assign boundary conditions when using periodic boundary conditions.
1 lines of code changed in 1 file:
Update LLNL path.
0 lines of code changed in 2 files:
Updating the job templates for Moab.
93 lines of code changed in 7 files:
Allocate patch boundary conditions on all patches for now.
This is hopefully a temperary patch that will aide in debugging another problem dealing with particles.
7 lines of code changed in 4 files:
Replaced the fort_prescoef routine with C++ equivalent.
This should not change the answers
27 lines of code changed in 5 files:
turn off Godunov sonic approximation in the face centered velocities
1 lines of code changed in 1 file:
throw an exception if the mpm section is missing from the amr section
6 lines of code changed in 1 file:
Don't push pdTdt through the heat conduction machinery anymore, just
increment the particle temperature directly.
14 lines of code changed in 3 files:
This update allows the Problem Spec Reader to find the .ups xml spec
file based on the location of the src tree. (Previously, it looked in
the current directory and thus only succeeded if you had 'inputs/'
there.) Now it will work no matter where you run from.
IMPORTANT NOTE:
To make this work, I had to call "create_sci_environment(...);"
at the beginning of sus. This should just work... but it is
possible that it will cause problems on some machines. Note,
create_sci_environment() will attempt to access a .scirunrc file,
which you can use to set environment variables that you want seen
in sus. This (assuming it really works) could mean that you don't
have to pass env vars via -X (or somesuch) in mpirun calls.
M Core/Util/Environment.cc
- Warn user if create_sci_environment() has NOT been called before
doing a sci_getenv().
- endl's are evil. :p ;) :)
- Indent.
M Packages/Uintah/CCA/Components/ProblemSpecification/ProblemSpecReader.cc
- Look for the ups_spec.xml file based on absolute path.
M Packages/Uintah/StandAlone/sus.cc
- Always call create_sci_environment(). (This shouldn't break
anything...but please verify before using in batch systems for big
runs.)
36 lines of code changed in 3 files:
This version is readable.
0 lines of code changed in 2 files:
Change the modifies to requires, etc, for gdTdt. It isn't really
modified, just used. This shouldn't change any answers.
7 lines of code changed in 1 file:
M uda2nrrd/handleVariable.cc
Print out the patch's index with respect to the level it is on.
(Display every 10th or 100th depending on number of patches.)
M uda2nrrd/uda2nrrd.cc
Fix usage text to be a little cleaner. Better error if '-v' not
specified.
38 lines of code changed in 2 files:
Fix problem with running pscp2 using a relative path.
14 lines of code changed in 1 file:
added bulletproofing.
Hypre pressure solver only works when there is an even number of cells on a patch.
Catch this and warn the user.
10 lines of code changed in 1 file:
pruned the #includes
formatting
56 lines of code changed in 2 files:
hyperSolver.cc & petsc solver.cc
problemSetup()
- added bulletproofing. Only supported solver/preconditioner are valid
options
All ups files:
- inside the <PressureSolver> section the xml tags have been changed.
<LinearSolver> -> <parameters>
<ksptype>cg</ksptype> -> <solver> cg </solver>
<pctype>jacobi</pctype> -> <preconditioner>jacobi</preconditioner>
</LinearSolver> -> </parameters>
134 lines of code changed in 5 files:
Merge of 41976
0 lines of code changed in 10 files:
Few more sub.mk cleanups (OSX).
70 lines of code changed in 2 files:
Added 'move light to eye' button.
31 lines of code changed in 3 files:
Needs THREAD_LIBRARY.
0 lines of code changed in 2 files:
Few more sub.mk file fixes (atlas).
29 lines of code changed in 2 files:
Better/more verbose error/info messages.
6 lines of code changed in 2 files:
Clean up compiler warning, catch bug (if it were to happen) sooner.
1 lines of code changed in 1 file:
Cleanup a few more sub.mk files.
39 lines of code changed in 5 files:
M configure.ac
M configure
M aclocal.m4
M configVars.mk.in
Clean up configure so that variables placed into configVars.mk only
specify the libraries for that variable (and not required libraries).
This helps clean up the configVars.mk file (makes it easier to see
specifically the libraries listed for a specific variable, and cleans
up the compile lines as libraries are not listed multiple times. This
was the way the system was supposed to be set up and how the comments
say it works, just not the way it was implemented (for some
variables).
With this change, there might be a few sub.mk files that need extra
make library variables listed in them so that all libraries can be
found to successfully link an executable.
M .../*/sub.mk
Now need to add $(THREAD_LIBRARY) to many sub.mk files. Also used
spacing/indention to make some files easier to read.
734 lines of code changed in 26 files:
Fix for f77 dependency generation flags for PGI fortran compiler (pgf77 on ranger). At some point we really will need to update configure to actually test for the F77 flags.
39 lines of code changed in 3 files:
Make archive (.a) creation output quieter... also fixed (I think) redirection to /dev/null... Seems to also fix the problem (on uP) of 'make sus' seeming to recreate the .a files multiple times.
0 lines of code changed in 2 files:
M Core/Exceptions/PetscError.cc ----renamed_to---> UintahPetscError.cc
M Core/Exceptions/PetscError.h ----renamed_to---> UintahPetscError.h
PetscError implies a function defined in Petsc (and actually, there is
a Petsc PetscError which caused a naming conflict with our PetscError.
So I renamed our PetscError to the more clear UintahPetscError.
M CCA/Components/Models/Radiation/Models_PetscSolver.cc
M CCA/Components/MPM/PetscSolver.cc
M CCA/Components/Arches/PetscSolver.cc
M CCA/Components/Arches/Radiation/RadLinearSolver.cc
M CCA/Components/Arches/Filter.cc
Using UintahPetscError. Some coding convention cleanups.
M CCA/Components/Models/Radiation/RadiationConstVariables.h
M CCA/Components/Arches/ArchesConstVariables.h
This file doesn't use PetscError, so doesn't need to include it.
ALSO, PLEASE don't place #includes above the '#ifndef .h file guard'
at the top of a .h file.
M CCA/Components/Models/Radiation/Models_HypreSolver.cc
Finish cleanup up what Todd started. ;) Removed references to
PetscError from this Hypre file. Rearranged the #includes to
be in a better order. Fixed #include "" to use #include <>.
M CCA/Components/Arches/Radiation/RadHypreSolver.cc
This file doesn't use PetscError, so don't #include it. Fixed
#include "" to be #include <>.
M CCA/Components/Arches/StencilMatrix.h
Don't use std::vector when it isn't used in the file.
M CCA/Components/Regridder/PatchFixer.cc
Untabify. Indent. Group using statements. Few coding standard
updates.
M Core/Exceptions/sub.mk
PetscError -> UintahPetscError. Clean up ordering of src files.
M Core/Grid/Variables/ReductionVariable_special.cc
Still trying to get the symbols to be defined correctly on all
compilers.
615 lines of code changed in 22 files:
- removed fortran normpress function. You don't need to call fortran code to
subtract a constant from an array
normPressure() & updatePressure()
- replaced nested loops with an iterator
- cleaned up prototype
21 lines of code changed in 6 files:
added periodic BC test to RT
0 lines of code changed in 2 files:
variables that are only used in one function shouldn't be declared as global.
(d_value)
-cleaned up the the #includes
17 lines of code changed in 2 files:
- removed unused variables (Why was there petsc variables in hypersolver.h?)
- clean up #includes.
5 lines of code changed in 1 file:
- replaced triple nested loops for iterators
- cleanup
101 lines of code changed in 1 file:
Bulletproofing.
0 lines of code changed in 2 files:
Use the basic 'ls', not (a, perhaps, fancy color adding,etc) ls.
1 lines of code changed in 1 file:
matrixCreate()
-comments
-add vertical and horizontal spaces
- minor variable name change
79 lines of code changed in 1 file:
formating
18 lines of code changed in 1 file:
Fix memory leak.
2 lines of code changed in 1 file:
Fixed a typo
1 lines of code changed in 1 file:
This is more likely the correct way to compute the offset.
2 lines of code changed in 1 file:
Fix indexing error discovered by Justin.
7 lines of code changed in 1 file:
A script to get stack traces from running jobs.
To run type execute this script with the following parameters
getstacktrace.ranger.sh <jobid> <executable name>
where <jobid> is the id of the job which can get obtained with the command 'qstat'.
and executable name is the name of the running executable.
For example
%getstacktrace.ranger.sh 181172 sus
The stack trace is set to stdout.
Similar scripts could be created for other servers with minimal effort.
65 lines of code changed in 1 file:
Don't call mpi functions if only using 1 processor. This should fix runing sus without mpirun for problems that use the DLB.
5 lines of code changed in 1 file:
More fixes to fixes for PGI compiler.
37 lines of code changed in 5 files:
Fixes to fixes for PGI compiler... to allow compilation at LLNL (Atlas/uP).
M StandAlone/regression/sub.mk
M Packages/Uintah/StandAlone/tools/compare_mms/sub.mk
M Packages/Uintah/StandAlone/tools/radiusMaker/sub.mk
M Packages/Uintah/testprograms/sub.mk
M Packages/Uintah/testprograms/PatchBVH/sub.mk
M Packages/Uintah/testprograms/TestFastMatrix/sub.mk
M Packages/Uintah/testprograms/BNRRegridder/sub.mk
M Packages/Uintah/testprograms/IteratorTest/sub.mk
Need to link Lapack too (when Blas is used).
M Packages/Uintah/Core/Grid/Variables/ugc_templates.cc
- The "using namespace Uintah" wasn't enough for the xlC (AIX
compiler)... Had to use "Uintah::" explicitly.
- Indent. Organize #includes.
M Packages/Uintah/Core/Grid/Variables/GridVariableBase.h
- Declare the parent classes allocate function. (Might not be
completely necessary, but before it was only declared in the parent
and in the subclass which made it kinda hard to figure out where
it was coming from.)
M Packages/Uintah/Core/Grid/Variables/GridVariableBase.cc
- More indention.
M Packages/Uintah/Core/Grid/Variables/GridVariable.h
- AIX (xlC) compiler doesn't like the "using" statement... complains
that it can't figure out which function is the right one.
- Indent. Untabify.
101 lines of code changed in 16 files:
Added, with Comer doing most of it, the ability to also read
in velocity from .pts files, in addtion to the handful of variables
already available.
68 lines of code changed in 10 files:
Fixes to allow Uintah to build using the PGI compiler:
M configure
M configure.ac
- Figure out size of 'long long' so that Endian.cc swapbytes() can be
set correctly... perhaps a bit of overkill, but...
- PGI compilers don't support -Wall, so don't use it.
- Better messages when determining dependency generation flag. Fix
grep for ":" as it sometimes is " :". See below (configVars.mk.in).
- pgf77 needs -lrt to link.
M configVars.mk.in
- ECHO should not be "echo -n" (no newline)... so named it more appropriately.
- Many compilers don't create dependency files (.d) with exactly "name.o : name.cc".
Then may use "name.o:name.cc". So don't use the ":" in the sed. This should
never cause a problem because of the "^".
- Added the dependency mode of: 'modify_and_move'. PGI compiler creates an invalid
.d file in the wrong place, so we have to fix it and move it.
- NOTE: the F77 dependency flag is currently (historically) just a copy of the CXX
flag... this has worked in the past and still works for everything but pgf77.
Soon (but not in this update) I will fix configure to do this correctly.
M StandAlone/regression/sub.mk
M Packages/Uintah/StandAlone/tools/compare_mms/sub.mk
M Packages/Uintah/StandAlone/tools/radiusMaker/sub.mk
- Need BLAS_LIBRARY to link... at least on Ranger using PGI.
- Please indent... it really does make it easier to read.
M Core/Malloc/Allocator.cc
Moved variable into the #if section that it is used in. Avoids compiler warning.
M Core/Util/Endian.cc
A Core/Util/testEndian.h.in
D Core/Util/Endian.h
- pgcc is requiring the swapbytes() for 'long long'... So add it
in. Since 'long long' size can be different on different machines,
use overkill method with configure figuring out size and setting it
for us.
- Moved Endian.h to testEndian.h.in to allow configure to modify it.
- Indented.
M Core/Util/sub.mk
M Packages/Uintah/Core/Grid/Variables/sub.mk
Untabified.
M Core/Util/Socket.cc
Fix compiler warning and possible 'random' error.
M Core/Math/MiscMath.cc
Fix PGI compiler issue.
M Packages/Uintah/CCA/Components/DataArchiver/DataArchiver.cc
M Packages/Uintah/CCA/Components/Schedulers/SchedulerCommon.cc
#include <time.h> is required for time functions.
M Packages/Uintah/CCA/Components/ICE/EOS/IdealGas.cc
M Packages/Uintah/CCA/Components/ICE/CustomBCs/sine.h
M Packages/Uintah/CCA/Components/ICE/CustomBCs/MMS_BCs.cc
M Packages/Uintah/CCA/Components/ICE/CustomBCs/microSlipBCs.cc
M Packages/Uintah/CCA/Components/ICE/BoundaryCond.cc
- Removed a bunch of definitions of "iter". (vector<IntVector>::const_iterator)...
probably a leftover from the iterator update a while back. In some cases,
renamed an interior (for loop) iterator from "iter" to "cIter" so that the
code would be a little more clear as to which iterator was being used
inside the inner for loop. Also, define some iterators in the for loop,
instead of above the loop. (for( vector::iterator iter...))
M Packages/Uintah/CCA/Components/ICE/AMRICE.h
M Packages/Uintah/Core/Grid/Variables/GridVariable.h
M Packages/Uintah/Core/Grid/Variables/GridVariableBase.h
Fix compiler warning about hidden parent class function.
M Packages/Uintah/CCA/Components/Arches/ExtraScalarSolver.h
Fix compiler warning about ineffectual use of a const return type. Eg:
const int doSomething() { return 1; }
doesn't mean anything... it doesn't make sense for the returned int to
be const. Should just be:
int doSomething() { return 1; }
M Packages/Uintah/CCA/Ports/SFC.h
Fix problem with nested comments. Don't use /* ... */ over many lines. Use #if 0.
M Packages/Uintah/StandAlone/tools/uda2nrrd/particles.cc
Comment about invalid code.
M Packages/Uintah/StandAlone/tools/puda/varsummary.cc
PGI compiler needs Min/Max defined.
M Packages/Uintah/StandAlone/tools/extractors/partextract.cc
#include <stdlib.h> for strtoll... Add hack to force (older (verion
7.1-2)) pgCC to allow strtoll.
M Packages/Uintah/Core/Grid/Patch.h
M Packages/Uintah/Core/Grid/AMR.h
Hack to remove PGI compiler warnings about unreachable code.
M Packages/Uintah/Core/Grid/Grid.h
Use white space... it is also your friend. Seriously (on a related
note ;) can someone tell me why they think "x=3;" is better than "x = 3;"?
M Packages/Uintah/Core/Grid/Variables/ReductionVariable_special.cc
Wow, this is an ugly file... Had to add some (templated) functions
that the PGI compiler was requiring.
M Packages/Uintah/Core/Grid/Variables/ComputeSet.h
Don't seem to need to #include the .cc file (for the templates) with
PGI anymore... at least not on Ranger using pgCC version 7.1-2.
M Packages/Uintah/Core/Grid/Variables/VarTypes.h
Needs the 'long long' var type.
M Packages/Uintah/Core/Grid/Variables/ComputeSet_special.cc
More use of white space, indentation, etc.
M Packages/Uintah/Core/DataArchive/DataArchive.cc
Added {} around what looks like a necessary block of code... strange
that this didn't cause hangs, etc in the code. Perhaps this section
of code isn't used that often? Hope the RT doesn't gripe
tomorrow... it's not my fault!
M Packages/Uintah/Core/Disclosure/TypeUtils.h
M Packages/Uintah/Core/Disclosure/TypeUtils.cc
Added 'long long' function. Organized the code a tad bit to make it
easier to see which functions (for which types) are defined.
M Packages/Uintah/testprograms/sub.mk
M Packages/Uintah/testprograms/PatchBVH/sub.mk
M Packages/Uintah/testprograms/TestFastMatrix/sub.mk
M Packages/Uintah/testprograms/BNRRegridder/sub.mk
M Packages/Uintah/testprograms/IteratorTest/sub.mk
Untabify. Clean up. Removed double definition of LIBS. Requires
BLAS_LIBRARY to link.
M Packages/Uintah/tools/BlasLapackTests/test_blas.c
Ranger's version of testcase... not sure I should have checked it
in... Probably need to have both with the #if separating them.
M Packages/Uintah/Dataflow/Modules/Selectors/ParticleFieldExtractor.h
Fix compiler warning about hidden function (update_progress).
M Packages/Uintah/Dataflow/Modules/Selectors/ParticleFieldExtractor.cc
Fix includes (better ordering). Fix (hack) PGI problem with finding atoll.
M Packages/Uintah/Dataflow/Modules/Selectors/FieldExtractor.h
More white space. Remove unused var. Move common code to above 'if'.
1096 lines of code changed in 69 files:
Add gTemperatureStar calc back in as it is used by MPMICE.
5 lines of code changed in 1 file:
remove quotation marks in exceptions Thanks Dav.
2 lines of code changed in 3 files:
Throw an exception instead of using exit.
On large processor runs when you use exit the job doesnt quit, instead it
just hangs.
15 lines of code changed in 2 files:
More tidying. No longer allocateAndPut gTemperatureStarLabel,
it was only used as a temporary variable, and is now treated
accordingly.
29 lines of code changed in 1 file:
Get rid of the temporary variable gpdTdt. What was I thinking?
9 lines of code changed in 1 file:
Verify that write permission is enabled for creating output files. Verify that '-p' was used when a particle variable is requested.
32 lines of code changed in 2 files:
Added some comments, and split the fracture stuff into
its own loops for readability and performance.
125 lines of code changed in 1 file:
Move scheduleComputeHeatExchange down with the rest of the
heat transfer stuff in scheduleTimeAdvance.
1 lines of code changed in 1 file:
Remove gratuitous exception.
0 lines of code changed in 1 file:
Avoid assigning a -1 to an unsigned int
0 lines of code changed in 2 files:
Another corrected version of this courtesy of Scott Bardenhagen.
0 lines of code changed in 4 files:
Undid last commit. noinline is not compatable with gcc....
1 lines of code changed in 1 file:
Do not allow operator< to be inlined. Static variables and inlining do not play well together.
3 lines of code changed in 1 file:
Set the grid pointer when using the copy constructor.
2 lines of code changed in 1 file:
Store a grid pointer with each patch. This was the way Uintah was prior to the patch changes. The current way of storing patches limits the number of grids at any one time to 2. This is a problem when using scirun with multiple extractors/udas/timesteps/etc.
26 lines of code changed in 21 files:
Move incrementGrid inside the critical section.
1 lines of code changed in 1 file:
quiet a compiler warning
2 lines of code changed in 1 file:
removed a check to see if an unsigned int was less than 0.
0 lines of code changed in 2 files:
Additional fixes for --disable-scirun
5219 lines of code changed in 2 files:
Alphabetized...
0 lines of code changed in 2 files:
Added an env variable for the uda2vis library and made the header file path relative
14 lines of code changed in 2 files:
Initialize variables to quite compiler warning... however, it is possible these will still be used before being set to something valid... at least NULL will cause sus to immediately die.
0 lines of code changed in 2 files:
The Mac is more stringent on what is needed to link, so had to trim
out some more libraries in order to turn off building DATAFLOW.
0 lines of code changed in 14 files:
M */sub.mk
Fix typo: need $(BUILD_DATAFLOW), not just $BUILD_DATAFLOW.
M Packages/Uintah/sub.mk
Fix make warnings, need: $(SRCDIR)/Dataflow, not just Dataflow.
M Core/Geom/sub.mk
Path.cc was listed twice.
17 lines of code changed in 22 files:
test that all p.xxxx.xml files have size > 0
10 lines of code changed in 1 file:
M configure configure.ac */sub.mk
Updated configure to make '--disable-dataflow' and '--disable-scirun'
mean the same thing. Fixed sub.mk files to only build non-scirun
(dataflow) stuff when one of these flags is used.
Mostly had to just add:
ifeq ($(BUILD_DATAFLOW),yes)
...
endif
to the sub.mk files and place any GL dependent files in that ifeq.
(Alphabetized the libraries listed in the sub.mks.)
M configVars.mk.in
Don't build the SCIRun/StandAlone directory if dataflow turned off.
We don't need anything in there and they all depend on things that
depend on GL. Could possibly get them to build, but it's not worth
the time.
M Packages/Uintah/sub.mk
Don't build Uintah SCIRun modules if scirun is disabled.
8442 lines of code changed in 18 files:
Don't allow mem usage to wrap below zero. This causes allocation to appear near max usage. I'm unsure what situtaions cause the memory freed to be greater than the memory allocated.
4 lines of code changed in 1 file:
missed a few typecasts
2 lines of code changed in 1 file:
typecast size_t variables to the proper int to ensure that printf plays nice.
41 lines of code changed in 1 file:
Added #include <Packages/Uintah/Core/Exceptions/ProblemSetupException.h> now that a routine is throwing a ProblemSetupException.
1 lines of code changed in 1 file:
Fixes to allow compilation on LLNL Purple.
5 lines of code changed in 3 files: