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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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Re: [Users] Some questions about new release 2013_05
by Petr Tsatsin 23 Jun '13

23 Jun '13

Hello Frank, Thank you for suggestions. On Wed, Jun 19, 2013 at 10:11 PM, Frank Loeffler <knarf(a)cct.lsu.edu> wrote: > Hi Petr, > > On Tue, Jun 18, 2013 at 02:42:07PM -0400, Petr Tsatsin wrote: > > 1) I just tried to run some of my "old" parameter files using the new ET > > release and I got some strange results. The parameter files which work > > completely fine for previous releases do not work anymore in a sense that > > for example for the binary neutron star simulations starting from LORENE > > initial data hamiltonian constraint blows up and central density become > nan > > shortly after the beginning. Thus, I have a question are there any > > essential changes I need to incorporate in my par files due to the new > > release or the old par files should in principle work and give same > results > > as before? > > With these symptoms I would first look at the initial data setup itself. > Are all past timelevels setup correctly? What is the best way to check if past time levels are initialized properly? I use the following parameters for the initial data: InitBase::initial_data_setup_method = "init_some_levels" ActiveThorns = "Meudon_Bin_NS" ADMBase::initial_data = "Meudon_Bin_NS" ADMBase::initial_lapse = "Meudon_Bin_NS" ADMBase::initial_shift = "Meudon_Bin_NS" ADMBase::initial_dtlapse = "Meudon_Bin_NS" ADMBase::initial_dtshift = "Meudon_Bin_NS" Hydrobase::initial_hydro = "Meudon_Bin_NS" Meudon_Bin_NS::filename = "path/to/file" > In principle, the Lorene thorns > should do that, but I could imagine tests not covering this. How does > the data differ between an evolution using the old and the new release? > I'm attaching the figure with minimum lapse evolution. it can be seen that lapse drops below 0.2 very quickly (several time steps). > > > 2) I'm trying to use ML_CCZ4 for the spacetime evolution and I found the > > example par file for BBH evolution in McLachlan/par/CCZ4/bbh_ccz4.par > which > > does not work. I figured that this file was for the old implementation of > > the ccz4 inside ML_BSSN thorn and if I replace ML_BSSN with ML_CCZ4 and > > comment some of the parameters it works. However, I was wondering if you > > could provide a working example of such a file with ML_CCZ4? > > I am sorry, I cannot directly help with this. I opened a ticket, which > might help others do it: https://trac.einsteintoolkit.org/ticket/1387 > Thank you. It would be very helpful to have working examples. > > Frank > > -- Petr Tsatsin Graduate Student - Department of Physics Charles E. Schmidt College of Science Florida Atlantic University (561)-297-3386 cell: 1-561-299-8048 ptsatin(a)fau.edu, ptsatsin(a)gmail.com

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Einstein Toolkit Conference Call
by Erik Schnetter 23 Jun '13

23 Jun '13

You are cordially invited to join our weekly Einstein Toolkit conference call at 10:00 US central time every Monday. This is the main weekly event for all Einstein Toolkit users and developers. We usually review the events of the previous week, and discuss ideas and proposal that may or may not have been mentioned on the mailing list. Feel free to bring any topics with you when you join the call. The next call is tomorrow morning. Instructions for joining this or other events are at <http://einsteintoolkit.org/community/support/>. The phone number for the upcoming call is +1-866-573-0359 (or +1-225-578-4942 from outside the US), and the conference ID is 118682#. -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/

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error in GRHydro
by Babiuc-Hamilton, Maria 20 Jun '13

20 Jun '13

Hello, When trying to compile the Gauss release of the ET arrangement on the Marshall U biggreen cluster, I get this error: Error: Cray pointer declaration at (1) requires -fcray-pointer flag make[3]: *** [GRHydro_Con2Prim.F90.o] Error 1 make[2]: *** [make.checked] Error 2 make[1]: *** [/home/babiuc/Cactus/configs/allthorns/lib/libthorn_GRHydro.a] Error 2 make: *** [allthorns] Error 2 What can be done to fix it? thanks, Maria

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Some questions about new release 2013_05
by Petr Tsatsin 18 Jun '13

18 Jun '13

Hello, 1) I just tried to run some of my "old" parameter files using the new ET release and I got some strange results. The parameter files which work completely fine for previous releases do not work anymore in a sense that for example for the binary neutron star simulations starting from LORENE initial data hamiltonian constraint blows up and central density become nan shortly after the beginning. Thus, I have a question are there any essential changes I need to incorporate in my par files due to the new release or the old par files should in principle work and give same results as before? 2) I'm trying to use ML_CCZ4 for the spacetime evolution and I found the example par file for BBH evolution in McLachlan/par/CCZ4/bbh_ccz4.par which does not work. I figured that this file was for the old implementation of the ccz4 inside ML_BSSN thorn and if I replace ML_BSSN with ML_CCZ4 and comment some of the parameters it works. However, I was wondering if you could provide a working example of such a file with ML_CCZ4? Thank you. -- Petr Tsatsin Graduate Student - Department of Physics Charles E. Schmidt College of Science Florida Atlantic University (561)-297-3386 cell: 1-561-299-8048 ptsatin(a)fau.edu, ptsatsin(a)gmail.com

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Meeting Minutes
by Roland Haas 17 Jun '13

17 Jun '13

Present: Vassili, Peter, Erik, Philipp, Yosef, Roland Tickets: * OMP collapse detection: want to use autoconf * vectors of vector groups: apply patches * implied SYNC removed from Carpet: actual simulation thorns seem fine, test in CarpetProlongateTest is not behaving like a typical simulation thorn * C89 vs. C99: have flesh add options to enable c99 automatically to compiler options * please review outstanding (old) patches: https://trac.einsteintoolkit.org/query?status=review&col=id&col=summary&col… Yours, Roland

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Einstein Toolkit Conference Call Reminder
by Erik Schnetter 17 Jun '13

17 Jun '13

You are cordially invited to join our weekly Einstein Toolkit conference call at 10:00 US central time every Monday. Instructions for joining this or other events are at <http://einsteintoolkit.org/community/support/>. The next call starts in about 20 minutes -- apologies for the late message. The phone number for the upcoming call is +1-866-573-0359 (or +1-225-578-4942 from outside the US), and the conference ID is 118682#. Feel free to bring any topics with you when you join the call. -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/

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OpenMP collapse directive disabled for C, but enabled for Fortran -- likely an error in the option list
by Jakob Hansen 15 Jun '13

15 Jun '13

Hi, I'm trying to compile Gauss release on our local machine (tachyon2), but I'm receiving errors like this : Checking status of thorn MPI ~/Cactus/configs/test/config-data/cctk_Config.h(397): catastrophic error: #error directive: "OpenMP collapse directive disabled for C, but enabled for Fortran -- likely an error in the option list" # error "OpenMP collapse directive disabled for C, but enabled for Fortran -- likely an error in the option list" and many errors similar to it. Possibly I need some changes to my optionlist (as suggested by the error). Any ideas which options need to be set in order to make a successful compile? My current option file looks something like this : ############################################ CPP = cpp FPP = cpp CC = /applic/compilers/intel/11.1/cce/bin/icc CXX = /applic/compilers/intel/11.1/cce/bin/icpc F77 = /applic/compilers/intel/11.1/fce/bin/ifort F90 = /applic/compilers/intel/11.1/fce/bin/ifort CPPFLAGS = -openmp -DMPICH_IGNORE_CXX_SEEK FPPFLAGS = -traditional -D_OPENMP CFLAGS = -openmp -g -traceback -debug all -align -std=gnu99 -ansi_alias -U__STRICT_ANSI__ CXXFLAGS = -openmp -g -traceback -debug all -align -restrict F77FLAGS = -openmp -g -traceback -debug all -align -pad -w95 -cm F90FLAGS = -openmp -g -traceback -debug all -align -pad -w95 -cm LDFLAGS = -Wl,-rpath,/applic/compilers/intel/11.1/mkl/lib/em64t -Wl,-rpath,/applic/compilers/intel/11.1/mpi/mvapich2/1.4/lib -Wl,-rpath,/applic/compilers/intel/11.1/cce/lib -Wl,-rpath,/applic/compilers/intel/11.1/fce/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.1.2 LIBDIRS = /usr/X11R6/lib64 /applic/compilers/intel/11.1/cce/lib /applic/compilers/intel/11.1/fce/lib C_LINE_DIRECTIVES = yes F_LINE_DIRECTIVES = yes 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 CXX_OPTIMISE_FLAGS = -O2 F77_OPTIMISE_FLAGS = -O2 F90_OPTIMISE_FLAGS = -O2 PROFILE = no C_PROFILE_FLAGS = -pg CXX_PROFILE_FLAGS = -pg F77_PROFILE_FLAGS = -pg F90_PROFILE_FLAGS = -pg WARN = yes BLAS_DIR = /applic/compilers/intel/11.1/mkl/lib/em64t BLAS_LIBS = mkl_solver_lp64 mkl_intel_lp64 mkl_intel_thread mkl_core iomp5 guide pthread HDF5_DIR = /home01/[user]/local/hdf5-1.8.11 LAPACK = yes LAPACK_DIR = /applic/compilers/intel/11.1/mkl/lib/em64t LAPACK_LIBS = mkl_solver_lp64 mkl_intel_lp64 mkl_intel_thread mkl_core iomp5 guide pthread MPI_DIR = /applic/compilers/intel/11.1/mpi/mvapich2/1.4 MPI_LIBS = mpich ibverbs ibumad rdmacm rt PTHREADS = yes ############################################ Any advices are much appreciated. Cheers, Jakob

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isnan & compile error: "'(' before 'Cactus'"?
by Scott Hawley 13 Jun '13

13 Jun '13

Hi, I'm confused as to why using "isnan" should produce an error involving "Cactus". I've pulled code out and reduced it to a mere isnan call, and even placed it within HAVE_ISNAN.... #ifdef HAVE_ISNAN if isnan(1.0) {} #endif (Ultimately I want isnan(gxx[CCTK_GFINDEX3D(cctkGH, i,j,k)]) in there...) Here's the error: %make bruiser SILENT=no .. COMPILING /Users/shawley/Cactus/arrangements/Bruiser/BruiserConstraints/src/BruiserUt il.cc current_wd=`pwd` ; cd /Users/shawley/Cactus/configs/bruiser/scratch ; /opt/local/bin/g++-mp-4.7 -m64 -fopenmp -g -O0 -O2 -c -o $current_wd/BruiserUtil.cc.o $current_wd/BruiserUtil.cc -I"/opt/local/include/openmpi" -I"/opt/local/include/openmpi" -I"/opt/local/include/openmpi" -I"/opt/local/include/openmpi" -I"/Users/shawley/Cactus/arrangements/Bruiser/BruiserConstraints/src" -I"/Users/shawley/Cactus/arrangements/Bruiser/BruiserConstraints/src/includ e" -I"/Users/shawley/Cactus/configs/bruiser/config-data" -I"/Users/shawley/Cactus/configs/bruiser/bindings/include" -I"/Users/shawley/Cactus/src/include" -I"/Users/shawley/Cactus/arrangements" -I"/Users/shawley/Cactus/configs/bruiser/bindings/Configuration/Thorns" -I"/Users/shawley/Cactus/configs/bruiser/bindings/include/BruiserConstraint s" -I"/opt/local/include/openmpi" -I"/opt/local/include/openmpi" -I"/opt/local/include/openmpi" -I"/opt/local/include/openmpi" -I"/Users/shawley/Cactus/arrangements/Bruiser/BruiserConstraints/src" -I"/Users/shawley/Cactus/arrangements/Bruiser/BruiserConstraints/src/includ e" -I"/Users/shawley/Cactus/configs/bruiser/bindings/include/BruiserConstraint s" -DCCODE /Users/shawley/Cactus/configs/bruiser/build/BruiserConstraints/BruiserUtil. cc: In function 'void BruiserF2CIBFillVar(cGH*, int, int, int, int, maskcodes_type)': /Users/shawley/Cactus/configs/bruiser/build/BruiserConstraints/BruiserUtil. cc:461:30: error: expected '(' before 'Cactus' make[3]: *** [BruiserUtil.cc.o] Error 1 make[2]: *** [make.checked] Error 2 Pulling the raw code itself shows no lines with "Cactus" in them, so apparently "isnan" has NOT been redefined by some header: % sed -n 460,462p /Users/shawley/Cactus/configs/bruiser/build/BruiserConstraints/BruiserUtil. cc #ifdef HAVE_ISNAN if isnan(6.0) {} #endif % I'm guessing this is one of those cases where the error being reported is not the "real" error. So I checked to make sure parentheses and curly braces are opened & closed appropriately. Any suggestions for how to fix this? Thanks.

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