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Error in compiling einsteintoolkit on Mac
by Babiuc-Hamilton, Maria 08 Feb '11

08 Feb '11

Hello, I have errors in compiling einsteintoolkit.th on a mac: First, it did not configure HDF5 Compiling einsteintoolkit CST error 1: -> Configuration script for thorn HDF5 returned exit code 1 Error message: 'Error while building HDF5. Aborting.' With external HDF5 directory, it complained Use external hdf5 --error libsz.dylib needed With external HDF5_DIR and LIBSZ_DIR the error is: Preprocessing /Users/babiuc/Cactus/arrangements/Carpet/CarpetIOBasic/src/iobasic.cc Compiling /Users/babiuc/Cactus/arrangements/Carpet/CarpetIOBasic/src/iobasic.cc /Users/babiuc/Cactus/arrangements/Carpet/CarpetIOBasic/src/iobasic.cc: In function 'bool CarpetIOBasic::UseScientificNotation(const T&) [with T = int]': /Users/babiuc/Cactus/arrangements/Carpet/Carpet/src/typecase:131:1: instantiated from here /Users/babiuc/Cactus/arrangements/Carpet/CarpetIOBasic/src/iobasic.cc:701:5: internal compiler error: in tsubst_copy_and_build, at cp/pt.c:13326 Please submit a full bug report, with preprocessed source if appropriate. See <http://gcc.gnu.org/bugs.html> for instructions. make[3]: *** [iobasic.cc.o] Error 1 make[2]: *** [make.checked] Error 2 make[1]: *** [/Users/babiuc/Cactus/configs/einsteintoolkit/lib/libthorn_CarpetIOBasic.a] Error 2 make: *** [einsteintoolkit] Error 2 please help, Maria PS: I am using the new gnu compilers: CC = gcc-mp-4.6 CXX = g++-mp-4.6 F77 = gfortran-mp-4.6 F90 = gfortran-mp-4.6 and the hdf5 is the one used by the visit2.2.0 binaries for mac x86_64: hdf5-1.8.4-x86_64 and required by CarpetHDF5.

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Meeting minutes
by Roland Haas 07 Feb '11

07 Feb '11

Present were: Frank, Tanja, Roland, Peter, Ian, Eloisa, Bruno, Erik ET paper: * no commits since last week * please have a look at your assigned section or if you feel you will not have time to work on it try to have it reassigned Visualization scripts: * three groups replied * please add your own methods, even if it is just "I do what XXX does" ET workshop: * will have a short workshop this year, will aim for a summer-school type event next year * target group: grad students/postdocs * topics: using ET (for "externals"), GRMHD (for us to attend) * possible to hold it at SDSC (Mike Norman), but would need to find someone to organize it. This would be more visible. Will look into it and come back next week. (Eloisa will look into this) * otherwise fall back to CalTech in the week of Oct 10-14th from Tue to Thu (11-13) ET GRMHD+EOS workshop: * meet sooner than ET workshop to smooth out issues with MHD and nuclear EOS * meet for 2-3 days * hosted at Atlanta (GT), date to be agreed upon, but likely around the dates of the APS meeting (not fixed though) * please indicate preferences here (APS Apr. 30 -- May 3): http://doodle.com/ayigys5kv7zzyxna * or via the email list if these dates are no good 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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Error in compiling einsteintoolkit on Ubuntu
by Babiuc-Hamilton, Maria 07 Feb '11

07 Feb '11

I'll install another compiler. Thanks. I have another question, though. I am trying to compile einsteintoolkit on Ubuntu, with gcc-4.4 compilers and I have this error: /home/babiuc/Cactus/configs/einsteintoolkit/build/AHFinder/AHFinder_int.f:1656.3: intarea=aux 1 Error: Non-numeric character in statement label at (1) /home/babiuc/Cactus/configs/einsteintoolkit/build/AHFinder/AHFinder_int.f:1656.9: intarea=aux 1 Error: Symbol 'ntarea' at (1) has no IMPLICIT type make[3]: *** [AHFinder_int.F.o] Error 1 make[2]: *** [make.checked] Error 2 The configuration file is: CPP = cpp-4.4 FPP = cpp-4.4 CC = gcc-4.4 CXX = g++-4.4 F77 = gfortran-4.4 F90 = gfortran-4.4 MPI = OpenMPI Thanks, Maria ________________________________________ From: Erik Schnetter [schnetter(a)cct.lsu.edu] Sent: Monday, February 07, 2011 1:02 PM To: Babiuc-Hamilton, Maria Cc: users(a)einsteintoolkit.org Subject: Re: [Users] Error in compiling einsteintoolkit on Mac Maria Your error message indicates that your compiler has a problem. You could install a different version of gcc, e.g. gcc 4.5.2 either from scratch or via MacPorts, and then use this compiler, which should work (I'm using it). You can have several versions of gcc installed at the same time. -erik On Mon, Feb 7, 2011 at 12:19 PM, Babiuc-Hamilton, Maria <babiuc(a)marshall.edu> wrote: > Hello, > > I have errors in compiling einsteintoolkit.th on a mac: > First, it did not configure HDF5 > Compiling einsteintoolkit > CST error 1: > -> Configuration script for thorn HDF5 returned exit code 1 > Error message: 'Error while building HDF5. Aborting.' > > With external HDF5 directory, it complained > Use external hdf5 --error libsz.dylib needed > > With external HDF5_DIR and LIBSZ_DIR the error is: > > Preprocessing /Users/babiuc/Cactus/arrangements/Carpet/CarpetIOBasic/src/iobasic.cc > Compiling /Users/babiuc/Cactus/arrangements/Carpet/CarpetIOBasic/src/iobasic.cc > /Users/babiuc/Cactus/arrangements/Carpet/CarpetIOBasic/src/iobasic.cc: In function 'bool CarpetIOBasic::UseScientificNotation(const T&) [with T = int]': > /Users/babiuc/Cactus/arrangements/Carpet/Carpet/src/typecase:131:1: instantiated from here > /Users/babiuc/Cactus/arrangements/Carpet/CarpetIOBasic/src/iobasic.cc:701:5: internal compiler error: in tsubst_copy_and_build, at cp/pt.c:13326 > Please submit a full bug report, > with preprocessed source if appropriate. > See <http://gcc.gnu.org/bugs.html> for instructions. > make[3]: *** [iobasic.cc.o] Error 1 > make[2]: *** [make.checked] Error 2 > make[1]: *** [/Users/babiuc/Cactus/configs/einsteintoolkit/lib/libthorn_CarpetIOBasic.a] Error 2 > make: *** [einsteintoolkit] Error 2 > > please help, > Maria > > PS: I am using the new gnu compilers: > CC = gcc-mp-4.6 > CXX = g++-mp-4.6 > F77 = gfortran-mp-4.6 > F90 = gfortran-mp-4.6 > and the hdf5 is the one used by the visit2.2.0 binaries for mac x86_64: hdf5-1.8.4-x86_64 and required by CarpetHDF5. > > > _______________________________________________ > Users mailing list > Users(a)einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users > -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/

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Meeting Reminder
by Frank Loeffler 06 Feb '11

06 Feb '11

Hi, This is a reminder about our usual Monday Einstein Toolkit phone call at 10 am US central time. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/info/support/ Some points of tomorrows discussion will be: - summarize the status of the ET paper - ET workshop ideas - visualization of simulation results Frank Loeffler

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VisIt could not read from the file
by Babiuc-Hamilton, Maria 04 Feb '11

04 Feb '11

Hello, I have problems trying to visualize in visit the h5 files created with the new HDF and zlib thorns. The errors are: $ visit -debug-5 Running: gui2.2.0 -debug-5 Running: viewer2.2.0 -host 127.0.0.1 -port 5600 -debug-5 -geometry 1558x1150+362+25 -borders 24,5,5,5 -shift 5,25 -preshift 0,-1 -defer Running: mdserver2.2.0 -host 127.0.0.1 -port 5601 -debug-5 HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0: #000: H5L.c line 1184 in H5Literate(): link iteration failed major: Symbol table minor: Iteration failed #001: H5G.c line 1532 in H5G_iterate(): error iterating over links major: Symbol table minor: Iteration failed #002: H5Gobj.c line 599 in H5G_obj_iterate(): can't iterate over symbol table major: Symbol table minor: Iteration failed #003: H5Gstab.c line 506 in H5G_stab_iterate(): unable to protect symbol table heap major: Symbol table minor: Protected metadata error #004: H5HL.c line 360 in H5HL_protect(): unable to load heap major: Heap minor: Unable to load metadata into cache #005: H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed. major: Object cache minor: Unable to protect metadata #006: H5C.c line 6160 in H5C_protect(): can't load entry major: Object cache minor: Unable to load metadata into cache #007: H5C.c line 10990 in H5C_load_entry(): unable to load entry major: Object cache minor: Unable to load metadata into cache #008: H5HLcache.c line 259 in H5HL_load(): bad heap free list major: Heap minor: Unable to load metadata into cache

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contributing to ET
by Yosef Zlochower 02 Feb '11

02 Feb '11

Hi, Jeff Winicour, Maria Babiuc-Hamilton, Bela Szilagyi, and I are working on an arrangement for Cauchy-Characteristic extraction. We were thinking of releasing it as an open source tool under the Einstein toolkit and were wondering about the procedure for getting the code included and suggestions for licenses (we would like to request that users of the code cite appropriate references). This arrangement, in conjunction with existing ET software, would include all the needed tools to perform CCE. -- 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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Re: [Users] merging of chunked hdf5 data
by Roland Haas 01 Feb '11

01 Feb '11

Hello Hee Il, > All the utility codes (hdf5_merge, hdf5_extract, & hdf5_double_to_single) > could be built on ET and could do someting e.g. merging chunked data but > they don't seem to match with current Carpet HDF5 format. I couldn't open > the combined file with Visit. Did you perhaps try the following (or similar)? hdf5_merge gxx.file_0.h5 gxx.file_1.h5 gxx.h5 That will not work since hdf5_merge does not adjust the field IOProcs in the files which tells the VisIt reader how many files to look for. What works is eg. hdf5_merge restart1/gxx.file_0.h5 restart2/gxx.file_0.h5 combined/gxx.file_0.h5 Instead you can use hdf5_slicer --match '.*' --out3d-cube gxx.file_0.h5 gxx.file_1.h5 gxx.h5 from carpetiohdf5. Neither one does any merging of patches, they simply copy datasets from one file to he other. 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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merging of chunked hdf5 data
by Hee Il Kim 01 Feb '11

01 Feb '11

Hi, HDF5 in ET does not have hdf5merge.cc hdf5extract.cc, etc. Building with old CactusExternal/HDF5 might be one solution but I'd like to know a newer method, if exists. Hee Il

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error: thorn HDF5
by Babiuc-Hamilton, Maria 31 Jan '11

31 Jan '11

Hello, I am trying to compile einsteintoolkit on a new cluster (http://www.marshall.edu/cyberinfrastructure/?page_id=5) and I have this error: CST error 1: -> Thorn 'HDF5' requires the capability 'zlib'. Please add a thorn that provides 'zlib' to your ThornList or remove 'HDF5' from it ! Please let me know how can be fixed. Also, when I using GetComponents I have a warning about "no darcs in..." thank you, Maria

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Meeting minutes
by Roland Haas 31 Jan '11

31 Jan '11

Meeting minutes: Present were: Frank, Roland, Peter, Josh, Tanja, Ian, Eloisa, Bruno, Erik, Yosef ET paper: * some commits were done during the week and weekend * please check if you are assigned to a section and expect to be bugged by Frank if things are still missing by the middle of the week New thorns: * do not include the Web 2.0 thorns into the ET thorn list but do include them into a (future) master thorn list * include SystemStatistics thorn * HDF5 now depends on a new thorn ZLIB which find libz Thornlists: * have two thornlists, a Einstein Toolkit (smaller list) one and a master one (everything) ET workshop: * we agree that workshop for ET beginners (but experienced grad students/postdocs), about issues with simulations, ideas on how to improve the toolkit is a good idea * have to decide where/when to hold it * check if we can get some funding from NSF * will come up with ideas for contents/location/participants during the week and discuss in the next meeting Visualization: * collect current practices of the groups in wiki https://docs.einsteintoolkit.org/et-docs/Visualization_of_simulation_results * visualization was part of the original proposal so we will have to think about it * include a simfactory "get" command to copy user specified data from a cluster Multipole: * please have a look at Erik's proposed patch New thorn submission policy (recap): * post intention on user mailing list and ask for discussion * if there is no discussion we will discuss the proposed thorn in the next meeting * we prefer full documentation and test suites but if the thorn was used in a publication we are willing to accept this as a "quality" measure instead 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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