- itaps-parallel - mailman3.cels.anl.gov

itaps mailing lists
by Lori A. Diachin 12 Nov '08

12 Nov '08

You should have received an email indicating that you have been added to two new mailing lists: - itaps-announce(a)lists.llnl.gov - itaps-user(a)lists.llnl.gov Here is the current list of subscribers for both lists: diachin2(a)llnl.gov isenburg1(a)llnl.gov miller86(a)llnl.gov tautges(a)mcs.anl.gov kraftche(a)cae.wisc.edu shephard(a)scorec.rpi.edu osahni(a)scorec.rpi.edu kjansen(a)scorec.rpi.edu txie(a)scorec.rpi.edu kddevin(a)sandia.gov vjleung(a)sandia.gov linli(a)ams.sunysb.edu rykauf(a)gmail.com khamaysehak(a)ornl.gov dealmeidav(a)ornl.gov het(a)pnl.gov If there is someone I obviously missed, my apologies - just send me a note and I'll add you to the list. If you would prefer not to be on this list, let me know that as well. Lori

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[Fwd: Speakers & hands on for SC08 tutorial]
by Lori A. Diachin 12 Nov '08

12 Nov '08

Here is the timeline for the tutorial on Sunday. SC08 Tutorial Morning Session (3.5 hours); starting at 8:30 Introduction, 30 minutes, Lori Overview of ITAPS services, 45 minutes, Mark Break 10 min Data Model, 45 minutes, Lori Basic Interface, 30 minutes, Tim Break (optional) 10 minutes Hands on, morning session, 40-50 minutes - Set up/test user environments - Hello iMesh and iMeshP (Karen) Afternoon Session (3.5 hrs) Advanced Interfaces, 25 minutes, Tim Parallel Interfaces, 30 minutes, Karen Software, 30 minutes, Lori and Karen Break 10 minutes Case Studies, 40 minutes, Mark and Tim Conclusions, 5 minutes, Lori Afternoon Hands On - 1 hr, 10 minutes, break as needed - Zoltan through iMeshP (Vitus) - Frontier (Ryan) - Smooth (Lori) - Adaptivity to a pre-defined mesh size field w/ Zoltan (Onkar)

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Notes from tutorial exercises
by Lori A. Diachin 12 Nov '08

12 Nov '08

Hi Vitus and all, I went through both tutorials this morning and overall think they're quite nice. I like that you provide the basics here in the second exercise - it's a very nice bridge between Hello and Smooth. I have a few minor notes (below). As a general comment to everyone - do we have any tutorial exercises that aren't in C++? I've gone through Hello, Load Balance and Smooth so far and I'm worried we'll give folks the wrong impression.. I see a .c file in the Hello directory -- would it be hard to add a fortran hello example? Lori Tutorial 1: Exercise 2: It's not clear to me where the MPI communicator is initialized in the test file? I assume it's COMM_WORLD, but you refer to 'initialized above' and I don't see it. I assume it's in the Init function, but it might be helpful to make it more explicit Exercise 3: Remind users how to get a string length; not all users will be c++ savy. In general it's not always clear to me why I'm doing something, getting the parts, getting various handles, etc - is it needed for Zoltan? If you can, it would be useful to add a sentence to the beginning of each exercise giving a bit of motivation for why I need to call this function. It will help folks think through it themselves later.. Tutorial 2: Might prefer to have different test file names in tutorial 1 and tutorial 2.... Actually, rather than switching files/directories, you could keep them all part of a single tutorial and just use the #define trick that Karen used in Hello. Is .vtu a vtk format? I'm not familiar with it and was surprised to see .vtu's... you might want to comment on what to expect in the notes for Exercise 1 ~

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Name mangling in MOAB
by Tim Tautges 12 Nov '08

12 Nov '08

Hi all, See http://trac.mcs.anl.gov/projects/ITAPS/browser/MOAB/trunk/configure.in, lines 31-33. If the script finds a fortran compiler, it runs that macro. That generates definitions for FC_FUNC and FC_FUNC_. Then, at line 869 in configure.in, AC_CONFIG_HEADERS is called to produce MBCN_FCDefs.h, which contains substituted definitions for FC_FUNC and FC_FUNC_. Those macros are used in iMesh_protos.h (http://trac.mcs.anl.gov/projects/ITAPS/browser/MOAB/trunk/tools/iMesh/iMesh…) to mangle the imesh function names. If you're doing this in FMDB, it's probably easier to eliminate going through MBCN_FCDefs.h or equivalent and call AC_CONFIG_HEADERS directly on iMesh.h, though you'll have to make a iMesh.h.in file for that to work properly. Any questions, let me know. - tim -- ================================================================ "You will keep in perfect peace him whose mind is steadfast, because he trusts in you." Isaiah 26:3 Tim Tautges Argonne National Laboratory (tautges(a)mcs.anl.gov) (telecommuting from UW-Madison) phone: (608) 263-8485 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706

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Pitch for folks to add Position Independent Code (PIC) by default
by Mark Miller 12 Nov '08

12 Nov '08

Hi All, I would like ask in the near future if folks wouldn't mind adding a feature to their Make/Configure/Build/Whatever to turn ON position independent code (PIC) by default. Some codes already have a --with-pic configure option and that is helpful. Other's don't have that option at all. But, as it turns out, most (if not all) the lib<whatever>.a files in /usr/local/itaps are not compiled with -fPIC. That means you cannot build a shared library linking against them and pretty much means I have to re-build everything there in order to link VisIt with those libs. So, I am making a pitch that a) folks add support for position independent code and b) that it gets turned ON by default. That way, whenever someone installs a lib, we'll be assured of getting a lib we can build shared libraries against. An alternative is to build shared libraries in addition to static. However, I believe that may be harder for folks as PIC is just an additional flag to compiler. This is NOT a tutorial-pressing need. It is just something I'd like to see if we can make start happening in Make/Configure/Build tools for our various pieces of software. Mark -- Mark C. Miller, Lawrence Livermore National Laboratory email: mailto:[email protected] (M/T/W) (925)-423-5901 (!!LLNL BUSINESS ONLY!!) (Th/F) (530)-753-8511 (!!LLNL BUSINESS ONLY!!)

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ITAPS Post-Tutorial Email Hotline
by Mark Miller 12 Nov '08

12 Nov '08

Hi All, Just to elaborate on my suggestion... You can offer tarballs on the web site for people to download with the caveat that the build process is not for the faint at heart. But, that ITAPS team 'promises' to respond within 1-2 hours to all emails sent to <blah-blah>@itaps-users.mcs.anl.gov (whatever) between Nov 17 and Dec 15 during normal business hours (8-12,1-5 PST) M-F. We can split up the next 4 weeks into 4 hour time slots (this is what we do on VisIt), that each of us can agree to take. Email that arrives OUT OF BAND gets dumped into the next slot's reponsibility (e.g. monday morning person handles everything that came in over the weekend). Between all of us, we can probably wind up having each person to have to handle only one or two time slots. Mark -- Mark C. Miller, Lawrence Livermore National Laboratory email: mailto:[email protected] (M/T/W) (925)-423-5901 (!!LLNL BUSINESS ONLY!!) (Th/F) (530)-753-8511 (!!LLNL BUSINESS ONLY!!)

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Tutorial Exercises Directory
by Lori A. Diachin 12 Nov '08

12 Nov '08

Hi All, I created a first pass of the Tutorial_Exercises directory in /usr/local/itaps on the mesh machine. I give a recommended order of performing the exercises and a brief description of each in the README. Please take a quick look, and if there are any issues we can correct them during the telecon. Tim, I'd like to add the Examples directory you're working on to this as well. We should talk about the best way to do that... can you create a HandsOn_Session.txt file to walk folks through what's in the directory, how to use it, and what libraries to link to? Finally - during the telecon, I'd like to revisit the notion of providing directions for folks to download and build an iMesh implementation on their own machine as part of the HandsOn directory. Will this be possible to achieve? Karen - you and I probably need to spend a few minutes on the phone this afternoon (or soon) to update the web pages with the new documentation for iMeshP. Also, were the issues with the iMesh doxy file resolved? BTW - I think I fixed the problem with the menuing system on the web itaps web pages (turns out internet explorer is pretty fragile when it comes to using stylesheets). If you still have problems with it, let me know. Lori

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[Fwd: [Fwd: [Fwd: Reminder - phone teleconference tomorrow]]]
by Lori A. Diachin 12 Nov '08

12 Nov '08

Reminder - telecon happening now... -------- Original Message -------- Subject: itaps-parallel [Fwd: [Fwd: Reminder - phone teleconference tomorrow]] Date: Tue, 11 Nov 2008 14:41:09 -0800 From: Lori A. Diachin <diachin2(a)llnl.gov> To: itaps-parallel(a)mcs.anl.gov <itaps-parallel(a)mcs.anl.gov> Hi All, A quick reminder that we have a telecon tomorrow (Wednesday, Nov 12) to discuss the status of the hands-on exercises for the SC08 tutorial along with any issues regarding the iMesh and iMeshP interfaces. It's scheduled for 11 am pacific. This will probably be close to our last chance to chat before the tutorial, so please be prepared with any issues that you feel need to be discussed. The LLNL telecon number is 866-914-3976 and the passcode is 662912# Lori

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FindConnect example ready
by Tim Tautges 12 Nov '08

12 Nov '08

Hi all, I've added ~tautges/ITAPS/SVN/Examples/IMESH/FindConnect to the examples on the mesh machine; this example shows how to use dynamically-allocated arrays in Fortran. Note the extra options passed to configure (see top of config.log) for specifying pointer size and cray pointer options to gfortran. I've added a note in the README file about that. Eventually, we'll get this fixed so the configure script figures that out. - tim -- ================================================================ "You will keep in perfect peace him whose mind is steadfast, because he trusts in you." Isaiah 26:3 Tim Tautges Argonne National Laboratory (tautges(a)mcs.anl.gov) (telecommuting from UW-Madison) phone: (608) 263-8485 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706

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Examples on mesh machine
by Tim Tautges 12 Nov '08

12 Nov '08

Hi all, I've put the HelloMesh on the mesh machine, in ~tautges/ITAPS/SVN/Examples and below. You should be able to copy that whole directory. See the README for instructions on how to build. Karen, the example there doesn't have any arrays, so it might not be sufficient for building your hello imeshp; I'll work on a more advanced example next. I haven't tried building with other implementations yet (besides MOAB), will try that next. Note, however, this test does depend on having iMesh-Defs.inc, so if it's not there yet, it won't work. - tim -- ================================================================ "You will keep in perfect peace him whose mind is steadfast, because he trusts in you." Isaiah 26:3 Tim Tautges Argonne National Laboratory (tautges(a)mcs.anl.gov) (telecommuting from UW-Madison) phone: (608) 263-8485 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706

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