ADIOS2 issueshttps://code.ornl.gov/pnb/ADIOS2/-/issues2019-06-24T18:25:19Zhttps://code.ornl.gov/pnb/ADIOS2/-/issues/15332.4.0-rc2?2019-06-24T18:25:19ZPodhorszki, Norbert2.4.0-rc2?*Created by: ax3l*
Hi,
are you planning to tag a `2.4.0-rc2` version before the release?
Currently, the `master` works for our downstream efforts (cc @franzpoeschel ) and a further release candidate would help us integrating it in...*Created by: ax3l*
Hi,
are you planning to tag a `2.4.0-rc2` version before the release?
Currently, the `master` works for our downstream efforts (cc @franzpoeschel ) and a further release candidate would help us integrating it in CI already.2.4.0 Production Releasehttps://code.ornl.gov/pnb/ADIOS2/-/issues/15912.4.0 release ReadMe.md shows circleci:failed badge2019-07-01T15:38:39ZPodhorszki, Norbert2.4.0 release ReadMe.md shows circleci:failed badge*Created by: germasch*
When going to the code view from the release page (https://github.com/ornladios/ADIOS2/tree/v2.4.0), the circleci badge shows "failed" -- and some of the other badges are broken links, which bothers me a little bi...*Created by: germasch*
When going to the code view from the release page (https://github.com/ornladios/ADIOS2/tree/v2.4.0), the circleci badge shows "failed" -- and some of the other badges are broken links, which bothers me a little bit ;)
It's probably too late to fix as the release is done, but on the odd chance that this can be fixed from the circleci config side, I thought I'd bring it up.https://code.ornl.gov/pnb/ADIOS2/-/issues/1374Ability to write already compressed image data2019-04-12T21:39:27ZPodhorszki, NorbertAbility to write already compressed image data*Created by: isosc*
When importing jpg images into adios, we want to avoid decompressing and then recompressing due to the loss of quality that would result. Instead, it should be possible to call put (or write in the hl python api) and...*Created by: isosc*
When importing jpg images into adios, we want to avoid decompressing and then recompressing due to the loss of quality that would result. Instead, it should be possible to call put (or write in the hl python api) and pass a buffer containing the already compressed data (along with any necessary compression related metadata). This is particularly useful for large tiled images such as TCGA (cancer images).https://code.ornl.gov/pnb/ADIOS2/-/issues/471Add ADIOS2.FlushAll() 2018-04-03T13:48:07ZPodhorszki, NorbertAdd ADIOS2.FlushAll() *Created by: pnorbert*
We need a function where the user can ask ADIOS to flush/sync all open file streams when e.g. they close the file for the checkpoint. This ensures that at the checkpoint, all other data streams are synced to the d...*Created by: pnorbert*
We need a function where the user can ask ADIOS to flush/sync all open file streams when e.g. they close the file for the checkpoint. This ensures that at the checkpoint, all other data streams are synced to the disk.
https://code.ornl.gov/pnb/ADIOS2/-/issues/1074Add a way to pin variables or steps in streaming mode to allow access to vari...2019-05-30T13:59:00ZPodhorszki, NorbertAdd a way to pin variables or steps in streaming mode to allow access to variables that are not sent at every step*Created by: fbudin69500*
It happens frequently that some data is saved or sent only at certain steps. For example, the geometry of the mesh is often only written on the first step.
When using a streaming engine like SST, one reader t...*Created by: fbudin69500*
It happens frequently that some data is saved or sent only at certain steps. For example, the geometry of the mesh is often only written on the first step.
When using a streaming engine like SST, one reader that connects later than when the data was written will miss this important piece of data that maybe is sent only once.
It would be convenient to have a way to pin some steps that are complete (contain all the variables), or individual variables that need to be read on the first step of the processing when a new reader connects.Eisenhauer, GregEisenhauer, Greghttps://code.ornl.gov/pnb/ADIOS2/-/issues/2023Add Engine::BlocksInfo to the python bindings2020-03-06T16:07:42ZPodhorszki, NorbertAdd Engine::BlocksInfo to the python bindings*Created by: isosc*
Engine::BlocksInfo() seems to be missing from the python bindings. This is essential for extracting metadata information to build skel I/O models.
This seems like it is a minor addition, but requires some knowled...*Created by: isosc*
Engine::BlocksInfo() seems to be missing from the python bindings. This is essential for extracting metadata information to build skel I/O models.
This seems like it is a minor addition, but requires some knowledge of the pybind tool.
https://code.ornl.gov/pnb/ADIOS2/-/issues/415Add Engine CurrentStep() inspection function2018-02-13T14:40:05ZPodhorszki, NorbertAdd Engine CurrentStep() inspection function*Created by: williamfgc*
Required to make it public information at the application level for all engines in streaming mode.*Created by: williamfgc*
Required to make it public information at the application level for all engines in streaming mode.https://code.ornl.gov/pnb/ADIOS2/-/issues/825Add error flags to C bindings2018-10-09T18:39:23ZPodhorszki, NorbertAdd error flags to C bindings*Created by: williamfgc*
`adios2_adios *adios2_init_config(const char *config_file, MPI_Comm mpi_comm, const adios2_debug_mode debug_mode)`
replace with:
`int adios2_init_config(adios2_adios* adios, const char *config_file, MPI_Comm...*Created by: williamfgc*
`adios2_adios *adios2_init_config(const char *config_file, MPI_Comm mpi_comm, const adios2_debug_mode debug_mode)`
replace with:
`int adios2_init_config(adios2_adios* adios, const char *config_file, MPI_Comm mpi_comm, const adios2_debug_mode debug_mode)`
To basically capture the C++11 library exceptionshttps://code.ornl.gov/pnb/ADIOS2/-/issues/324Add functionality to remove variables and attributes2017-12-05T00:16:36ZPodhorszki, NorbertAdd functionality to remove variables and attributes*Created by: williamfgc*
*Created by: williamfgc*
https://code.ornl.gov/pnb/ADIOS2/-/issues/2003Add generated folders from docs to .gitignore2020-03-03T13:51:41ZPodhorszki, NorbertAdd generated folders from docs to .gitignore*Created by: NAThompson*
After building the docs, multiple generated directories are added:
```
docs/bin/
docs/lib/
docs/pyvenv.cfg
```
These should be in the `.gitignore`.*Created by: NAThompson*
After building the docs, multiple generated directories are added:
```
docs/bin/
docs/lib/
docs/pyvenv.cfg
```
These should be in the `.gitignore`.https://code.ornl.gov/pnb/ADIOS2/-/issues/1500add inConfigFile option to declareIO in fortran 2019-06-24T18:26:21ZPodhorszki, Norbertadd inConfigFile option to declareIO in fortran *Created by: guj*
Would be nice to have in Fortran:
When initiating adios2 from xml config,
the declare_io function should make sure IO names are in the config file.
(or have a way to check) *Created by: guj*
Would be nice to have in Fortran:
When initiating adios2 from xml config,
the declare_io function should make sure IO names are in the config file.
(or have a way to check) https://code.ornl.gov/pnb/ADIOS2/-/issues/1102Add MGARD as a dependency to CI tests2019-06-27T18:17:16ZPodhorszki, NorbertAdd MGARD as a dependency to CI tests*Created by: williamfgc*
@chuckatkins I added some tests in #1101 that are only tested locally. I need your help to add to the CI build from the https://github.com/CODARcode/MGARD mgard3 branch. Thanks!*Created by: williamfgc*
@chuckatkins I added some tests in #1101 that are only tested locally. I need your help to add to the CI build from the https://github.com/CODARcode/MGARD mgard3 branch. Thanks!https://code.ornl.gov/pnb/ADIOS2/-/issues/781add mgard support under adios2 thirdparty2018-12-07T21:49:19ZPodhorszki, Norbertadd mgard support under adios2 thirdparty*Created by: williamfgc*
@chuckatkins this is just to formalize mgard support inside adios2. Thanks!*Created by: williamfgc*
@chuckatkins this is just to formalize mgard support inside adios2. Thanks!https://code.ornl.gov/pnb/ADIOS2/-/issues/460Add remove variable functionality in Fortran API2018-02-28T20:08:49ZPodhorszki, NorbertAdd remove variable functionality in Fortran API*Created by: williamfgc*
*Created by: williamfgc*
https://code.ornl.gov/pnb/ADIOS2/-/issues/1361AddressSanitizer: container-overflow2019-04-09T19:24:09ZPodhorszki, NorbertAddressSanitizer: container-overflow*Created by: NAThompson*
In the CMakeLists.txt add the line
```
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address")
```
and then run the unit tests. Then we obtain the container-overflow error
```
284: Process wran...*Created by: NAThompson*
In the CMakeLists.txt add the line
```
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address")
```
and then run the unit tests. Then we obtain the container-overflow error
```
284: Process wrank 0 rank 0 calls MainWriters
284: There are 1 Writers
284: Process wrank 1 rank 0 calls MainReaders
284: There are 1 Readers
284: =================================================================
284: ==99274==ERROR: AddressSanitizer: container-overflow on address 0x60200002e310 at pc 0x000109eca751 bp 0x7ffee7018
0 sp 0x7ffee7017c30
284: WRITE of size 4 at 0x60200002e310 thread T0
284: =================================================================
284: ==99273==ERROR: AddressSanitizer: container-overflow on address 0x60200002e3d0 at pc 0x00010baf5751 bp 0x7ffee53f6
0 sp 0x7ffee53f5ed0
284: WRITE of size 4 at 0x60200002e3d0 thread T0
284: #0 0x10baf5750 in wrap_memcpy (libclang_rt.asan_osx_dynamic.dylib:x86_64h+0x1e750)
284: #1 0x10c9aaed3 in non_overlap_copy_content_same_ddt (libopen-pal.40.dylib:x86_64+0x1aed3)
284: #2 0x10b9d4397 in ompi_datatype_sndrcv (libmpi.40.dylib:x86_64+0x2c397)
284: #3 0x10b9e6a5e in MPI_Gather (libmpi.40.dylib:x86_64+0x3ea5e)
284: #4 0x10b3eeef7 in adios2::insitumpi::FindPeers(ompi_communicator_t*, std::__1::basic_string<char, std::__1::ch
_traits<char>, std::__1::allocator<char> > const&, bool, ompi_communicator_t*) (libadios2.2.dylib:x86_64+0xaadef7)
284: #5 0x10b385250 in adios2::core::engine::InSituMPIWriter::InSituMPIWriter(adios2::core::IO&, std::__1::basic_st
ng<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, adios2::Mode, ompi_communicator_t*) (libadios
2.dylib:x86_64+0xa44250)
284: #6 0x10aac12b3 in adios2::core::IO::Open(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::a
ocator<char> > const&, adios2::Mode, ompi_communicator_t*) (libadios2.2.dylib:x86_64+0x1802b3)
284: #7 0x10b563fe1 in adios2::IO::Open(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocat
<char> > const&, adios2::Mode, ompi_communicator_t*) (libadios2.2.dylib:x86_64+0xc22fe1)
284: #8 0x10a815fad in TestStagingMPMD::MainWriters(ompi_communicator_t*, unsigned long, unsigned long, int, unsign
int) (TestStagingMPMD:x86_64+0x10000ffad)
284: #9 0x10a80d8e2 in TestStagingMPMD::TestCommon(RunParams, int, unsigned int, unsigned int, float) (TestStagingM
D:x86_64+0x1000078e2)
284: #10 0x10a80d02e in TestStagingMPMD_SingleStep_Test::TestBody() (TestStagingMPMD:x86_64+0x10000702e)
```
Or, a somewhat different route to nullptr segfault:
```bash
build/bin$ ./TestStagingMPMD
AddressSanitizer:DEADLYSIGNAL
=================================================================
==1299==ERROR: AddressSanitizer: SEGV on unknown address 0x000000000000 (pc 0x7fff589be712 bp 0x7ffee40d0f40 sp 0x7ffee40d0f40 T0)
==1299==The signal is caused by a READ memory access.
==1299==Hint: address points to the zero page.
#0 0x7fff589be711 in _platform_strlen (libsystem_platform.dylib:x86_64+0x1711)
#1 0x10ce0eed8 in wrap_strlen (libclang_rt.asan_osx_dynamic.dylib:x86_64h+0x17ed8)
#2 0x10bb38faf in main (TestStagingMPMD:x86_64+0x10000afaf)
#3 0x7fff587dc3d4 in start (libdyld.dylib:x86_64+0x163d4)
==1299==Register values:
rax = 0x000000010daa250c rbx = 0x00007ffee40d1900 rcx = 0x0000000000000000 rdx = 0x0000000000000000
rdi = 0x0000000000000000 rsi = 0x0000000000000000 rbp = 0x00007ffee40d0f40 rsp = 0x00007ffee40d0f40
r8 = 0x0000000000000000 r9 = 0xffffffff00000000 r10 = 0x0000000112be0c30 r11 = 0x000000010cd048d8
r12 = 0x0000000000000000 r13 = 0x00001fffdc81a2f8 r14 = 0x0000000000000000 r15 = 0x000000010daa2508
AddressSanitizer can not provide additional info.
SUMMARY: AddressSanitizer: SEGV (libsystem_platform.dylib:x86_64+0x1711) in _platform_strlen
==1299==ABORTING
[:01299] *** Process received signal ***
[:01299] Signal: Abort trap: 6 (6)
[:01299] Signal code: (0)
[:01299] *** End of error message ***
[1] 1299 abort ./TestStagingMPMD
```https://code.ornl.gov/pnb/ADIOS2/-/issues/1343Add support for local values in Fortran2019-04-02T17:06:51ZPodhorszki, NorbertAdd support for local values in Fortran*Created by: williamfgc*
*Created by: williamfgc*
https://code.ornl.gov/pnb/ADIOS2/-/issues/220Add support for version checking in FindZFP2019-09-25T16:32:51ZPodhorszki, NorbertAdd support for version checking in FindZFP*Created by: chuckatkins*
Minimum version required is 0.5.1, but FindZFP doesn't currently handle version checking*Created by: chuckatkins*
Minimum version required is 0.5.1, but FindZFP doesn't currently handle version checking2.5.0 Production Releasehttps://code.ornl.gov/pnb/ADIOS2/-/issues/1166add tests after doing a make install on CI2019-06-26T18:34:52ZPodhorszki, Norbertadd tests after doing a make install on CI*Created by: williamfgc*
Not sure if possible, but maybe it is time for external tests. Current master is broken after `make install` as we are not testing outside local ctest.*Created by: williamfgc*
Not sure if possible, but maybe it is time for external tests. Current master is broken after `make install` as we are not testing outside local ctest.2.4.0 Production Releasehttps://code.ornl.gov/pnb/ADIOS2/-/issues/2039Add the building of Docker images to CI2020-03-13T18:38:38ZPodhorszki, NorbertAdd the building of Docker images to CI*Created by: HannoSpreeuw*
I could add the building of Docker images to your CI system, if you would like that.
This is in relation to issue #2038, so to prevent this from occurring again. *Created by: HannoSpreeuw*
I could add the building of Docker images to your CI system, if you would like that.
This is in relation to issue #2038, so to prevent this from occurring again. https://code.ornl.gov/pnb/ADIOS2/-/issues/440Add updated User Guide documentation2019-01-11T17:02:17ZPodhorszki, NorbertAdd updated User Guide documentation*Created by: williamfgc*
*Created by: williamfgc*
Eisenhauer, GregEisenhauer, Greg