Update Silo and HDF5 by markcmiller86 · Pull Request #20752 · visit-dav/visit

markcmiller86 · 2025-12-08T12:27:34Z

Description

Updates Silo to 4.12.0 and CMake
Updates HDF5 to 2.0 and CMake
Patches build of Xdmf 2.1.1 for HF5-2.0
Fixes a few HDF5 plugins for HDF5-2.0
Patches and or adjusts bv_xxx.sh for some HDF5 dependent TPLs

Type of change

Bug fix~~
New feature~~
Documentation update~~
Other~~

How Has This Been Tested?

Reminders:

Please follow the style guidelines of this project.
Please perform a self-review of your code before submitting a PR and asking others to review it.
Please assign reviewers (see VisIt's PR procedures for more information).

Checklist:

I have commented my code where applicable.~~
I have updated the release notes.~~
I have made corresponding changes to the documentation.~~
I have added debugging support to my changes.~~
I have added tests that prove my fix is effective or that my feature works.~~
I have confirmed new and existing unit tests pass locally with my changes.~~
I have added new baselines for any new tests to the repo.~~
I have NOT made any changes to protocol or public interfaces in an RC branch.~~

src/tools/dev/scripts/bv_support/bv_hdf5.sh

cyrush · 2025-12-08T16:26:35Z

So far looks great! I recommend we create a ticket that lists plugins that still need to use old HDF5 APIs via defines.

src/tools/dev/scripts/bv_support/bv_hdf5.sh

markcmiller86 · 2025-12-08T21:45:07Z

Almost certainly no. For most of its life szip was inconveniently licensed. Truly open source alternatives for it have emerged only recently say within the last few years. It was closely associated with the hdf5 library however because I think NASA had a lot of initial interest in it. And they were a big early user and sponsor of hdf5. My understanding is it excels mostly at integer or integer like data and not floating point data. So my belief is that no llnl SIM codes have ever used it. That said it may be worth checking with Kathryn Mohror to ask if she is aware of ever having encountered it in some of their work on SCR.

…

On Mon, Dec 8, 2025, 1:24 PM Cyrus Harrison ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In src/tools/dev/scripts/bv_support/bv_hdf5.sh <#20752 (comment)>: > if [[ "$DO_ZLIB" == "yes" ]]; then info "Configuring HDF5 with ZLib support." - cf_zlib="--with-zlib=\"${VISITDIR}/zlib/${ZLIB_VERSION}/${VISITARCH}\"" + cmk_opts="${cmk_opts} \ I think it is unlikely that a user will understand they have an szip file and be able to create the lib and set up the env vars. That said, if these files are very rare -- I am open to dropping support. Mark do you know if LLNL sim codes used szip? — Reply to this email directly, view it on GitHub <#20752 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLUUZD2QSA5W6OL6GAOGE34AXT7ZAVCNFSM6AAAAACOL3TFYOVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZTKNJUGEZDCMRVGY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

markcmiller86 · 2025-12-09T16:47:03Z

I was trying to build Xdmf against the one, parallel HDF5-2.0 I have installed and that fails, even after my patches for HDF5-2.0. Why? It fails because including hdf5.h in Xdmf sources causes a #include <mpi.h> and bv_xdfm.py ordinarily doesn't deal with building Xdmf against a parallel HDF5. Xdmf's CMake logic is very, very old. It is not using find_package() for HDF5 and so doesn't prime itself properly when building against a parallel-enabled HDF5.

There are a few options for situations like this...

Simply adjust bv_hdf5.sh to install both hdf5 and hdf5_mpi as before (which was the plan last week and my intention if I keep hitting issues like this).
There is a swizzle on the above I've at least tested with Xdmf and that is to arrange for H5_HAVE_PARALLEL to be #undef'd in HDF5 headers when building a serial lib like Xdmf against HDF5. This seems to work!
When building for parallel, inject -I/path/to/mpi/headers into Xdmf CMAKE_CXX_FLAGS
- Note: Xdmf 2.1.1 does have some MPI functionality in it but it is related to their network-distributed global memory (NDGM) and unrelated to our needs for simple Xdmf I/O.

markcmiller86 · 2025-12-10T09:19:03Z

To get Xdmf library to add -I/path/to/mpi/includes when HDF5 library it is using is parallel enabled, I added some logic to use CMake to probe the HDF5 installation. That seems to work.

markcmiller86 · 2025-12-11T05:15:16Z

Ok, netcdf requires more love because it a) assumes hid_t is an int and in HDF5-2.0 that type was changed to int64_t and it has the same H5Oget_info...() issues seen in other libs.

I suspect HDF5-2.0 has a bug in the API mapping macros for H5Oget_info... methods. I've submitted an inquiry to The HDF Group about it. Its popping up in a lot of places due to a missing arg when compiling against 2.0.

biagas · 2025-12-11T15:37:42Z

You might try Netcdf 4.5.0. That's what I've been using on Windows (for ease of building). I had no issues with the VisIt using this version, nor with building it against HDF5 2.0 in my test builds this week.

src/tools/dev/scripts/bv_support/bv_hdf5.sh

markcmiller86 · 2025-12-12T09:04:11Z

You might try Netcdf 4.5.0. That's what I've been using on Windows (for ease of building). I had no issues with the VisIt using this version, nor with building it against HDF5 2.0 in my test builds this week.

So, the set of patches needed for netcdf-4.1.1 (now ~15 years old) with HDF5-2.0 is getting larger and more complex. I am close to having it working but I kinda like @biagas suggestion. @cyrush do you have strong opinions?

cyrush · 2025-12-12T15:48:03Z

@markcmiller86 I think we should try the new version, would be good to remove ancient patches and have same code used on windows as linux if possible.

markcmiller86 · 2025-12-13T02:20:50Z

So, I was 4 patches in and apparently 2 patches away from a successful netcdf-4.1.1 build with HDF5-2.0. So, I've currently got that in this PR. I will revisit the issue before taking out of draft mode. But, for time being, I think its working now.

markcmiller86 · 2025-12-15T20:03:54Z

I added logic to silo plugin to provide a little more info about the file (and plugin) software versions...

cyrush · 2026-01-09T00:19:05Z

documenting a snag on macOS:

[harrison37@zeliak hdf5-2.0.0-build (feat-mcm86-04dec25-upd-hdf5-2.0-and-friends)]$ cat bv_run_cmake.sh 
"/Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/cmake/3.31.8/darwin-arm64/bin/cmake" -DBUILD_TESTING:BOOL=OFF -DHDF5_BUILD_CPP_LIB:BOOL=OFF -DHDF5_BUILD_JAVA:BOOL=OFF -DHDF5_BUILD_EXAMPLES:BOOL=OFF -DHDF5_BUILD_TOOLS:BOOL=ON -DHDF5_ENABLE_SUBFILING_VFD:BOOL=OFF -DCMAKE_C_COMPILER:STRING=clang -DCMAKE_CXX_COMPILER:STRING=clang++ -DCMAKE_C_FLAGS:STRING="-Wno-error=implicit-function-declaration -O2 " -DCMAKE_CXX_FLAGS:STRING="-O2 " -DCMAKE_INSTALL_PREFIX:PATH=/Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/hdf5/2.0.0/darwin-arm64 -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_STATIC_LIBS:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=ON -DONLY_SHARED_LIBS:BOOL=ON -DHDF5_BUILD_HL_LIB:BOOL=ON -DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=ON -DZLIB_INCLUDE_DIR:PATH="/Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/zlib/1.3.1/darwin-arm64/include" -DZLIB_LIBRARY_RELEASE:FILEPATH="/Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/zlib/1.3.1/darwin-arm64/lib/libz.dylib" -DHDF5_BUILD_FORTRAN:BOOL=OFF -DHDF5_ENABLE_PARALLEL:BOOL=ON -DMPI_C_COMPILER:PATH="/Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/mpich/3.3.1/darwin-arm64/bin/mpicc" -DMPI_CXX_COMPILER:PATH="/Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/mpich/3.3.1/darwin-arm64/bin/mpic++" -DMPI_C_COMPILER_INCLUDE_DIRS:STRING="" -DMPI_C_HEADER_DIR:PATH="" ../hdf5-2.0.0

-- Configuring incomplete, errors occurred!
[harrison37@zeliak hdf5-2.0.0-build (feat-mcm86-04dec25-upd-hdf5-2.0-and-friends)]$ ./bv_run_cmake.sh 
-- Final: share
-- Checking if complex number support is available
-- Using C99 complex number types
-- Checking if _Float16 support is available
-- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) 
-- ....All Warnings are enabled
-- Could NOT find MPI_C (missing: MPI_C_HEADER_DIR) (found version "3.1")
CMake Error at /Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/cmake/3.31.8/darwin-arm64/share/cmake-3.31/Modules/FindPackageHandleStandardArgs.cmake:233 (message):
  Could NOT find MPI (missing: MPI_C_FOUND) (found version "3.1")
Call Stack (most recent call first):
  /Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/cmake/3.31.8/darwin-arm64/share/cmake-3.31/Modules/FindPackageHandleStandardArgs.cmake:603 (_FPHSA_FAILURE_MESSAGE)
  /Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/cmake/3.31.8/darwin-arm64/share/cmake-3.31/Modules/FindMPI.cmake:1842 (find_package_handle_standard_args)
  CMakeLists.txt:784 (find_package)

I think this logic is not quite correct

    if [[ "$PAR_INCLUDE" != "" ]] ; then
         cmk_opts="${cmk_opts} \
             -DMPI_C_COMPILER_INCLUDE_DIRS:STRING=\"${PAR_INCLUDE_PATH}\" \
             -DMPI_C_HEADER_DIR:PATH=\"${PAR_INCLUDE_PATH}\""
     fi
    
     if [[ "$PAR_LIBS" != "" ]] ; then
         cmk_opts="${cmk_opts} -DMPI_C_LINK_FLAGS:STRING=\"${PAR_LINKER_FLAGS}\""
     fi

because we end up with:

-DMPI_C_COMPILER_INCLUDE_DIRS:STRING="" -DMPI_C_HEADER_DIR:PATH=""

which short circuits the mpi detection logic and creates the failure.

markcmiller86 · 2026-01-09T02:40:14Z

Ok, so that is the build of HDF5-2.0.0 then via bv_hdf5.sh. I thought I copied that logic verbatim from bv_conduit.sh. What was your build_visit command-line and env?

cyrush · 2026-01-09T19:07:53Z

I am confused as to why those flags are getting set since they seem to be empty.

I also hit issues with ADIOS2 and CGNS, here are the CGNS issues:

Configuring CGNS . . .
Invoking command to configure CGNS
CMake Error at /Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/cmake/3.31.8/darwin-arm64/share/cmake-3.31/Modules/FindPackageHandleStandardArgs.cmake:233 (message):
  Could NOT find MPI (missing: MPI_C_FOUND)
Call Stack (most recent call first):
  /Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/cmake/3.31.8/darwin-arm64/share/cmake-3.31/Modules/FindPackageHandleStandardArgs.cmake:603 (_FPHSA_FAILURE_MESSAGE)
  /Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/cmake/3.31.8/darwin-arm64/share/cmake-3.31/Modules/FindMPI.cmake:1842 (find_package_handle_standard_args)
  /Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/hdf5/2.0.0/darwin-arm64/cmake/hdf5-config.cmake:120 (find_package)
  /Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/cmake/3.31.8/darwin-arm64/share/cmake-3.31/Modules/FindHDF5.cmake:513 (find_package)
  CMakeLists.txt:3 (find_package)


HDF5 MPI include flag detected as ""

CGNS actually has a cmake build system, but it seems we are calling cmake via make and config.
We may want to directly use cmake.

I am going to try to get further w/o solving ADIOS2 or CGNS now.

cyrush · 2026-01-09T19:12:10Z

Silo failed as well.

I think anything downstream of HDF5 that is cmake and that is not setting up MPI - or perhaps is setting it up after it looks for HDF5) is failing.

I don't understand the logic for multiple versoins of hdf5 (one with mpi and one without), but could things be crossed? I

CMake'ing Silo
"/Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/cmake/3.31.8/darwin-arm64/bin/cmake" -DCMAKE_INSTALL_PREFIX:PATH="/Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/silo/4.12.0/darwin-arm64" -DBUILD_TESTING:BOOL=OFF -DSILO_ENABLE_INSTALL_LITE_HEADERS:BOOL=ON -DCMAKE_BUILD_TYPE:STRING=Release -DSILO_ENABLE_FORTRAN:BOOL=OFF -DSILO_ENABLE_PYTHON_MODULE:BOOL=ON -DSILO_PYTHON_DIR:PATH="/Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/python/3.13.9/darwin-arm64" -DSILO_ENABLE_SHARED:BOOL=ON -DSILO_ENABLE_HDF5:BOOL=ON -DSILO_HDF5_DIR:PATH="/Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/hdf5/2.0.0/darwin-arm64" -DSILO_HDF5_SZIP_DIR:PATH="/Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/szip/2.1/darwin-arm64" -DSILO_BUILD_FOR_BSD_LICENSE:BOOL=OFF -DSILO_ENABLE_HZIP:BOOL=ON -DSILO_ENABLE_FPZIP:BOOL=ON -DSILO_ZLIB_DIR:PATH="/Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/zlib/1.3.1/darwin-arm64" ../Silo-4.12.0
bash bv_run_cmake.sh
-- The CXX compiler identification is AppleClang 17.0.0.17000404
-- The C compiler identification is AppleClang 17.0.0.17000404
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
CMake Error at /Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/cmake/3.31.8/darwin-arm64/share/cmake-3.31/Modules/FindPackageHandleStandardArgs.cmake:233 (message):
  Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND)
Call Stack (most recent call first):
  /Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/cmake/3.31.8/darwin-arm64/share/cmake-3.31/Modules/FindPackageHandleStandardArgs.cmake:603 (_FPHSA_FAILURE_MESSAGE)
  /Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/cmake/3.31.8/darwin-arm64/share/cmake-3.31/Modules/FindMPI.cmake:1842 (find_package_handle_standard_args)
  /Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/hdf5/2.0.0/darwin-arm64/cmake/hdf5-config.cmake:120 (find_package)
  /Users/harrison37/Work/github/visit-dav/visit/build-mb-develop-darwin-22-arm64/thirdparty_shared/third_party/cmake/3.31.8/darwin-arm64/share/cmake-3.31/Modules/FindHDF5.cmake:513 (find_package)
  CMake/SiloFindHDF5.cmake:65 (find_package)
  CMakeLists.txt:229 (include)

cyrush · 2026-03-05T01:41:51Z

resolves #20727

…com:visit-dav/visit into feat-mcm86-04dec25-upd-hdf5-2.0-and-friends

Fix zlib fighting error by finding ZLib before MPI.

JustinPrivitera · 2026-03-07T01:51:24Z

src/config-site/dane1.cmake

+# Temporary install of these libs...
+# qt  szip  vtk  zlib
+SET(HDF52O_BUILD_TMP /g/g11/miller86/visit/visit/build-Xdmf/my_install)


Is this a public location?

Is this needed only for dane? Why is that?

Correct...not a public location. It was for when I was first building just a portion of the TPLs involving some kind of HDF5 dependence. I have a public install of all TPLs now in 3.5.0-hdf5200 and will update the daneX.cmake files for that shortly.

JustinPrivitera · 2026-03-07T01:52:17Z

src/config-site/rzwhippet10.cmake

-### NOTE: Modified from build_visit output
-#-------
-##
-## Turn on DDT support.
-##
-VISIT_OPTION_DEFAULT(VISIT_DDT ON TYPE BOOL)
-#-------
-


why turn DDT off now? Was this an oversight when copying the new config site in?

Good catch Justin. Will put this back. Thanks!

JustinPrivitera · 2026-03-07T01:56:17Z

src/databases/CarpetHDF5/avtCarpetHDF5FileFormat.C


   float** data = NULL;
-   int dims[3] = {1, 1, 1};
+   //int dims[3] = {1, 1, 1};


can we just delete this line instead of commenting it out?

I didn't want to because I wanted it to be consistent with other portions of the file where this same coding was used including a commented out identical line.

JustinPrivitera · 2026-03-07T01:56:53Z

src/databases/CosmosPP/avtCosmosPPFileFormat.C

        bounds[0] = (x < bounds[0] ? x : bounds[0]);
        bounds[1] = (x > bounds[1] ? x : bounds[1]);
-        float y = current_tmp[0];
+        float y = (rank > 1 ? current_tmp[1] : 0.0f);


why make this change?

I agree. I will revert. This was part of an AI assisted change to fix hid_t/int confusions and open/close pairings.

JustinPrivitera · 2026-03-07T01:57:18Z

src/databases/CosmosPP/avtCosmosPPFileFormat.C

    if (rank < 3)
-    {
-        bounds[4] = -(bounds[1]-bounds[0])*0.5;
-        bounds[5] = +(bounds[1]-bounds[0])*0.5;
-    }
-    else
    {
        // HACK!  The VTK point locator doesn't work very well with 2D objects,
        // so make this appear to be 3D by using the X-coordinate.
        bounds[4] = bounds[0];
        bounds[5] = bounds[1];
    }
+    else
+    {
+        bounds[4] = -(bounds[1]-bounds[0])*0.5;
+        bounds[5] = +(bounds[1]-bounds[0])*0.5;
+    }


why swap the if condition logic?

This is supposed to handle the case where there are less than 3 dimensions (rank < 3). Looking, neither the original nor my (AI assisted) swap makes sense. The original set the Z min to minus 1/2 the X range and the Z max to plus 1/2 the X range if there rank < 3 and set Z min to X min and Z max to X max when rank >= 3. Neither of those make sense to me but neither does reversing it.

JustinPrivitera · 2026-03-07T01:57:37Z

src/databases/Denovo/avtDenovoFileFormat.C

-        H5Dclose(coordMetaData[i].varId);
+        /*H5Dclose(coordMetaData[i].varId);*/


do we need to leave this comment or can we delete?

First, unfort. we have no test data for this plugin. I think this and a few other HDF5 plugins should be wholly removed. I don't think this is being used.

That said, the actual close for coordMetaData[i].varId I think occurs elsewhere (FreeUpResources or maybe the destructor). So, there should be a note there explaining why we don't close it here and I left it in commented to suggest that. But, lemme make that clearer

JustinPrivitera · 2026-03-07T01:58:51Z

src/databases/OpenPMD/OpenPMDClasses/PMDIteration.C

 				err = H5Oget_info_by_name(groupId,
 										objectName,
 										&objectInfo,
+                                                                                H5O_INFO_ALL,


formatting?

src/doc/building_visit/Building_Directly_With_CMake.rst

src/doc/getting_started/Installing_VisIt.rst

…com:visit-dav/visit into feat-mcm86-04dec25-upd-hdf5-2.0-and-friends

cyrush · 2026-03-09T18:43:00Z

Re DDT support, I am not sure it matters if we keep it on for rzwhippet.
We should discuss.

Co-authored-by: Justin Privitera <35237779+JustinPrivitera@users.noreply.github.com>

Ensure all hdf5-dependent libraries find/use the same zlib. Modified our Find zlib to use find_package(ZLIB). Replaced use of ZLIB_LIB in DataManualExamples to ZLIB_LIBRARY to match rest of VisIt.

Add zlib patch for silo. Tweak xdmf settings.

…com:visit-dav/visit into feat-mcm86-04dec25-upd-hdf5-2.0-and-friends

cyrush · 2026-03-11T02:56:40Z

Success!

markcmiller86 added 4 commits December 5, 2025 22:25

upd to version 2.0

020fc54

upd to 4.12.0; repl autotools w/cmake

3f3e415

fix for HDF5-2.0

c4dce63

fix for HDF5-2.0

8509801

biagas reviewed Dec 8, 2025

View reviewed changes

src/tools/dev/scripts/bv_support/bv_hdf5.sh Outdated Show resolved Hide resolved

biagas reviewed Dec 8, 2025

View reviewed changes

src/tools/dev/scripts/bv_support/bv_hdf5.sh Show resolved Hide resolved

make work with hdf5-2.0

a68bedd

markcmiller86 added 4 commits December 10, 2025 11:09

add comments

3eaf8c2

rm unnecessary CMakeLists.txt patch

47e867e

fix for HDF5-2.0

ee2312f

adj handling of HDF5 mpi dep

374173b

cyrush reviewed Dec 11, 2025

View reviewed changes

src/tools/dev/scripts/bv_support/bv_hdf5.sh Outdated Show resolved Hide resolved

fix zlib option

62618ea

markcmiller86 added 2 commits December 12, 2025 18:15

fix for HDF5-2.0

979b7e9

fix logic; imprv comment

ad857d6

imprv db-comment

6068fd3

markcmiller86 and others added 2 commits March 4, 2026 12:22

do not set MPI_HOME

af56f69

Update container tag.

11adfcf

markcmiller86 and others added 9 commits March 4, 2026 19:57

fix open/close pairings; int/hid_t confusions

e816f69

Merge branch 'feat-mcm86-04dec25-upd-hdf5-2.0-and-friends' of github.…

609afdf

…com:visit-dav/visit into feat-mcm86-04dec25-upd-hdf5-2.0-and-friends

fix int/hid_t

06357b0

add note about delayed startup

2d98131

discuss config-site contents

0f66aac

fix build error; add INCDEP remarks

7436a4e

fix spelling

6fd29c6

Modify CGNS/CFITSIO build_visit modules to use CMake.

acd834c

Fix zlib fighting error by finding ZLib before MPI.

Undo fix-for-zlib-fighting to get build working again.

6a242e2

JustinPrivitera requested changes Mar 7, 2026

View reviewed changes

markcmiller86 added 2 commits March 7, 2026 09:46

fix VTK libnames

3559e83

Merge branch 'feat-mcm86-04dec25-upd-hdf5-2.0-and-friends' of github.…

79a3538

…com:visit-dav/visit into feat-mcm86-04dec25-upd-hdf5-2.0-and-friends

markcmiller86 and others added 8 commits March 9, 2026 13:02

Apply suggestion from @JustinPrivitera

4f9fc19

Co-authored-by: Justin Privitera <35237779+JustinPrivitera@users.noreply.github.com>

Apply suggestion from @JustinPrivitera

040e235

Co-authored-by: Justin Privitera <35237779+JustinPrivitera@users.noreply.github.com>

Apply suggestion from @JustinPrivitera

1fc473c

Co-authored-by: Justin Privitera <35237779+JustinPrivitera@users.noreply.github.com>

Fix zlib-fighting issues with third party libraries.

19eaa39

Ensure all hdf5-dependent libraries find/use the same zlib. Modified our Find zlib to use find_package(ZLIB). Replaced use of ZLIB_LIB in DataManualExamples to ZLIB_LIBRARY to match rest of VisIt.

Update CFITSIO version in rzwhippet config-site.

a755a8a

Remove zlib patch from hdf5.

6723135

Add zlib patch for silo. Tweak xdmf settings.

Fix bounds changes

c706e45

Merge branch 'feat-mcm86-04dec25-upd-hdf5-2.0-and-friends' of github.…

c40c38b

…com:visit-dav/visit into feat-mcm86-04dec25-upd-hdf5-2.0-and-friends

cyrush merged commit a6c0c30 into develop Mar 11, 2026
7 checks passed

cyrush deleted the feat-mcm86-04dec25-upd-hdf5-2.0-and-friends branch March 11, 2026 02:57

This was referenced Mar 11, 2026

macOS engine_ser and engine_par appearing in dock #20840

Closed

Update to latest HDF5 and remove serial/parallel builds of various dependencies #20109

Closed

JustinPrivitera mentioned this pull request Mar 17, 2026

Upgrade to Silo 4.12 #20727

Closed

		H5Dclose(coordMetaData[i].varId);
		/H5Dclose(coordMetaData[i].varId);/

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How Has This Been Tested?

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