': /Users/shawley/Cactus/configs/texmex/build/TexMEx/initial.cc:1059:47: error: 'ADMMass' has not been declared Can someone set me straight on this? Thanks. Also if I try "INHERITS: ADMMass", I get CST error 1: -> Unknown line in param.ccl for thorn TexMEx "INHERITS: ADMMass"

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(no subject)
by Babiuc-Hamilton, Maria 21 May '12

21 May '12

Hello, Does anybody know why I am getting all those NaNs and what shall I do about it? -> NaN caught in variable 'CARPET::local_interior_points_per_second' -> NaN caught in variable 'CARPET::total_interior_points_per_second' -> NaN caught in variable 'CARPET::local_interior_point_updates_count' -> NaN caught in variable 'CARPET::total_interior_point_updates_count' thanks, Maria

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Users May 2012