sensei issueshttps://gitlab.kitware.com/sensei/sensei/-/issues2019-04-22T14:05:11-04:00https://gitlab.kitware.com/sensei/sensei/-/issues/39document ascent stuff2019-04-22T14:05:11-04:00Burlen Loringdocument ascent stuffdocument how to configure, build, and use sensei with the ascent back end. this should go in the read the docs user guide.document how to configure, build, and use sensei with the ascent back end. this should go in the read the docs user guide.DavidDavidhttps://gitlab.kitware.com/sensei/sensei/-/issues/38ascent dependency & exports (cmake)2019-04-22T14:03:40-04:00Burlen Loringascent dependency & exports (cmake)Add ascent exports to our cmake use file. test this by moving a copy of the `oscillator` mini app outside the source dir and compiling it. this test is what would be done by some one instrumenting a sim.Add ascent exports to our cmake use file. test this by moving a copy of the `oscillator` mini app outside the source dir and compiling it. this test is what would be done by some one instrumenting a sim.DavidDavidhttps://gitlab.kitware.com/sensei/sensei/-/issues/37ascent dependency & exports (sensei_config)2019-04-22T14:01:15-04:00Burlen Loringascent dependency & exports (sensei_config)`sensei_config` is the command line program that propagates library and header dependency from our cmake scripts to something that can be used in GNU make based projects. `sensei_config` is a shell script generated by CMake. Add all of ...`sensei_config` is the command line program that propagates library and header dependency from our cmake scripts to something that can be used in GNU make based projects. `sensei_config` is a shell script generated by CMake. Add all of the libs & includes needed to link AMReX against SENSEI compiled with ascent are in `sensei_config`.DavidDavidhttps://gitlab.kitware.com/sensei/sensei/-/issues/36make sure stuff doesn't use MPI after finalize2021-02-01T19:14:47-05:00Burlen Loringmake sure stuff doesn't use MPI after finalizeuse new end point. Test with VTKPostHoc I/Ouse new end point. Test with VTKPostHoc I/Ohttps://gitlab.kitware.com/sensei/sensei/-/issues/35Improve the web site random image feature2021-02-01T19:18:55-05:00Burlen LoringImprove the web site random image feature@patrick\-oleary @ewbethel @dcthomp
The web site random image currently does a true random walk through the image collection. This is problematic because many duplicate images are displayed. For example the first image may appear multi...@patrick\-oleary @ewbethel @dcthomp
The web site random image currently does a true random walk through the image collection. This is problematic because many duplicate images are displayed. For example the first image may appear multiple times in the first few transitions.
A simple fix would be to apply an a fixed/pre-determined cyclic order on the images and pick the starting point at random. from the randomly chosen starting point, the predetermined cyclic order would be followed. this would maximize time between repeated images, and give all the images fair air time.https://gitlab.kitware.com/sensei/sensei/-/issues/34Add images to the web site2019-04-23T13:46:09-04:00Burlen LoringAdd images to the web site@dcthomp @patrick\-oleary @ewbethel
David Can you please make sure the following images get put on the web site. We had spoke on 10/26 about this, but with all the chaos around SC I think it fell off our radars. I'm moving our email co...@dcthomp @patrick\-oleary @ewbethel
David Can you please make sure the following images get put on the web site. We had spoke on 10/26 about this, but with all the chaos around SC I think it fell off our radars. I'm moving our email conversation to the issue tracker here so that we do not forget.
Thank you for your help
Burlen
In situ rendering of a Rayleigh-Taylor instability computed with the AMReX IAM compressible Navier-Stokes simulation code with 4 levels of refinement using 2048 cores on NERSC Cori.
![rt_contour_00500](/uploads/208fbddd90277d18c3f13947f9215ba5/rt_contour_00500.png)
![image_000500](/uploads/e37e1aae1f5ac8e5209de314e25d7c35/image_000500.png)
In situ rendering of relativistic Laser Plasma Accelerator(LPA) simulation with WarpX on NERSC Cori.
![beam_j_pin_00800](/uploads/62ecd9d16879c2068720aff678e91e95/beam_j_pin_00800.png)
![beam_j_catalyst_00800](/uploads/e0da059d16a89a897dd553c28ca42703/beam_j_catalyst_00800.png)David ThompsonDavid Thompsonhttps://gitlab.kitware.com/sensei/sensei/-/issues/33Catalyst Warning2021-02-01T19:15:38-05:00Burlen LoringCatalyst Warning@patrick\-oleary @ewbethel
Hi Patrick,
With the update to ParaView 5.6.0 I am seeing warnings every time Catalyst executes. We are passing the correct time step, ParaView warns that it only sees the previous value. However, the correc...@patrick\-oleary @ewbethel
Hi Patrick,
With the update to ParaView 5.6.0 I am seeing warnings every time Catalyst executes. We are passing the correct time step, ParaView warns that it only sees the previous value. However, the correct time value(the one we pass) is used by ParaView during the execution so that this is more of an annoyance. However, the AMReX folks use the output put streams for diagnostic and profiling data so this is a real problem for them.
It would be a big help if Kitware could help track down the problem. Is that something you can do?
```bash
STEP 22 starts ...
STEP 22 ends. TIME = 9.556420749e-15 DT = 4.343827613e-16
Walltime = 145.8195755 s; This step = 0.203643828 s; Avg. per step = 6.628162524 s
SENSEI Begin update...
Warning: In /work/SENSEI/ParaView/ParaViewCore/VTKExtensions/Core/vtkPVTrivialProducer.cxx, line 95
vtkPVTrivialProducer (0x1c35b100): Requesting time 9.12204e-15 but only 9.55642e-15 is available
SENSEI update complete (6.599138309 sec)
```https://gitlab.kitware.com/sensei/sensei/-/issues/32VTKPosthocIO create output dir if it does not exist2018-12-17T13:43:03-05:00Burlen LoringVTKPosthocIO create output dir if it does not existthis can be done in the initialize methodthis can be done in the initialize methodhttps://gitlab.kitware.com/sensei/sensei/-/issues/31using output_dir attribute in the VTKPostHoc writer breaks visit and pvd files2018-10-28T17:08:22-04:00Burlen Loringusing output_dir attribute in the VTKPostHoc writer breaks visit and pvd filesfix the pvd/visit file generationfix the pvd/visit file generationhttps://gitlab.kitware.com/sensei/sensei/-/issues/30oscillator crash2019-12-17T13:20:41-05:00Junmin Guoscillator crashmy command:
srun -n 4 ./oscillator -s 64,64,64 -b 64 -t 5 -f h5-osc.xml sample.osc
output:
```
WARNING: No subset specified. Writing all available data
Error: could not find appropriate neighbor for particle: (id 2780, position: (32.303...my command:
srun -n 4 ./oscillator -s 64,64,64 -b 64 -t 5 -f h5-osc.xml sample.osc
output:
```
WARNING: No subset specified. Writing all available data
Error: could not find appropriate neighbor for particle: (id 2780, position: (32.303, 11.4627, 55.0531), velocity: (-3.68322, -4.93237, 1.67584))
=========================================================
Process id 63460 Caught SIGABRT
Program Stack:
WARNING: The stack trace will not use advanced capabilities because this is a release build.
0x2aaaaaf8dc10 : ??? [(???) ???:-1]
0x2aaab2b28f67 : gsignal [(libc.so.6) ???:-1]
0x2aaab2b2a33a : abort [(libc.so.6) ???:-1]
0x475054 : Block::move_particles(float, diy::Master::ProxyWithLink const&) [(oscillator) ???:-1]
0x4551f3 : diy::Master::ProcessBlock::operator()() [(oscillator) ???:-1]
0x4573bf : diy::Master::execute() [(oscillator) ???:-1]
0x4576c3 : void diy::Master::foreach_<Block>(std::function<void (Block*, diy::Master::ProxyWithLink const&)> const&, std::function<bool (int, diy::Master const&)> const&) [(oscillator) ???:-1]
0x44545d : main [(oscillator) ???:-1]
0x2aaab2b14725 : __libc_start_main [(libc.so.6) ???:-1]
0x447bd9 : _start [(oscillator) ???:-1]
```David ThompsonDavid Thompsonhttps://gitlab.kitware.com/sensei/sensei/-/issues/29handle LINK_ONLY in sensei config2018-09-18T12:49:13-04:00Burlen Loringhandle LINK_ONLY in sensei configmany entries such this are showing up in the static catalyst versions
`:$<LINK_ONLY:vtkPythonInterpreter>`
I think these can be removedmany entries such this are showing up in the static catalyst versions
`:$<LINK_ONLY:vtkPythonInterpreter>`
I think these can be removedhttps://gitlab.kitware.com/sensei/sensei/-/issues/28sensei + vtkm build fail2018-09-13T15:43:39-04:00Burlen Loringsensei + vtkm build fail```
In file included from /work/SENSEI/sensei/sensei/VTKmVolumeReductionAnalysis.cxx:1:
/work/SENSEI/sensei/sensei/VTKmVolumeReductionAnalysis.h:5:10: fatal error: vtkm/cont/Field.h: No such file or directory
#include <vtkm/cont/Field.h...```
In file included from /work/SENSEI/sensei/sensei/VTKmVolumeReductionAnalysis.cxx:1:
/work/SENSEI/sensei/sensei/VTKmVolumeReductionAnalysis.h:5:10: fatal error: vtkm/cont/Field.h: No such file or directory
#include <vtkm/cont/Field.h>
^~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [sensei/CMakeFiles/senseiCore.dir/build.make:193: sensei/CMakeFiles/senseiCore.dir/VTKmVolumeReductionAnalysis.cxx.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/Makefile2:263: sensei/CMakeFiles/senseiCore.dir/all] Error 2
make: *** [Makefile:130: all] Error 2
```https://gitlab.kitware.com/sensei/sensei/-/issues/27fix vtkm documentation2018-09-13T15:44:15-04:00Burlen Loringfix vtkm documentationREADME.md incorrectly implies that use3 of VTKm in sensei depends on VTK, we have also used a VTKm clone outside of VTK, and need to support that use case.README.md incorrectly implies that use3 of VTKm in sensei depends on VTK, we have also used a VTKm clone outside of VTK, and need to support that use case.https://gitlab.kitware.com/sensei/sensei/-/issues/26fix broken vtkm accelerators2018-09-13T14:03:18-04:00Burlen Loringfix broken vtkm acceleratorslibraries are not linkedlibraries are not linkedhttps://gitlab.kitware.com/sensei/sensei/-/issues/25use interface library for vtkm dependencies2018-09-13T15:44:46-04:00Burlen Loringuse interface library for vtkm dependenciesIn `CMake/vtkm.cmake` define an interface library that encapsulates our usage of VTKm. Make sure that SENSEICOnfig includes the exported libnrary so that external projects can link to sensei built with VTKm features.
see for example `CM...In `CMake/vtkm.cmake` define an interface library that encapsulates our usage of VTKm. Make sure that SENSEICOnfig includes the exported libnrary so that external projects can link to sensei built with VTKm features.
see for example `CMake/vtk.cmake`, `CMake/mpi.cmake`, `CMake/adios.cmake` for examples of how this is done.https://gitlab.kitware.com/sensei/sensei/-/issues/24Update autocorrelation analysis to handle oscillator's ucdmesh2018-12-10T15:20:15-05:00Aron HelserUpdate autocorrelation analysis to handle oscillator's ucdmeshucdmesh is an unstructured grid.
@mrzv said this in an email thread:
> The way autocorrelation was written was that each block (stored in the master) stores a grid of values, where it updates the autocorrelation values. If you change f...ucdmesh is an unstructured grid.
@mrzv said this in an email thread:
> The way autocorrelation was written was that each block (stored in the master) stores a grid of values, where it updates the autocorrelation values. If you change from a structured grid to something else, a similar structure needs to be mirrored in the blocks.
If you try to run the autocorrelation analysis on the "ucdmesh", it currently crashes, because it tries to look up a block based on an 'lid' of -1, which doesn't exist.
This feature will probably not be needed for the aug 2018 miniapp scaling runs.https://gitlab.kitware.com/sensei/sensei/-/issues/23raise exceptions in DataAdaptor wrappers2018-08-13T19:33:50-04:00Burlen Loringraise exceptions in DataAdaptor wrappersThe API had to be massaged because Python doesn't do pass by reference at the expense of the error return code. Instead we can raise exceptions in DataAdaptor wrappers when an error occurs. currently we are reporting the error but raisin...The API had to be massaged because Python doesn't do pass by reference at the expense of the error return code. Instead we can raise exceptions in DataAdaptor wrappers when an error occurs. currently we are reporting the error but raising an exception.https://gitlab.kitware.com/sensei/sensei/-/issues/22segv in parallel3d with histogram2021-02-01T19:16:12-05:00Burlen Loringsegv in parallel3d with histogram```bash
$gdb --args ./bin/3D_Grid -g 1x1x1 -l 1x1x1 -f ../sensei_2/configs/3dgrid.xml
Global Dimensions 1X1X1: Local Dimensions 1X1X1
Total Blocks are 1X1X1
STATUS: [0][/home/sensei/sc17/software/sensei/builds/sensei_2/sensei/Configur...```bash
$gdb --args ./bin/3D_Grid -g 1x1x1 -l 1x1x1 -f ../sensei_2/configs/3dgrid.xml
Global Dimensions 1X1X1: Local Dimensions 1X1X1
Total Blocks are 1X1X1
STATUS: [0][/home/sensei/sc17/software/sensei/builds/sensei_2/sensei/ConfigurableAnalysis.cxx:198][v1.1.0-57-ga2bf4db]
STATUS: Configured histogram with 10 celldata array pressure on mesh mesh
STATUS: [0][/home/sensei/sc17/software/sensei/builds/sensei_2/sensei/ConfigurableAnalysis.cxx:198][v1.1.0-57-ga2bf4db]
STATUS: Configured histogram with 10 celldata array density on mesh mesh
STATUS: [0][/home/sensei/sc17/software/sensei/builds/sensei_2/sensei/ConfigurableAnalysis.cxx:198][v1.1.0-57-ga2bf4db]
STATUS: Configured histogram with 10 celldata array temperature on mesh mesh
Program received signal SIGSEGV, Segmentation fault.
0x000000000053c118 in sensei::VTKHistogram::Internals::operator()<double> (this=0xaa4340, array=...)
at /home/sensei/sc17/software/sensei/builds/sensei_2/sensei/VTKHistogram.cxx:115
115 ++this->Histogram[bin];
Missing separate debuginfos, use: dnf debuginfo-install libuuid-2.30-1.fc26.x86_64 python2-libs-2.7.13-11.fc26.x86_64
(gdb) where
#0 0x000000000053c118 in sensei::VTKHistogram::Internals::operator()<double> (this=0xaa4340, array=...)
at /home/sensei/sc17/software/sensei/builds/sensei_2/sensei/VTKHistogram.cxx:115
#1 0x000000000053a4ed in vtkDataArrayDispatcher<sensei::VTKHistogram::Internals, void>::Go (this=0x7fffffffccc0, lhs=0xaa3c10)
at /home/sensei/sc17/software/paraview/builds/ParaView/VTK/Common/DataModel/vtkDataArrayDispatcher.h:170
#2 0x00000000005393bd in sensei::VTKHistogram::Compute (this=0xaa3440, da=0xaa3c10, ghostArray=0x0)
at /home/sensei/sc17/software/sensei/builds/sensei_2/sensei/VTKHistogram.cxx:218
#3 0x0000000000538e70 in sensei::Histogram::Execute (this=0xaa2cb0, data=0xaa3020)
at /home/sensei/sc17/software/sensei/builds/sensei_2/sensei/Histogram.cxx:197
#4 0x000000000050145b in sensei::ConfigurableAnalysis::Execute (this=0xaa2c80, data=0xaa3020)
at /home/sensei/sc17/software/sensei/builds/sensei_2/sensei/ConfigurableAnalysis.cxx:741
#5 0x00000000004f8c62 in bridge_update (tstep=0, time=0) at /home/sensei/sc17/software/sensei/builds/sensei_2/miniapps/parallel3d/Bridge.cxx:59
#6 0x00000000004f37fa in main (argc=<optimized out>, argv=<optimized out>)
at /home/sensei/sc17/software/sensei/builds/sensei_2/miniapps/parallel3d/parallel_3D.c:162
(gdb) p bin
$12 = -2147483648
```https://gitlab.kitware.com/sensei/sensei/-/issues/21test with binary installs2018-07-10T13:49:42-04:00Burlen Loringtest with binary installsin #19 a user reported that sensei fails to build with debian and homebrew installed vtk. we should test those as this will lower the barrier to get startedin #19 a user reported that sensei fails to build with debian and homebrew installed vtk. we should test those as this will lower the barrier to get startedhttps://gitlab.kitware.com/sensei/sensei/-/issues/20master branch fails to build with ENABLE_PYTHON=OFF2018-07-10T13:40:18-04:00Silvio Rizzimaster branch fails to build with ENABLE_PYTHON=OFFmaster branch
commit ac2c52f94b1b7c5658ed614a9000bb0c9f86f101
With ENABLE_PYTHON=OFF I get the following error:
```
[ 64%] Building CXX object sensei/CMakeFiles/sensei.dir/ConfigurableAnalysis.cxx.o
/projects/visualization/srizz...master branch
commit ac2c52f94b1b7c5658ed614a9000bb0c9f86f101
With ENABLE_PYTHON=OFF I get the following error:
```
[ 64%] Building CXX object sensei/CMakeFiles/sensei.dir/ConfigurableAnalysis.cxx.o
/projects/visualization/srizzi/BUILDS/sensei/sensei/sensei/ConfigurableAnalysis.cxx(618): error: identifier "PythonAnalysis" is undefined
vtkNew<PythonAnalysis> pyAnalysis;
^
/soft/visualization/vtk/include/vtk-8.1/vtkNew.h(62): error: name followed by "::" must be a class or namespace name
vtkNew() : Object(T::New())
^
detected during instantiation of "vtkNew<T>::vtkNew() [with T=<error-type>]" at line 618 of "/projects/visualization/srizzi/BUILDS/sensei/sensei/sensei/ConfigurableAnalysis.cxx"
compilation aborted for /projects/visualization/srizzi/BUILDS/sensei/sensei/sensei/ConfigurableAnalysis.cxx (code 2)
sensei/CMakeFiles/sensei.dir/build.make:62: recipe for target 'sensei/CMakeFiles/sensei.dir/ConfigurableAnalysis.cxx.o' failed
make[2]: *** [sensei/CMakeFiles/sensei.dir/ConfigurableAnalysis.cxx.o] Error 2
CMakeFiles/Makefile2:286: recipe for target 'sensei/CMakeFiles/sensei.dir/all' failed
```