Users March 2011

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15 participants
25 discussions

Meeting minutes
by Roland Haas 01 Apr '11

01 Apr '11

Meeting minutes: Present were: Frank, Tanja, Bruno, Roland, Christian, Eloisa, Peter, Yosef, Ian, Erik upcoming ET release: * updated release timeline https://trac.einsteintoolkit.org/wiki/ReleasePlan * release will not include python simfactory or the Mercurial version of Carpet, but we will switch to those about two weeks after the release * major new feature of release: EOS_Omni * will write transition guide to be either part of EOS_Omni documentation or on the ET website (or both) * MHD is still being tested and not yet ready for official release ** presentation of status at CIGR workshop * testuites: ** remove obsolete machines: Abe, damiana ** add new machines: Datura (Ian Hinder), Lonestar and Hopper (Erik Schnetter), Trestles (Christian Ott) incl. only if straightforward to do, Pandora (Peter Diener) ** test with OpenMP (release with OMP only if no problems are found): 1 process+1 thread total, 1 process+2 threads total, 2 processes+2 threads total ET paper: * publish independent of ET release (with timetable from Meeting Reminder): April 04: Most text included, or sections get reassigned April 11: All text included, data from example sections mostly there April 18: Results from example sections included, or dropped April 25: Text and data complete - "public review" May 09: Addressed incoming comments, publish along with new release 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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EOS_Omni parameter file conversion guide draft
by Erik Schnetter 31 Mar '11

31 Mar '11

I began to write an EOS_Omni parameter file conversion guide, mostly because I needed it myself. I am writing this guide as part of the EOS_Omni documentation. While writing this guide, I also wanted to document some of the details of EOS_Omni, and I found some unexpected behaviour. I attach my current draft; I would appreciate it if someone with more experience than me could have a look at it, correct the larger errors, and then commit it to the thorn. I am particularly confused about the meaning of the *_ini parameters (nothing in this thorn makes a distinction between initial data and time evolution), and the meaning of have_temp (which seems to ignore the temperature either way). -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 27 Mar '11

27 Mar '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/info/support/ I short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. Some points of tomorrows discussion will be: 1) ET release plan for ET_2011_05 see https://trac.einsteintoolkit.org/wiki/ReleasePlan 2) ET paper plan: April 04: Most text included, or sections get reassigned April 11: All text included, data from example sections mostly there April 18: Results from example sections included, or dropped April 25: Text and data complete - "public review" May 09: Addressed incoming comments, publish along with new release Frank Loeffler

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Checking out multiple git branches but defaulting to master
by Yosef Zlochower 24 Mar '11

24 Mar '11

Hi, I have a git repository with multiple branches. I want to use GetComponents to checkout some of the branches but also have the repository default to master. Right now, the repository will default to the last branch listed in !REPO_BRANCH, which apparently cannot be set to master. -- Dr. Yosef Zlochower Center for Computational Relativity and Gravitation Assistant Professor School of Mathematical Sciences Rochester Institute of Technology 85 Lomb Memorial Drive Rochester, NY 14623 Office:74-2067 Phone: +1 585-475-6103 yosef(a)astro.rit.edu CONFIDENTIALITY NOTE: The information transmitted, including attachments, is intended only for the person(s) or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and destroy any copies of this information.

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Meeting minutes
by Roland Haas 22 Mar '11

22 Mar '11

Meeting minutes: Present were: Frank, Peter, Tanja, Roland, Erik, Ian, Eloisa, Christian ET paper: * LRR: ** proposal writing has not yet started ** would need method to give credit to contributors, LRR is problematic because the number of authors is limited (3, at most 5 authors possible), try for authors list of current draft (7-10), acknowledge past contributors, sort out off-line ** also review work done using the Einstein Toolkit ** better to go use a series of ordinary papers, with an baseline paper first and additional papers later on describing new modules / modifications ** publish in LRR if possible, otherwise choose traditional publication * paper draft in repository needs to be finished ** add more details, remove 20 pages goal ** preferred way to ensure proper credit to contributors (fairness issue with small number of authors in LRR) ** ask authors to put in at least a skeleton section within 2 weeks ** suggest reassignment of sections if no change after these two weeks and no data for when the section will be written is given ** re-add deadline and section authors to paper draft ET spring workshop: * transportation from CalTech to Anaheim: best to use public transportation, taking Metro Gold line to Union station, then train to Anaheim, then cab or walk for 2miles. 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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ET paper
by Frank Loeffler 22 Mar '11

22 Mar '11

Hi As discussed I added names to every section, and an approximate length. You don't absolutely have to meet that, but you should arrive somewhere around that number. Please let me know now if you don't think you can write your contribution within the next two weeks, or if you are interested to take over or add another part. When you use references, you have to add them to einsteintoolkit.bib, using its format. Figures go into the 'figures' subdirectory. Please use pdf, png or jpeg (e.g. not eps), and don't use the file extensions in the latex source. If possible, add the source for the figures as well. This also includes data (if small enough) and scripts to generate plots. This also includes the parameter files for the examples - which should only contain ET components. Frank

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 21 Mar '11

21 Mar '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/info/support/ I short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. Some points of tomorrows discussion will be: 1) ET living review proposal 2) ET paper news? 3) ET developer workshop in April - logistics (e.g. how to go from CalTech to Anaheim) I am sorry for the late reminder this time (15 minutes to the meeting). Frank Löffler

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config file for lonestar
by Yosef Zlochower 18 Mar '11

18 Mar '11

Hi, I am trying some simulations on lonestar using the config file below. I noticed that my simulations hang when I choose large numbers of cores. I haven't yet determined where they hang (the same executable and parfile combination does not hang on fewer cores). Is there a standard config file for lonestar? CPP = cpp FPP = cpp CC = /opt/apps/intel/11.1/bin/intel64/icc CXX = /opt/apps/intel/11.1/bin/intel64/icpc F77 = /opt/apps/intel/11.1/bin/intel64/ifort F90 = /opt/apps/intel/11.1/bin/intel64/ifort # -inline-debug-info leads to compiler crashes when used with optimisation CPPFLAGS = -DMPICH_IGNORE_CXX_SEEK FPPFLAGS = -traditional #CFLAGS = -g -debug all -traceback -align -std=gnu99 -ansi_alias CFLAGS = -g -debug all -traceback -align -std=c99 -ansi_alias CXXFLAGS = -g -debug all -traceback -align -restrict F77FLAGS = -g -debug all -traceback -align -pad -w95 -cm F90FLAGS = -g -debug all -traceback -align -pad -w95 -cm C_LINE_DIRECTIVES = yes F_LINE_DIRECTIVES = yes LDFLAGS = -Wl,-rpath,/opt/apps/intel11_1/mvapich2/1.6/lib -Wl,-rpath,/opt/apps/ intel/11.1/lib/intel64/lib # Include hypre, SPAI, Chaco, spooles, SuperLU_DIST, MUMPS, ParMetis, SCALAPACK, blacs, g2c, and X11 for PETSc LIBDIRS = /opt/apps/intel/11.1/lib/intel64/lib # -check-uninit aborts for uninitialised variables, which is too strict 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 # -O3 miscompiles parts of CarpetLib # -ip leads to wrong physics when OpenMP is used OPTIMISE = yes CPP_OPTIMISE_FLAGS = # -DCARPET_OPTIMISE -DNDEBUG FPP_OPTIMISE_FLAGS = # -DCARPET_OPTIMISE -DNDEBUG C_OPTIMISE_FLAGS = -O2 -xW CXX_OPTIMISE_FLAGS = -O2 -xW F77_OPTIMISE_FLAGS = -O2 -xW F90_OPTIMISE_FLAGS = -O2 -xW 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 = F77_WARN_FLAGS = F90_WARN_FLAGS = BLAS_DIR = HDF5 = yes HDF5_DIR = BUILD #Previously: #GSL_DIR = /opt/apps/gsl/1.11 GSL_DIR = BUILD LAPACK_DIR = MPI = CUSTOM MPI_INC_DIRS = /opt/apps/intel11_1/mvapich2/1.6/include/ MPI_LIB_DIRS = /opt/apps/intel11_1/mvapich2/1.6/lib/ /opt/ofed/lib64/ MPI_LIBS = mpich rt rdmacm ibverbs ibumad PTHREADS = yes -- Dr. Yosef Zlochower Center for Computational Relativity and Gravitation Assistant Professor School of Mathematical Sciences Rochester Institute of Technology 85 Lomb Memorial Drive Rochester, NY 14623 Office:74-2067 Phone: +1 585-475-6103 yosef(a)astro.rit.edu CONFIDENTIALITY NOTE: The information transmitted, including attachments, is intended only for the person(s) or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and destroy any copies of this information.

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CarpetIOHDF5 error at recovery
by Hee Il Kim 18 Mar '11

18 Mar '11

Hi, I'm sorry this has been discussed already. I got the error message below when I tried to restart from (chuncked) checkpoint files. I can't say whether the files are corrupted or not. I just checked they didn't show any problematic messages from "h5ls --errors checkpt_files". The error occurs because the checkpoint files are corrupted or any other reason? ### Error mesages ### cactus_bns_et: /home01/r632kgw/khi/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Input.cc:302: int CarpetIOHDF5::Recover(_cGH *, const char *, int): Assertion `called_from == CP_RECOVER_PARAMETERS or called_from == FILEREADER_DATA' failed. Cheers, Hee Il

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Re: [Users] numrel/simfactory SVN commit 1296: /branches/PYSIM_2010/mdb/optionlists/
by Ian Hinder 16 Mar '11

16 Mar '11

Hi, What is the reason for requiring the Fortran and C++ bindings to be present in everyones' HDF5 library? ExternalLibraries/HDF5 now expects these to be present. Since not all thorns need these, I think having them should be optional. If you try to use a thorn which tries to include the C++ header, for example, then it should be very clear what is going on. On 16 Mar 2011, at 17:22, knarf(a)cct.lsu.edu wrote: > User: knarf > Date: 2011/03/16 10:22 AM > > Modified: > /branches/PYSIM_2010/mdb/optionlists/ > debian-lenny-gcc.cfg > > Log: > Don't rely on the hdf5 intallation of a debian system as it usually doesn't contain the fortran bindings (needed atm) > > File Changes: > > Directory: /branches/PYSIM_2010/mdb/optionlists/ > ================================================ > > File [modified]: debian-lenny-gcc.cfg > Delta lines: +1 -1 > =================================================================== > --- branches/PYSIM_2010/mdb/optionlists/debian-lenny-gcc.cfg 2011-03-14 21:17:04 UTC (rev 1295) > +++ branches/PYSIM_2010/mdb/optionlists/debian-lenny-gcc.cfg 2011-03-16 16:22:38 UTC (rev 1296) > @@ -51,7 +51,7 @@ > > BLAS_LIBS = > > -HDF5 = yes > +HDF5_DIR = BUILD > > LAPACK = yes > LAPACK_LIBS = lapack > -- Ian Hinder ian.hinder(a)aei.mpg.de

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