Users June 2013

users@lists.einsteintoolkit.org

13 participants
24 discussions

Einstein Toolkit Meeting Reminder
by Frank Loeffler 14 May '15

14 May '15

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 contains: - Fall workshop - PLEASE let us know if you come [1]! - Hotel booking - Release planning - release date: Mon Oct 24 2011 - freeze date: Mon Sep 26 - the day of the call! - branch name: ET_2011_10 - List of release-concerning bugs [2] - ET paper: proposed "freeze" by Oct 3rd (Mon after this call) As always: feel free to add to this list. Frank Loeffler [1] https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Fall_2011#Fall_Einstei… [2] https://trac.einsteintoolkit.org/query?status=!closed&milestone=ET_2011_11&…

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strong scaling tests on Stampede (TACC)
by Bruno Giacomazzo 19 Sep '13

19 Sep '13

Hi, I did some strong scaling tests on Stampede (https://www.xsede.org/tacc-stampede) with both Whisky and GRHydro (using the development version of ET in both cases). I used a Carpet par file that Roberto DePietri provided me and that he used for similar tests on an Italian cluster (I have attached the GRHydro version, the Whisky one is similar except for using Whisky instead of GRHydro). I used both Intel MPI and Mvapich and I did both pure MPI and MPI/OpenMP runs. I have attached a text file with my results. The first column is the name of the run (if it starts with mvapich it used mvapich otherwise it used Intel MPI), the second one is the number of cores (option --procs in simfactory), the third one the number of threads (--num-threads), the fourth one the time in seconds spent in CCTK_EVOL, and the fifth one the walltime in seconds (i.e., the total time used by the run as measured on the cluster). I have also attached a couple of figures that show CCTK_EVOL vs #cores and walltime vs #cores (only for Intel MPI runs). First of all, in pure MPI runs (--num-threads=1) I was unable to run on more than 1024 cores using Intel MPI (the run was just crashing before iteration zero or hanging up). No problem instead when using --num-threads=8 or --num-threads=16. I also noticed that scaling was particularly bad in pure MPI runs and that a lot of time was spent outside CCTK_EVOL (both with Intel MPI and MVAPICH). After speaking with Roberto, I found out that the problem is due to 1D ASCII output (which is active in that parfile) and that makes the runs particularly slow above ~100 cores on this machine. In plot_scaling_walltime_all.pdf I plot also two pure MPI runs, but without 1D ASCII output and the scaling is much better in this case (the time spent in CCTK_EVOL is identical to the case with 1D output and hence I didn't plot them in the other figure). I didn't try using 1D hdf5 output instead, does anyone use it? According to my tests, --num-threads=16 performs better than --num-threads=8 (which is the current default value in simfactory) and Intel MPI seems to be better than MVAPICH. Is there a particular reason for using 8 instead of 16 threads as the default simfactory value on Stampede? Let me know if you have any comment or suggestion. Cheers, Bruno Dr. Bruno Giacomazzo JILA - University of Colorado 440 UCB Boulder, CO 80309 USA Tel. : +1 303-492-5170 Fax : +1 303-492-5235 email : bruno.giacomazzo(a)jila.colorado.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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Simfactory/Mojave: machine name error
by Scott Hawley 10 Jul '13

10 Jul '13

Ok, this is pretty low-priority. Working around it no big deal, but it would be nice to have things configured so this didn't come up: I'm at a coffee shop and for some reason simfactory is pulling a weird machine name based on the local subnet. Never seen this before. I'm building from within Eclipse using Mojave. Here's the console log from Mojave->Build... /usr/bin/python simfactory/lib/sim.py build --mdbkey=make -j 1 --verbose bruiser --thornlist /Users/shawley/ThornLists/ThornListBruiser --optionlist /Users/shawley/options.bruiser.mac IN DIRECTORY: /Users/shawley/Cactus Unknown machine name provision.forbidden.wifi-zones.com<http://provision.forbidden.wifi-zones.com> Error: Unknown local machine provision.forbidden.wifi-zones.com<http://provision.forbidden.wifi-zones.com>. Please use 'sim setup' to create a local machine entry from the generic template. Aborting Simfactory. But when I check my environment I can't find any reference to said machine. Mojave->Env yields % env ... HOST=provision In fact there's no reference to that domain... % env | grep wifi % ?? And my machine name file is there % ls ~/Cactus/simfactory/mdb/machines/provision.ini /Users/shawley/Cactus/simfactory/mdb/machines/provision.ini Any suggestions for a solution that works automatically, all the time? For now I just turned my wifi off and it works fine... Thanks, Scott

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CarpetHDF5 compilation error
by Babiuc-Hamilton, Maria 02 Jul '13

02 Jul '13

Hi, I'm getting this error when compiling the CarpetHDF5 plugging for Visit: clang: warning: argument unused during compilation: ----------------------------------------------------------------- Plugin: CarpetHDF5 ("Carpet AMR/curvilinear HDF5 output generated by the Cactus Computational Toolkit", type=database) -- version 2.1 Attribute: () -- The C compiler identification is Clang 4.2.0 -- The CXX compiler identification is Clang 4.2.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Configuring done -- Generating done -- Build files have been written to: /Users/maria/GaussCactus/CarpetHDF5 Scanning dependencies of target ECarpetHDF5Database_par [ 6%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5EnginePluginInfo.C.o clang: warning: argument unused during compilation: '-L/Users/maria/Desktop/VisIt.app/Contents/Resources/2.6.2/darwin-x86_64/include/hdf5/include' [ 12%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5PluginInfo.C.o clang: warning: argument unused during compilation: '-L/Users/maria/Desktop/VisIt.app/Contents/Resources/2.6.2/darwin-x86_64/include/hdf5/include' [ 18%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5CommonPluginInfo.C.o clang: warning: argument unused during compilation: '-L/Users/maria/Desktop/VisIt.app/Contents/Resources/2.6.2/darwin-x86_64/include/hdf5/include' In file included from /Users/maria/GaussCactus/CarpetHDF5/CarpetHDF5CommonPluginInfo.C:40: /Users/maria/GaussCactus/CarpetHDF5/avtCarpetHDF5FileFormat.h:59:10: fatal error: 'hdf5.h' file not found #include "hdf5.h" ^ 1 error generated. make[2]: *** [CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5CommonPluginInfo.C.o] Error 1 make[1]: *** [CMakeFiles/ECarpetHDF5Database_par.dir/all] Error 2 make: *** [all] Error 2 Maria

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Latest GetComponents broken?
by Ben Bernard 01 Jul '13

01 Jul '13

I am attempting to use the GetComponents script on Queen Bee to install the latest Einstein Toolkit, using the commands on the Tutorial for new users. Unfortunately it seems that the GetComponents script cannot find many of the components, and locks up after a few of them. Has anyone else encountered this issue? Regards, Benjamin Bernard

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Einstein Toolkit Meeting Reminder
by Roland Haas 30 Jun '13

30 Jun '13

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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/ In short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. Topics to discuss include the new tickets in Trac, the upcoming ET developer's workshop, and plans on possibly cleaning up GRHydro. Roland Haas -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAlHQqOAACgkQTiFSTN7SboUaZwCbBbaXB80cGJS0W3rKjhynOMb6 FssAn1qdT87PXDyYdZLmZTxjEODycZSf =H3Ul -----END PGP SIGNATURE-----

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EXTRA_CFLAGS
by Erik Schnetter 30 Jun '13

30 Jun '13

We discussed recently how CFLAGS and other compiler options should be handled when configuring Cactus. On one hand, Cactus should automatically determine certain necessary settings depending on compiler vendor and operating system (e.g. choosing -std=c99). On the other hand, the user should have an easy way to add to these flags, as well as the possibility to override the automatically chosen flags. I suggest the following way to do this. This roughly follows autoconf conventions (see e.g. < http://www.gnu.org/software/autoconf/manual/autoconf-2.67/html_node/Preset-… >): CCTK_CFLAGS is a Cactus variable that is automatically set to something reasonable to make things work. CFLAGS is a "user" variable. It defaults to being empty; the user can leave it unset, or can use it to add to CCTK_CFLAGS. The Makefile will use $(CCTK_CFLAGS) $(CFLAGS) when building. Cactus will never set CFLAGS. If the user sets CCTK_CFLAGS, then this completely overrides Cactus -- this is for experts, or for emergency cases where Cactus doesn't get it right, e.g. when porting Cactus to a new system. This would apply to all variables where multiple values make sense. It would e.g. not apply to CC or DEBUG. -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/

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Re: [Users] CarpetHDF5 compilation error
by Frank Löffler 29 Jun '13

29 Jun '13

Hi This error indicates that clang couldn't find your hdf5 include files. Usually, you tell this the compiler using the -L flag. Your warnings indicate that clang isn't using the path you give for hdf5 using -L. I didn't use clang yet so I don't know for sure whether it uses -L options but I would be surprised if not. Can you check whether hdf5 is in fact installed where you tell it it should: /Users/maria/Desktop/VisIt.app/Contents/Resources/2.6.2/darwin-x86_64/include/hdf5/include ? Frank "Babiuc-Hamilton, Maria" <babiuc(a)marshall.edu> schrieb: >Hi, > >I'm getting this error when compiling the CarpetHDF5 plugging for Visit: > >clang: warning: argument unused during compilation: > >----------------------------------------------------------------- > >Plugin: CarpetHDF5 ("Carpet AMR/curvilinear HDF5 output generated by the Cactus Computational Toolkit", type=database) -- version 2.1 > Attribute: () > >-- The C compiler identification is Clang 4.2.0 >-- The CXX compiler identification is Clang 4.2.0 >-- Check for working C compiler: /usr/bin/cc >-- Check for working C compiler: /usr/bin/cc -- works >-- Detecting C compiler ABI info >-- Detecting C compiler ABI info - done >-- Check for working CXX compiler: /usr/bin/c++ >-- Check for working CXX compiler: /usr/bin/c++ -- works >-- Detecting CXX compiler ABI info >-- Detecting CXX compiler ABI info - done >-- Configuring done >-- Generating done >-- Build files have been written to: /Users/maria/GaussCactus/CarpetHDF5 >Scanning dependencies of target ECarpetHDF5Database_par >[ 6%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5EnginePluginInfo.C.o >clang: warning: argument unused during compilation: '-L/Users/maria/Desktop/VisIt.app/Contents/Resources/2.6.2/darwin-x86_64/include/hdf5/include' >[ 12%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5PluginInfo.C.o >clang: warning: argument unused during compilation: '-L/Users/maria/Desktop/VisIt.app/Contents/Resources/2.6.2/darwin-x86_64/include/hdf5/include' >[ 18%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5CommonPluginInfo.C.o >clang: warning: argument unused during compilation: '-L/Users/maria/Desktop/VisIt.app/Contents/Resources/2.6.2/darwin-x86_64/include/hdf5/include' >In file included from /Users/maria/GaussCactus/CarpetHDF5/CarpetHDF5CommonPluginInfo.C:40: >/Users/maria/GaussCactus/CarpetHDF5/avtCarpetHDF5FileFormat.h:59:10: fatal error: > 'hdf5.h' file not found >#include "hdf5.h" > ^ >1 error generated. >make[2]: *** [CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5CommonPluginInfo.C.o] Error 1 >make[1]: *** [CMakeFiles/ECarpetHDF5Database_par.dir/all] Error 2 >make: *** [all] Error 2 > > >Maria >_______________________________________________ >Users mailing list >Users(a)einsteintoolkit.org >http://lists.einsteintoolkit.org/mailman/listinfo/users

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Fw: Latest GetComponents broken?
by Ben Bernard 27 Jun '13

27 Jun '13

----- Forwarded Message ----- From: Erik Schnetter <schnetter(a)cct.lsu.edu> To: Ben Bernard <Ben_the_Lucky(a)yahoo.com> Sent: Thursday, June 27, 2013 10:12 AM Subject: Re: [Users] Latest GetComponents broken? Ben Please forward this message to the mailing list. -erik On Thu, Jun 27, 2013 at 8:58 AM, Ben Bernard <Ben_the_Lucky(a)yahoo.com> wrote: It seemed to work much better. Here is the summary: >----------------------------------------------------------------- > 162 components checked out. > 0 components updated. > > Unable to process EinsteinAnalysis/Outflow: symlinks may be broken > Unable to process EinsteinExact/doc: symlinks may be broken > Unable to process KrancNumericalTools/GenericFD: symlinks may be broken > Unable to process McLachlan/doc: symlinks may be broken > Unable to process Carpet/doc: symlinks may be broken > Unable to process GetComponents: symlinks may be broken > >Summary of Warnings: > >Could not checkout EinsteinAnalysis/Outflow, unable to switch to tag . Any existing symlinks to EinsteinAnalysis/Outflow will be broken >Could not checkout EinsteinExact/doc, unable to switch to tag . Any existing symlinks to EinsteinExact/doc will be broken >Could not checkout KrancNumericalTools/GenericFD, unable to switch to tag . Any existing symlinks to KrancNumericalTools/GenericFD will be broken >Could not checkout McLachlan/doc, unable to switch to tag . Any existing symlinks to McLachlan/doc will be broken >Could not checkout Carpet/doc, unable to switch to tag . Any existing symlinks to Carpet/doc will be broken >Could not checkout GetComponents, unable to switch to tag . Any existing symlinks to GetComponents will be broken > Time Elapsed: 11 minutes, 28 seconds > > >Thank you for your help. > >I am going to attempt to build and run the static tov. > >Ben > > >From: Erik Schnetter <schnetter(a)cct.lsu.edu> >To: Ben Bernard <Ben_the_Lucky(a)yahoo.com> >Sent: Wednesday, June 26, 2013 11:51 PM > >Subject: Re: [Users] Latest GetComponents broken? > > > >Ben > > >I can reproduce your problem on my laptop. The actual error messages are different, but are definitively there. > > >I have had success when I leave out the "--parallel" option. I usually don't use it, which is why I didn't notice this problem earlier. > > >Can you try without --parallel? You may need to start from scratch, i.e. without an existing "Cactus" directory that may contain incomplete repositories. > > >-erik > > > > > >On Wed, Jun 26, 2013 at 4:18 PM, Ben Bernard <Ben_the_Lucky(a)yahoo.com> wrote: > >Erik, >> >>To answer your questions, I used the tutorial at >> >>https://docs.einsteintoolkit.org/et-docs/Tutorial_for_New_Users >> >>After logging in using ssh -Y, I enter >> >>$ wget --no-check-certificate https://raw.github.com/gridaphobe/CRL/ET_2013_05/GetComponents >>$ ./GetComponents --parallel https://svn.einsteintoolkit.org/manifest/branches/ET_2013_05/einsteintoolki… >> >> >> >>The output then is >> Do you want to update all existing components? yes, no [no] : no >>----------------------------------------------------------------- >>Checking out module: EinsteinAnalysis/Outflow >>from repository: git://github.com/rhaas80/Outflow.git >>into: Cactus/arrangements >>----------------------------------------------------------------- >>Checking out module: EinsteinExact/doc >>from repository: git://github.com/barrywardell/EinsteinExact >>into: Cactus/arrangements >>----------------------------------------------------------------- >>Checking out module: KrancNumericalTools/GenericFD >>from repository: git://github.com/ianhinder/Kranc.git >>into: Cactus/arrangements >>----------------------------------------------------------------- >>Checking out module: McLachlan/doc >>from repository: git://carpetcode.org/McLachlan >>into: Cactus/arrangementsWarning: Could not update McLachlan. Could not stash local changes. Error message was 'fatal: bad revision 'HEAD' >>fatal: bad revision 'HEAD' >>fatal: Needed a single revision >>You do not have the initial commit yet >>'. >>----------------------------------------------------------------- >>Checking out module: McLachlan/m >>from repository: git://carpetcode.org/McLachlan >>into: Cactus/arrangements >>Use of uninitialized value in concatenation (.) or string at ./GetComponents line 1440, <STDIN> line 1.Warning: Could not checkout EinsteinAnalysis/Outflow, unable to switch to tag . Any existing symlinks to EinsteinAnalysis/Outflow will be broken >>Switched to branch "ET_2013_05" >>Switched to branch "master" >>Use of uninitialized value in concatenation (.) or string at ./GetComponents line 1440, <STDIN> line 1.Warning: Could not checkout KrancNumericalTools/GenericFD, unable to switch to tag . Any existing symlinks to KrancNumericalTools/GenericFD will be broken >> >> >> >>The script hangs there. >> >> >>Ben >> >> >> >> >>From: Erik Schnetter <schnetter(a)cct.lsu.edu> >>To: Ben Bernard <Ben_the_Lucky(a)yahoo.com> >>Cc: "users(a)einsteintoolkit.org" <users(a)einsteintoolkit.org> >>Sent: Wednesday, June 26, 2013 11:06 AM >>Subject: Re: [Users] Latest GetComponents broken? >> >> >> >>Ben >> >> >>The script works for me. Let me ask for some further information to be able to help you: >>- What web site has the instructions that you are following? >>- From what url did you download GetComponents? >>- From what url did you get the thorn list? >>- What errors are you seeing? >> >> >>-erik >> >> >> >> >> >>On Wed, Jun 26, 2013 at 9:55 AM, Ben Bernard <Ben_the_Lucky(a)yahoo.com> wrote: >> >>I am attempting to use the GetComponents script on Queen Bee to install the latest Einstein Toolkit, using the commands on the Tutorial for new users. Unfortunately it seems that the GetComponents script cannot find many of the components, and locks up after a few of them. Has anyone else encountered this issue? >>> >>>Regards, >>> >>>Benjamin Bernard >>>_______________________________________________ >>>Users mailing list >>>Users(a)einsteintoolkit.org >>>http://lists.einsteintoolkit.org/mailman/listinfo/users >>> >>> >> >> >> >>-- >>Erik Schnetter <schnetter(a)cct.lsu.edu> >>http://www.perimeterinstitute.ca/personal/eschnetter/ >> >> > > > >-- >Erik Schnetter <schnetter(a)cct.lsu.edu> >http://www.perimeterinstitute.ca/personal/eschnetter/ > > -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/

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Meeting Minutes
by Roland Haas 24 Jun '13

24 Jun '13

Present: Vassili, Peter, Erik, Philipp, Yosef, Roland new Carpet version: * Philipp observed increased memory consumption (run terminated by Out-Of-Memory killer) and a run speed that was continuously decreasing over the time of the run on bluewaters. This used the Intel compiler and ~8000 cores * Roland looked at differences in data between "old" and "new" versions, sees roundoff level differences in rho (for a NsNs run) but larger ones in eps. Could just be the usual case of eps being more sensitive. Roundoff level differences are expected due to different processor decomposition New thorns: * Erik proposed a MemSpeed thorn on trac * Yosef's ParitySymmetry thorn is still up for review * please review the changes to Regrid2 for ParitySymmetry Calls: * very little to discuss these days, consider having the meeting only every two weeks? Please comment. Yours, Roland

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Users June 2013