35521dd | Eh Tan | 05 December 2006, 05:04:14 UTC | Removed sections about HDFView. HDFView by default displays the dataset in a 2D table, which can be very confusing when working on multidimensional dataset. "h5ls -r" is a better tool for discovering the group structure and dataset dimension. | 05 December 2006, 05:04:14 UTC |
e8a02da | Eh Tan | 05 December 2006, 04:19:42 UTC | * Renamed estimate.py to estimate_size.py * Added license text * Update for new HDF5 layout | 05 December 2006, 04:19:42 UTC |
318477c | Luis Armendariz | 05 December 2006, 00:46:40 UTC | Changed code in A.1.1 and A.1.2 to use small font with typewriter style. | 05 December 2006, 00:46:40 UTC |
ee84bec | Eh Tan | 05 December 2006, 00:40:12 UTC | Mentioned change of naming scheme for capfiles in NEWS | 05 December 2006, 00:40:12 UTC |
ad9f299 | Sue Kientz | 05 December 2006, 00:31:25 UTC | fixed quotes; added degree symbols as requested | 05 December 2006, 00:31:25 UTC |
0c3e62b | Eh Tan | 05 December 2006, 00:14:58 UTC | Finished the GMT script section | 05 December 2006, 00:14:58 UTC |
c4f1afa | Eh Tan | 04 December 2006, 23:47:57 UTC | Renamed "center" to "starting point" | 04 December 2006, 23:47:57 UTC |
90487f5 | Sue Kientz | 04 December 2006, 22:42:59 UTC | minor sentence/word form changes in 5.1 and 5.2 | 04 December 2006, 22:42:59 UTC |
b3365ac | Sue Kientz | 04 December 2006, 22:33:47 UTC | reformatted column names in c.4.9 | 04 December 2006, 22:33:47 UTC |
f4f3bca | Eh Tan | 04 December 2006, 22:19:15 UTC | Revised Chapter 5 and Appendix A * Minor revision of post-processing * Update OpenDX section for new HDF5 layout * Briefly mentioned GMT scripts (unfinished) * Described new viscosity laws * Using Greek letter eta in the viscosity equations | 04 December 2006, 22:19:15 UTC |
2457cf3 | Sue Kientz | 04 December 2006, 20:33:20 UTC | fixed more quotes, fixed table breaks, lines in table missing, other minor format problems | 04 December 2006, 20:33:20 UTC |
1daa462 | Luis Armendariz | 04 December 2006, 19:48:19 UTC | Added OpenHDF5 and OpenVTK actions for mayavi2 | 04 December 2006, 19:48:19 UTC |
a7c9af3 | Luis Armendariz | 04 December 2006, 17:24:39 UTC | Fixes to manual | 04 December 2006, 17:24:39 UTC |
d0d65c0 | Luis Armendariz | 04 December 2006, 17:24:24 UTC | Fixed typos | 04 December 2006, 17:24:24 UTC |
192f787 | Luis Armendariz | 04 December 2006, 16:54:12 UTC | Added vim modeline | 04 December 2006, 16:54:12 UTC |
02556dd | Luis Armendariz | 04 December 2006, 14:21:20 UTC | Mayavi2 UI customizations | 04 December 2006, 14:21:20 UTC |
7fcb642 | Luis Armendariz | 04 December 2006, 14:11:12 UTC | Added python module namespace for the citcoms mayavi2 plugins | 04 December 2006, 14:11:12 UTC |
586ea34 | Luis Armendariz | 04 December 2006, 13:43:01 UTC | Removed executable permissions | 04 December 2006, 13:43:01 UTC |
33b38bf | Eh Tan | 02 December 2006, 07:41:50 UTC | Update for new HDF5 layout | 02 December 2006, 07:41:50 UTC |
a822c42 | Eh Tan | 02 December 2006, 07:14:16 UTC | * Removed obsolete parameters * Added new parameters * Only one "parameter=value" per line | 02 December 2006, 07:14:16 UTC |
59540cb | Eh Tan | 02 December 2006, 06:04:50 UTC | Updated for new HDF5 layout | 02 December 2006, 06:04:50 UTC |
409e719 | Eh Tan | 02 December 2006, 06:04:05 UTC | Minor tweaks | 02 December 2006, 06:04:05 UTC |
737d6d7 | Eh Tan | 02 December 2006, 04:43:50 UTC | Moved utility functions to h5util.c | 02 December 2006, 04:43:50 UTC |
c9f5f73 | Eh Tan | 02 December 2006, 04:15:26 UTC | Fixed a bug of counting argc | 02 December 2006, 04:15:26 UTC |
95de6c6 | Eh Tan | 02 December 2006, 00:57:22 UTC | Added more rheology options, which is required for benchmarks rheol=1: visc = visc0 * exp(viscE * (viscT - T)) rheol=2: visc = visc0 * exp(-T / viscT) | 02 December 2006, 00:57:22 UTC |
9dc129b | Eh Tan | 02 December 2006, 00:38:50 UTC | Updated h5tocap.py for new layout of HDF5 files | 02 December 2006, 00:38:50 UTC |
d5da530 | Eh Tan | 02 December 2006, 00:03:01 UTC | Added a program to convert h5 file to velo files for restart | 02 December 2006, 00:03:01 UTC |
6d40d87 | Sue Kientz | 01 December 2006, 23:34:49 UTC | removed todo at 4.5.1, no issue there | 01 December 2006, 23:34:49 UTC |
6f8787c | Leif Strand | 01 December 2006, 22:00:25 UTC | Fix for infinite regress when builddir == srcdir. !@#$%* The .pth/sitedir/sys.path/PYTHONPATH aspect of eggs is really irritating. I hope setuptools becomes a part of the standard Python distro, as the Python core developers are likely to accept it uncritically and unmodified (as they are wont to do, apparently -- judging by all the other crap that is in the standard library). God willing, this will further accelerate the death of the language. | 01 December 2006, 22:00:25 UTC |
a348cee | Eh Tan | 01 December 2006, 21:56:58 UTC | Added samples of HDF5 output | 01 December 2006, 21:56:58 UTC |
99f6b02 | Leif Strand | 01 December 2006, 21:33:03 UTC | builddir != srcdir works again. The use of setup.py/distutils/setuptools forces the creation of files in srcdir. This bugs me. | 01 December 2006, 21:33:03 UTC |
72eaebe | Leif Strand | 01 December 2006, 04:40:37 UTC | The "make install" command now works again. | 01 December 2006, 04:40:37 UTC |
4602470 | Sue Kientz | 30 November 2006, 23:38:30 UTC | fixed sentence in A.1.2 last row | 30 November 2006, 23:38:30 UTC |
e83fdc3 | Eh Tan | 30 November 2006, 23:08:42 UTC | Updated Chapter 6 * sync'd the manual with the cookbook scripts * improving the resolution of cookbook5.2.eps is left until the next release Also, fixed table borders in Appendix A. | 30 November 2006, 23:08:42 UTC |
68ecca0 | Eh Tan | 30 November 2006, 22:55:21 UTC | Moved path name of restart file to "datadir_old" | 30 November 2006, 22:55:21 UTC |
7b4029c | Eh Tan | 30 November 2006, 22:53:31 UTC | Fixed issue63, Change "monitoringfrequency" comment in citcoms cookbooks | 30 November 2006, 22:53:31 UTC |
bfd0022 | Luis Armendariz | 30 November 2006, 22:21:14 UTC | Done with Chapter 4 references. | 30 November 2006, 22:21:14 UTC |
91e3d58 | Eh Tan | 30 November 2006, 21:16:44 UTC | The concept of caps is explained in section 1.7 | 30 November 2006, 21:16:44 UTC |
31ea96a | Luis Armendariz | 30 November 2006, 21:10:38 UTC | Removing obsolete program h5steps.c | 30 November 2006, 21:10:38 UTC |
1b23e41 | Eh Tan | 30 November 2006, 20:57:36 UTC | Updated Appendices | 30 November 2006, 20:57:36 UTC |
bbe34e1 | Eh Tan | 30 November 2006, 20:26:51 UTC | Updated section 3.6.1 | 30 November 2006, 20:26:51 UTC |
63b4155 | Leif Strand | 28 November 2006, 23:28:36 UTC | Fixed some bugs, some of which were introduced during the C -> C++ transition. Using a pidXXXX.cfg file as input should "work" now, although it still doesn't reproduce the original simulation, since at least one parameter is missing ('steps'). I maintain that dumping the configuration is really the job of the framework (Pyre). Unfortunately, Pyre's current capabilities in this area are buggy in the case of '.pml' files, and non-existent in the case of '.cfg' files. Note: 'nproc_surf' is now a real inventory item, instead of a fake one. It looks like it doesn't belong in the inventory at all, though. (I left it there to avoid breakage.) | 28 November 2006, 23:28:36 UTC |
08658cd | Leif Strand | 28 November 2006, 21:08:18 UTC | Checked-in a virus, a worm, a Trojan horse, and some other malware. LyX doesn't support copy & paste between applications, so this check-in may have introduced some bugs as well. | 28 November 2006, 21:08:18 UTC |
b1196e7 | Sue Kientz | 28 November 2006, 19:26:20 UTC | various edits to 3.6.1 and 3.7 | 28 November 2006, 19:26:20 UTC |
e195f6d | Leif Strand | 28 November 2006, 07:33:41 UTC | Rewrote expand_str() in order to: 1) avoid potential buffer overflow; 2) avoid the use of non-standard strndup(); 3) avoid the use of the heap altogether. (Prompted by unresolved strndup on Mac OS X.) | 28 November 2006, 07:33:41 UTC |
6da3152 | Eh Tan | 28 November 2006, 05:00:42 UTC | Clarified the comment | 28 November 2006, 05:00:42 UTC |
408a073 | Eh Tan | 28 November 2006, 04:42:18 UTC | Updated for new features | 28 November 2006, 04:42:18 UTC |
172b656 | Eh Tan | 28 November 2006, 04:41:56 UTC | Added a reference to NEWS | 28 November 2006, 04:41:56 UTC |
573d06e | Eh Tan | 28 November 2006, 03:34:23 UTC | Chapter 3 updated | 28 November 2006, 03:34:23 UTC |
80c8616 | Leif Strand | 28 November 2006, 03:01:37 UTC | Changes related to Pythia v0.8.1.0b7, which CitcomS now requires: 'journal' is no longer a part of an application's inventory, and pyre.applications.start() is now responsible for calling run(). | 28 November 2006, 03:01:37 UTC |
f503267 | Eh Tan | 28 November 2006, 02:57:07 UTC | Updated the dimensional const | 28 November 2006, 02:57:07 UTC |
2d35142 | Eh Tan | 28 November 2006, 02:55:44 UTC | Updated to be consistent with the manual | 28 November 2006, 02:55:44 UTC |
61249ec | Eh Tan | 27 November 2006, 23:09:42 UTC | Changed the default value of "datadir" to "." | 27 November 2006, 23:09:42 UTC |
944d4da | Eh Tan | 27 November 2006, 22:37:27 UTC | Changed postprocessing scripts for the new "datadir" parameter | 27 November 2006, 22:37:27 UTC |
510c2e5 | Eh Tan | 27 November 2006, 21:27:15 UTC | Fix for POSIX-compliant arithmetic expression The "sh" shell on my Ubuntu 6.10 doesn't have the "let" command. That's how I found that "let" is not in the POSIX standard. Use "$((expression))" instead. | 27 November 2006, 21:27:15 UTC |
baf9708 | Eh Tan | 27 November 2006, 20:05:42 UTC | Added extern program to determine "datadir" | 27 November 2006, 20:05:42 UTC |
2cd498c | Eh Tan | 27 November 2006, 20:05:11 UTC | Changes how to specify output directory * "output_format" must be either "ascii" (the default) or "hdf5", the "ascii-local" option is gone * "datafile" becomes the prefix of the filename and cannot contain "/" * "datadir" becomes mandatory input parameters * If "datadir" is "%DATADIR", the output directory is determined by an external program "citcoms_datadir" * Special substrings "%RANK", "%HOSTNAME" in datadir will be substituted by mpi rank, machine's hostname, $DATADIR environment variable, respectively. * These special strings start with "%", rather than "$", becuase it's very difficult to input "$" from the command line. | 27 November 2006, 20:05:11 UTC |
eaffb18 | Eh Tan | 22 November 2006, 21:26:09 UTC | Changed the convergence criterion of Stokes solver: * stop iterations if delta(v) or delta(p) becomes too small (i.e., v or p has converged) * this is suggested by Shijie Zhong | 22 November 2006, 21:26:09 UTC |
26f0c05 | Eh Tan | 22 November 2006, 21:25:47 UTC | Ignoring overlapping nodes when counting # of global nodes | 22 November 2006, 21:25:47 UTC |
5c19bff | Sue Kientz | 22 November 2006, 20:25:40 UTC | typo; made references into an itemized list | 22 November 2006, 20:25:40 UTC |
32fc3c9 | Eh Tan | 22 November 2006, 20:05:23 UTC | Removed unused codes and files | 22 November 2006, 20:05:23 UTC |
2d8467a | Eh Tan | 22 November 2006, 19:41:43 UTC | Refactored geoid calculation | 22 November 2006, 19:41:43 UTC |
8463943 | Luis Armendariz | 21 November 2006, 23:03:38 UTC | Expanded section on optimizing parallel I/O. | 21 November 2006, 23:03:38 UTC |
91c9c75 | Eh Tan | 21 November 2006, 20:18:02 UTC | Added scripts for 2D temperature plots, using GMT commands | 21 November 2006, 20:18:02 UTC |
201713b | Eh Tan | 20 November 2006, 19:24:40 UTC | Forgot to declare function prototype | 20 November 2006, 19:24:40 UTC |
401efaa | Eh Tan | 18 November 2006, 05:17:07 UTC | Disabled a debugging output, which is not protected by a "if(E->control.verbose)" and caused Segmentation Fault. | 18 November 2006, 05:17:07 UTC |
1433785 | Leif Strand | 18 November 2006, 01:29:12 UTC | The function loadObject() has been moved from Pythia to Merlin. | 18 November 2006, 01:29:12 UTC |
7d6ea27 | Eh Tan | 18 November 2006, 00:48:49 UTC | Updated the vbc files and input file | 18 November 2006, 00:48:49 UTC |
a4596a5 | Eh Tan | 18 November 2006, 00:41:52 UTC | Updated the vbc files and input file. | 18 November 2006, 00:41:52 UTC |
63a29c8 | Eh Tan | 18 November 2006, 00:20:26 UTC | HDF5 output for geoid is working | 18 November 2006, 00:20:26 UTC |
4b8c00e | Luis Armendariz | 17 November 2006, 22:37:12 UTC | Cleaned up 'svn status' by updating svn:ignore property | 17 November 2006, 22:37:12 UTC |
1d9227a | Eh Tan | 17 November 2006, 20:25:45 UTC | HDF5 output of surf, botm, horiz_avg are working now. * Time and timestep infomation is written as scalar attributes "time" and "timestep" in / group. * Set MPI_Info according to input parameters "cb_block_size" and "cb_buffer_size" * I decided not to write surf, botm, and horiz_avg coordinates. This coordinate can be retrieved from the 3D coordinate very easily by this pseudo-code: surf_coord = coord[cap=all, x=all, y=all, z=1] z_coord = coord[cap=1, x=1, y=1, z=all] Remainging works: geoid for hdf5, update the manual | 17 November 2006, 20:25:45 UTC |
c947d7a | Eh Tan | 17 November 2006, 06:26:37 UTC | HDF5 output reloaded. See issue4 for reasoning. Most data outputs are working. Remaining works: * How to deal with time output? (Maybe not output at all? Time info is always written in the .time file anyway.) * Where to put 2d and 1d coordinate output? (Maybe output with the data? These datasets are small and won't take too much space anyway.) * Geoid output | 17 November 2006, 06:26:37 UTC |
30bb98f | Leif Strand | 17 November 2006, 05:34:42 UTC | Fixed a minor bug in Output.py. | 17 November 2006, 05:34:42 UTC |
7da74a3 | Leif Strand | 17 November 2006, 02:24:51 UTC | Revised everything having to do with runtime configuration: launcher.xxx, scheduler.xxx, and job.xxx. Lowered the prominence/importance given to .pml files... and resisted my temptation to delete all reference to them :-) (I think I'm pretty much done with the v2.1 manual at this point. Reading the manual makes me tired, because it reminds me of how much work remains to be done on the code itself. Ease-of-use could be substantially improved...) | 17 November 2006, 02:24:51 UTC |
86701e5 | Leif Strand | 16 November 2006, 21:58:42 UTC | Reverted another recent decision of mine: Always build the legacy drivers, 'CitcomSFull' and 'CitcomSRegional'. I took these out of the Pyre build to avoid confusion; but now -- thinking of shared installations of CitcomS on clusters -- I think they should always be built (as they were before) so that users have the option. | 16 November 2006, 21:58:42 UTC |
6d6764b | Leif Strand | 16 November 2006, 21:36:50 UTC | Install examples under PREFIX/share/CitcomS/examples, as now documented in the manual. This is for the benefit of users of shared installations of CitcomS. I also sync'd the file list in examples/Makefile.am. Note: the file velbc_regional.tar.gz seems to be corrupt!!! | 16 November 2006, 21:36:50 UTC |
d5b200b | Leif Strand | 16 November 2006, 21:25:54 UTC | Corrections with respect to r5302: the binaries/scripts are now once again built under the 'bin' subdirectory. Also reviewed all references to PREFIX. | 16 November 2006, 21:25:54 UTC |
a1e12dc | Leif Strand | 16 November 2006, 14:40:41 UTC | Re-created 'bin' subdirectory to avoid filename conflict on case-sensitive filesystems (Mac, Windows): "CitcomS" == "citcoms". Fixed egg-related bugs which prevented 'configure' from succeeding when buildir != srcdir (another BuildBot test vector). Call addsitedir() in the 'citcoms' script. I guess this is now necessary since "site.py" is no longer in the same directory as "citcoms". (*) Note that there is currently a bug in Merlin which prevents 'citcoms' from running ("No module named pkg_resources"). The work-around is to manually add the merlin egg to the merlin-install.pth file. There are more bugs which prevent running on Mac OS X at all (still investigating). (*) I'm becoming annoyed with setuptools' use of .pth files as a sys.path/PYTHONPATH persistence mechanism, mainly because of the accompanying hacks which are used to turn ordinary directories into "site" directories (i.e., directories where .pth files work) -- these ugly, confusing hacks include the fake site.py, "virtual python", etc. I think Merlin will only use .pth files in real site directories. It will use clear, straitforward, direct sys.path manipulation everywhere else. | 16 November 2006, 14:40:41 UTC |
2642094 | Eh Tan | 16 November 2006, 03:04:21 UTC | Forgot to commit module/ directory | 16 November 2006, 03:04:21 UTC |
6602642 | Eh Tan | 16 November 2006, 03:01:59 UTC | Declared function prototype at the top | 16 November 2006, 03:01:59 UTC |
3cfe216 | Eh Tan | 16 November 2006, 02:07:09 UTC | Forgot to commit python files | 16 November 2006, 02:07:09 UTC |
785021d | Eh Tan | 16 November 2006, 02:07:00 UTC | Declared function prototype at the top | 16 November 2006, 02:07:00 UTC |
1bd5e68 | Eh Tan | 16 November 2006, 01:52:25 UTC | Implemented geoid calculation, see issue64. User visible changes include: * "output_optional" can include string "geoid", which will enable geoid output * new input parameters: radius, density_above, density_below * removed input parameters: layerd, wdensity, llmax, nlong, nlati * moved input parameter "output_ll_max" from Sphere.py to Output.py * sync'd the defalut values of input parameters in Const.py and Instructions.c TODO: h5output_geoid() not finished | 16 November 2006, 01:52:25 UTC |
4aa72aa | Leif Strand | 15 November 2006, 22:01:35 UTC | Elaborated a bit on .egg download, and clarified that CitcomS needs Pythia v0.8.1.x (instead of 0.8). | 15 November 2006, 22:01:35 UTC |
f245f79 | Leif Strand | 15 November 2006, 21:18:52 UTC | Re-read the stuff I worked on yesterday, making minor corrections: "is in your PATH" -> "is on your PATH", inserted the word "Section" before section references, other minor changes. | 15 November 2006, 21:18:52 UTC |
465cdc7 | Sue Kientz | 15 November 2006, 20:40:13 UTC | a few typos fixed, http removed from htmlurl tags (not needed and lengthen name in line); pdf regen | 15 November 2006, 20:40:13 UTC |
0693207 | Leif Strand | 15 November 2006, 02:06:20 UTC | Corrections to the section, "Changing Parameters". | 15 November 2006, 02:06:20 UTC |
901d882 | Leif Strand | 15 November 2006, 01:14:49 UTC | Updated the installation chapter. | 15 November 2006, 01:14:49 UTC |
80a98d3 | Leif Strand | 14 November 2006, 03:25:28 UTC | Pythia v0.8.1.0b4: Fixed bugs relating to MPI launching: Fix sys.path/PYTHONPATH automatically; don't touch 'argv' until after MPI_Init(). Next, I may try to slurp 'pycitcoms.c' into the framework... it contains a lot of implementation details which have everything to do with Pyre and nothing to do with CitcomS. | 14 November 2006, 03:25:28 UTC |
4bd3a75 | Leif Strand | 11 November 2006, 03:34:08 UTC | Use the new merlin (the setuptools clone). Download Python dependencies automatically during 'configure' (This doesn't work for "make install" yet.) The Dynamo BuildBot might even succeed after this check-in... fingers crossed... | 11 November 2006, 03:34:08 UTC |
79e53b1 | Sue Kientz | 10 November 2006, 19:20:56 UTC | created formulas for sec a.1.11 | 10 November 2006, 19:20:56 UTC |
8cac7ae | Sue Kientz | 10 November 2006, 18:54:31 UTC | cookbook 6 graphic edited, various small tweaks | 10 November 2006, 18:54:31 UTC |
fdd2455 | Sue Kientz | 10 November 2006, 01:59:45 UTC | finished various typos and fixes after checking with Luis on questions | 10 November 2006, 01:59:45 UTC |
897706c | Sue Kientz | 09 November 2006, 19:37:41 UTC | various typos and fixes | 09 November 2006, 19:37:41 UTC |
967ea83 | Eh Tan | 07 November 2006, 19:33:31 UTC | * Fixed a few typos * Added "TODO" in front of all unfinished text. | 07 November 2006, 19:33:31 UTC |
f89ab8a | Leif Strand | 07 November 2006, 02:30:04 UTC | Moved CitcomS HDF5 macros to cs/autoconf. | 07 November 2006, 02:30:04 UTC |
02fbe2f | Leif Strand | 07 November 2006, 01:33:06 UTC | Took a step backwards so that I can take a more conservative approach to build/install. Also, temporarily deleted 'Exchanger' and all references to it, to avoid confusion. We can always go back in time and retrieve it later. | 07 November 2006, 01:33:06 UTC |
c20d5e5 | Sue Kientz | 07 November 2006, 00:49:42 UTC | pdf generated | 07 November 2006, 00:49:42 UTC |
bd49eb5 | Sue Kientz | 07 November 2006, 00:49:04 UTC | gurnis edits, new pdf | 07 November 2006, 00:49:04 UTC |