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[Commits] New changesets in Carpet Mercurial
by Erik Schnetter 19 Mar '12

19 Mar '12

Luca In general, the system should provide good settings, and you would not use this parameter. In some cases, the system may have a problem, and then this parameter can provide a work-around. For example, we recently identified a change of behaviour on Kraken at TACC, and were able to use this parameter to work around a problem. (In the mean time, we found the correct solution for Kraken.) -erik On Fri, Mar 16, 2012 at 8:37 PM, Luca Baiotti <baiotti(a)ile.osaka-u.ac.jp> wrote: > Hello Erik, > > is set_cpu_affinity (already) recommended for production runs? What > could one expect from it? > > Best, > > Luca > > > > On 17/3/12 12:16 AM, Carpet mercurial repositories wrote: >> changeset: 3492:0a4e0bb3448a >> parent: 3490:c81ef26b02ec >> user: Erik Schnetter<schnetter(a)gmail.com> >> date: Fri Mar 16 11:09:48 2012 -0400 >> summary: Carpet: Add parameter set_cpuaffinity >> >> changeset: 3493:26551c89c940 >> parent: 3492:0a4e0bb3448a >> parent: 3491:e8512ecd6c79 >> user: Erik Schnetter<schnetter(a)gmail.com> >> date: Fri Mar 16 11:15:28 2012 -0400 >> summary: Merge >> >> changeset: 3494:b85d9ecd647a >> tag: tip >> user: Erik Schnetter<schnetter(a)gmail.com> >> date: Fri Mar 16 11:16:19 2012 -0400 >> summary: Carpet: Add example parameter files for CPU affinity handling >> >> _______________________________________________ >> Commits mailing list >> Commits(a)einsteintoolkit.org >> http://lists.einsteintoolkit.org/mailman/listinfo/commits >> > > -- > Thanks for saving energy! > _______________________________________________ > 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/

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Meeting Minutes
by Roland Haas 19 Mar '12

19 Mar '12

Present were: Roland, Frank, Josh, Bruno, Tanja, Yosef * there are currently a number of branches of ET thorns at various institutions, there is a suggestion to instead work on branches inside of the ET repositories. A suggestion was made to have a concerted effort to merge these private changes back into the public repository. ET workshop: * Cactus virtual machines will be available for download soon * please test them in particular if you are handling a hands on session * please add any slides you would like to use to the workshop repository https://svn.einsteintoolkit.org/documents/Workshop_Spring_2012/ * there are currently about 20 registered participants Yours, Roland

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Einstein Toolkit Meeting
by Frank Loeffler 18 Mar '12

18 Mar '12

On Sun, Mar 11, 2012 at 11:22:44PM -0500, Frank Loeffler wrote: 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#. We are heading full-speed (time-wise) towards the spring ET workshop [1]. Let's go through the planned activities and see who managed to prepare what already. Of course, feel free to bring up any other bugging issue as well. Also note, that the US is on daylight savings time already (most of it anyways), but Europe or other parts of the world might not be. [1] https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Spring_2012 Frank Loeffler

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Re: [Users] [Commits] New changesets in Carpet Mercurial
by Luca Baiotti 16 Mar '12

16 Mar '12

Hello Erik, is set_cpu_affinity (already) recommended for production runs? What could one expect from it? Best, Luca On 17/3/12 12:16 AM, Carpet mercurial repositories wrote: > changeset: 3492:0a4e0bb3448a > parent: 3490:c81ef26b02ec > user: Erik Schnetter<schnetter(a)gmail.com> > date: Fri Mar 16 11:09:48 2012 -0400 > summary: Carpet: Add parameter set_cpuaffinity > > changeset: 3493:26551c89c940 > parent: 3492:0a4e0bb3448a > parent: 3491:e8512ecd6c79 > user: Erik Schnetter<schnetter(a)gmail.com> > date: Fri Mar 16 11:15:28 2012 -0400 > summary: Merge > > changeset: 3494:b85d9ecd647a > tag: tip > user: Erik Schnetter<schnetter(a)gmail.com> > date: Fri Mar 16 11:16:19 2012 -0400 > summary: Carpet: Add example parameter files for CPU affinity handling > > _______________________________________________ > Commits mailing list > Commits(a)einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/commits > -- Thanks for saving energy!

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SubstepOutput
by Ian Hinder 16 Mar '12

16 Mar '12

Hi all, I have a small thorn which might be useful for debugging. It enables output of grid variables on each MoL substep, so you can see what is happening on each one. The variables are output into files with the substep number appended, so you get, for example, phi.x.asc phi_0.x.asc phi_1.x.asc phi_2.x.asc for a 3-step method (e.g. RK3). The first step is 0 (in contrast to how MoL counts internally, which is backwards). This happens in MoL_Step after MoL_RHSBoundaries before MoL_NaNCheck which should be sufficient. You could also manually modify the schedule to investigate at other points, if that is useful to you. You use the thorn by setting the parameter SubstepOutput::vars to the list of variables or groups you want to output, for example SubstepOutput::vars = "Wave::phi Wave::pi Wave::phirhs Wave::pirhs" You can also set the output method to use: SubstepOutput::output_method = "IOHDF5" It defaults to IOASCII_1D. You can get this thorn using git clone https://bitbucket.org/ianhinder/substepoutput.git SubstepOutput It might be appropriate for this functionality to be implemented in MoL instead. -- Ian Hinder http://numrel.aei.mpg.de/people/hinder

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Re: [Users] simfactory configuration for kraken
by Roland Haas 15 Mar '12

15 Mar '12

Hello Bernard, > Actually, Roland, do you know if this applies for the PGI compilers as > well? Because that's what I was using. I do not know if it applies to the PGI compiler as well. NICS'sannouncement before the upgrade (in one of the weekly ones) said that at least a re-link, possibly a full recompile is required. We no longer use PGI because it was found to be slower than Intel. You can certainly pull the individual cfg file out of the trunk repository (https://svn.cct.lsu.edu/repos/numrel/simfactory2/trunk/mdb/optionlists/krak…) or do a switch of branch just for simfactory (most likely by removing your current simfactory checkout, changing the URL in the Thornlist to trunk and using GetComponent again). The same applis to the updated machine.ini and Kraken.sub files (minor changes only in them, ini file changes name of option list, Kraken.sub updates path to qsub). The other option is for me to put the new config files into the Maxwell branch as well. Updates such as this were one reason why we used branches rather than tags I believe. For the maintainers: any objections to this plan? My understanding is that I would also create a new tag ET_2011_10_v1 for this, yes? Yours, Roland -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://keys.gnupg.net.

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Using gmake - Re: ETK in NERSC machines (Hopper/Carver) does not work properly
by Jose Fiestas Iquira 15 Mar '12

15 Mar '12

Hello Ian, all, I am trying now to use gmake to create an executable using McLachlan for a simulation of binary coalescence. When I do: gmake grbinary I obtain: ..... CST finished. /global/u1/f/fiestas/CACTUS/Cactus/arrangements/Carpet/CarpetLib/src/make.configuration.defn:5: *** Configuration error: The Carpet thorns require MPI. Please configure with MPI, or remove the Carpet thorns from the ThornList.. Stop. gmake: *** [grbinary] Error 2 .......... I checked the configuration and I found following line while doing: gmake grbinary-config thornlist='thornlists/grbinary.th' ............ Configuring without MPI ............ So, I tried: export mpi=native gmake grbinary-config and - setting mpi=native in a config. file and using it gmake grbinary-config options='grbinary-config.txt' Initially looks OK: fiestas@hopper09:~/CACTUS/Cactus> gmake grbinarypgi-config options='grbinary-config-pgi' Cactus - version: 4.0.0 Reconfiguring grbinarypgi. Adding configuration options from 'grbinary-config-pgi'... Setting mpi to 'native' Setting CC to 'mpicc' Setting CXX to 'mpicxx' End of options from 'grbinary-config-pgi'. .... but later I get again the message: ........... Configuring without MPI ........ Am I doing something wrong? Btw, if I configure with my own thronlist and add it as above, it keeps reading all thorns in the arrangements directory while compiling. So, I copied my thornlist in configs/grbinary/ to force the compilation using my thornlist. Is it normal? Thanks, Jose On Mon, Mar 12, 2012 at 4:24 AM, Ian Hinder <ian.hinder(a)aei.mpg.de> wrote: > > On 10 Mar 2012, at 01:41, Jose Fiestas Iquira wrote: > > > Dear colleagues, > > > > I was trying the last days to install an own application based on ETK in > > NERSC machines (Hopper/Carver), having some problems during the > compilation. > > Before trying to find the real problem, I started from scratch and > realize > > I can not even checkout ETK properly. > > Does somebody tried it in machines different as LONI machines since the > > last release? Would appreciate any experience about it. > > Below my steps: > > > > > > 1. GetComponents <Einstein Toolkit> (release version) > > curl -O https://raw.github.com/gridaphobe/CRL/master/GetComponents > > .............................. > > *183 components checked out.* > > * 0 components updated.* > > * > > * > > * Unable to process simfactory2* > > * Unable to process LSUThorns/QuasiLocalMeasures* > > * Unable to process LSUThorns/SummationByParts* > > * Unable to process LSUThorns/Vectors* > > These are all hosted on svn.cct.lsu.edu, which we have found to be very > unreliable. It might be that the machine (or connection) was down when you > tried it. Can you try it again? > > We might want to think about moving these repositories to a more reliable > server, for example svn.einsteintoolkit.org. > > Alternatively, it might be that there is a routing problem between NERSC > and CCT. Can you try > > ping svn.cct.lsu.edu > > from one of the affected machines? > > PS: your WaveDemo build fails because the wavedemo thornlist is not up to > date. It needs to be modified to include the Vectors thorn (see the ET > thornlist for an example). > > The Cactus thornlists are out of date - see > > https://trac.einsteintoolkit.org/ticket/663 > > and > > https://trac.einsteintoolkit.org/ticket/641 > > > * > > * > > *Summary of Warnings:* > > * > > * > > *Could not checkout module simfactory2* > > * > > * > > * > > * > > *Could not checkout module LSUThorns/QuasiLocalMeasures* > > * > > * > > * > > * > > *Could not checkout module LSUThorns/SummationByParts* > > * > > * > > * > > * > > *Could not checkout module LSUThorns/Vectors* > > * > > * > > > > * Time Elapsed: 26 minutes, 19 seconds* > > .............................................. > > > > 2. GetComponent <WaveDemo> > > ./GetComponents > > http://cactuscode.org/documentation/tutorials/wavetoydemo/WaveDemo.th > > > > * Went OK* > > * > > * > > 3. cd Cactus > > gmake WaveDemo-config > > gmake WaveDemo > > > > > > *------------------------------------------------------* > > *Warnings were generated during execution of the CST* > > *------------------------------------------------------* > > * > > * > > * > > * > > *CST error 1:* > > * -> Duplicate thornname LocalReduce in CactusBase and CactusNumerical* > > * > > * > > * > > * > > *CST error 2:* > > * -> Thorn 'CarpetLib' requires the capability 'Vectors'.* > > * Please add a thorn that provides 'Vectors' to your ThornList or > > remove 'CarpetLib' from it !* > > * > > * > > * > > * > > *CST error 3:* > > * -> Thorn 'ML_BSSN' requires the capability 'Vectors'.* > > * Please add a thorn that provides 'Vectors' to your ThornList or > > remove 'ML_BSSN' from it !* > > * > > * > > * > > * > > *CST error 4:* > > * -> Thorn 'ML_BSSN_O2' requires the capability 'Vectors'.* > > * Please add a thorn that provides 'Vectors' to your ThornList or > > remove 'ML_BSSN_O2' from it !* > > * > > * > > * > > * > > *CST error 5:* > > * -> ID_BIN_BH (thorn Meudon_Bin_BH) inherits from SummationByParts* > > * No thorn in your current ThornList implements SummationByParts* > > * Either remove Meudon_Bin_BH, or add a thorn to your* > > * ThornList implementing SummationByParts* > > * Available thorns in arrangements directory implementing > > SummationByParts:* > > * LSUThorns/SummationByParts* > > * > > * > > * > > * > > *CST error 6:* > > * -> MEUDON_BIN_NS (thorn Meudon_Bin_NS) inherits from SummationByParts* > > * No thorn in your current ThornList implements SummationByParts* > > * Either remove Meudon_Bin_NS, or add a thorn to your* > > * ThornList implementing SummationByParts* > > * Available thorns in arrangements directory implementing > > SummationByParts:* > > * LSUThorns/SummationByParts* > > * > > * > > * > > * > > *CST error 7:* > > * -> Configuration script for thorn BLAS returned exit code 1* > > * Error message: 'Error while building BLAS. Aborting.'* > > * > > * > > * > > * > > *CST error 8:* > > * -> Configuration script for thorn LAPACK returned exit code 1* > > * Error message: 'Error while building LAPACK. Aborting.'* > > * > > * > > *------------------------------------------------------* > > * > > * > > *gmake[1]: *** > > > [/project/projectdirs/snfactry/hshukla/CACTUS/Cactus/configs/WaveDemo/config-data/make.thornlist] > > Error 1* > > *gmake: *** [WaveDemo] Error 2* > > * > > * > > * > > * > > * > > 4. Copied LSUThorns by hand and repeated step 3 and got the same errors. > > * > > > > *183 components checked out.* > > * 0 components updated.* > > * > > * > > * Unable to process simfactory2* > > * Unable to process LSUThorns/QuasiLocalMeasures* > > * Unable to process LSUThorns/SummationByParts* > > * Unable to process LSUThorns/Vectors* > > * > > * > > *Summary of Warnings:* > > * > > * > > *Could not checkout module simfactory2* > > * > > * > > * > > * > > *Could not checkout module LSUThorns/QuasiLocalMeasures* > > * > > * > > * > > * > > *Could not checkout module LSUThorns/SummationByParts* > > * > > * > > * > > * > > *Could not checkout module LSUThorns/Vectors* > > * > > * > > > > * Time Elapsed: 26 minutes, 19 seconds* > > > > Best, > > Jose > > _______________________________________________ > > Users mailing list > > Users(a)einsteintoolkit.org > > http://lists.einsteintoolkit.org/mailman/listinfo/users > > -- > Ian Hinder > http://numrel.aei.mpg.de/people/hinder > >

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output not overwritten anymore?
by Christian Reisswig 14 Mar '12

14 Mar '12

Hi, I am wondering if the default behavior of Cactus output has been changed recently. When starting a simulation from scratch (i.e. no recovery), already existing output files used to get overwritten. Instead now, Cactus appends data to the end of the files. How can I change this behavior? Is there a parameter for this? Thanks, Christian

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Re: [Users] [Commits] [svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 313)
by Joshua Faber 13 Mar '12

13 Mar '12

I believe it is the standard version, at least when T mu nu is stored, for which T_mu nu = rho h u_mu u_nu + P g_mu nu, and you need to include the 8 pi terms any time it appears as the RHS of the Einstein equation. I don't know personally how McLachlan actually calculates the RHS of the field equations in detail. -J On Tue, Mar 13, 2012 at 4:35 PM, Roland Haas <roland.haas(a)physics.gatech.edu> wrote: > Hello Josh, all, > >> Fixed factors of 8 pi in definition of matter sources > Just out of (morbid) curiosity: what is actually used in the code? > > Yours, > Roland > > -- > My email is as private as my paper mail. I therefore support encrypting > and signing email messages. Get my PGP key from http://keys.gnupg.net. > > > _______________________________________________ > Commits mailing list > Commits(a)einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/commits >

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simfactory configuration for kraken
by Cody Simmons 13 Mar '12

13 Mar '12

Hi all, I've gotten Cactus to compile on Kraken using the updated configuration file below. However, I am having trouble successfully running a simulation. When I run "./simfactory/bin/sim whoami" , it returns "Current machine: franklin". Any ideas? -Cody Simmons # kraken-intel # Whenever this version string changes, the application is configured # and rebuilt from scratch VERSION = 2012-03-12 CPP = cpp FPP = cpp CC = /opt/intel/composer_xe_2011_sp1.8.273/bin/intel64/icc CXX = /opt/intel/composer_xe_2011_sp1.8.273/bin/intel64/icpc F77 = /opt/intel/composer_xe_2011_sp1.8.273/bin/intel64/ifort F90 = /opt/intel/composer_xe_2011_sp1.8.273/bin/intel64/ifort CPPFLAGS = -D__CRAYXT -D__CRAYXT_COMPUTE_LINUX_TARGET -D__TARGET_LINUX__ -DMPICH_IGNORE_CXX_SEEK FPPFLAGS = -traditional CFLAGS = -g -debug all -traceback -msse3 -align -std=c99 -ansi_alias -U__STRICT_ANSI__ CXXFLAGS = -g -debug all -traceback -msse3 -align -restrict -D_intel_fast_memcpy=memcpy -D_intel_fast_memset=memset F77FLAGS = -g -debug all -traceback -msse3 -align -pad -w95 -cm F90FLAGS = -g -debug all -traceback -msse3 -align -pad -w95 -cm CUCC = /opt/intel/composer_xe_2011_sp1.8.273/bin/intel64/icpc CUCCFLAGS = -x c++ -D__CRAYXT -D__CRAYXT_COMPUTE_LINUX_TARGET -D__TARGET_LINUX__ -DMPICH_IGNORE_CXX_SEEK -g -debug all -traceback -msse3 -align -std=c99 -ansi_alias -U__STRICT_ANSI__ -openmp CUCC_DEBUG_FLAGS = -DCARPET_DEBUG -O0 CUCC_OPTIMISE_FLAGS = -O2 -override-limits CUCC_WARN_FLAGS = CU_DEPEND = /opt/intel/composer_xe_2011_sp1.8.273/bin/intel64/icpc -M -x c++ -D__CRAYXT -D__CRAYXT_COMPUTE_LINUX_TARGET -D__TARGET_LINUX__ -DMPICH_IGNORE_CXX_SEEK -openmp SYS_INC_DIRS = /opt/cray/mpt/5.3.5/xt/seastar/mpich2-intel/120/include LDFLAGS = -static LIBDIRS = /opt/cray/mpt/5.3.5/xt/seastar/mpich2-intel/120/lib /opt/cray/mpt/5.3.5/xt/seastar/sma/lib64 /opt/cray/portals/2.2.0-1.0301.26633.6.9.ss/lib64 /opt/cray/pmi/2.1.4-1.0000.8596.15.1.ss/lib64 /opt/xt-libsci/default/intel/lib /opt/xt-pe/2.2.48B/lib /opt/xt-pe/default/lib /opt/xt-pe/2.2.48B/lib/snos64 /opt/xt-pe/default/lib/snos64 /usr/lib/alps /nics/b/home/eschnett/petsc/lib LIBS = -Wl,--start-group sci_istanbul_mp ifcore mpichcxx mpich rt sma portals pmi alpslli alpsutil pthread imf m mpl -Wl,--end-group iomp5 pthread DISABLE_REAL16 = yes # MPI doesn't support this type C_LINE_DIRECTIVES = yes F_LINE_DIRECTIVES = yes VECTORISE = yes VECTORISE_ALIGNED_ARRAYS = no VECTORISE_INLINE = no DEBUG = no CPP_DEBUG_FLAGS = -DCARPET_DEBUG FPP_DEBUG_FLAGS = -DCARPET_DEBUG C_DEBUG_FLAGS = -O0 # -check-uninit CXX_DEBUG_FLAGS = -O0 # -check-uninit F77_DEBUG_FLAGS = -O0 -check bounds -check format # -check all F90_DEBUG_FLAGS = -O0 -check bounds -check format # -check all OPTIMISE = yes CPP_OPTIMISE_FLAGS = # -DCARPET_OPTIMISE -DNDEBUG FPP_OPTIMISE_FLAGS = # -DCARPET_OPTIMISE -DNDEBUG C_OPTIMISE_FLAGS = -O2 -override-limits CXX_OPTIMISE_FLAGS = -O2 -override-limits F77_OPTIMISE_FLAGS = -O2 -override-limits F90_OPTIMISE_FLAGS = -O2 -override-limits PROFILE = no CPP_PROFILE_FLAGS = FPP_PROFILE_FLAGS = C_PROFILE_FLAGS = -pg CXX_PROFILE_FLAGS = -pg F77_PROFILE_FLAGS = -pg F90_PROFILE_FLAGS = -pg OPENMP = yes CPP_OPENMP_FLAGS = -openmp FPP_OPENMP_FLAGS = -D_OPENMP C_OPENMP_FLAGS = -openmp CXX_OPENMP_FLAGS = -openmp F77_OPENMP_FLAGS = -openmp F90_OPENMP_FLAGS = -openmp WARN = yes CPP_WARN_FLAGS = FPP_WARN_FLAGS = C_WARN_FLAGS = CXX_WARN_FLAGS = F90_WARN_FLAGS = F77_WARN_FLAGS = BLAS_DIR = /opt/intel/composer_xe-2011_sp1.8.273/mkl/lib/intel64/ BLAS_LIBS = -Wl,--start-group mkl_intel_lp64 mkl_intel_thread mkl_core -Wl,--end-group iomp5 pthread FFTW_DIR = /opt/fftw/3.3.0.0/x86_64/lib GSL_DIR = /sw/xt-cle3.1/gsl/1.14/cnl3.1_intel12.0.4.191/lib HDF5_DIR = BUILD # IPM_DIR = /sw/xt-cle3.1/gsl/1.14/cnl3.1_intel12.0.4.191/lib LAPACK_DIR = /sw/xt-cle3.1/gsl/1.14/cnl3.1_intel12.0.4.191/lib LAPACK_LIBS = -Wl,--start-group mkl_intel_lp64 mkl_intel_thread mkl_core -Wl,--end-group MPI = NATIVE PAPI_DIR = /opt/cray/papi/4.1.4/perfmon/2.82/lib PAPI_LIBS = papi pfm PETSC_DIR = /opt/petsc/3.2.00/real/INTEL/ PETSC_ARCH = cray-xt PETSC_ARCH_LIBS = craypetsc HYPRE cmumps dmumps smumps zmumps mumps_common parmetis metis pord superlu_4.0 superlu_dist_2.3 sci mpich pmi rt PTHREADS = yes SSL_DIR = /nics/b/home/tradke/install/openssl-0.9.8i # TAU_MAKEFILE = /sw/xt5/tau/2.18.1/cnl2.1_intel7.2.5/tau-2.18.1p2/craycnl/lib/Makefile.tau-multiplecounters-mpi-papi-pdt-intel

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