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Update AMReX, E3SM, and OpenPMD submodules #104

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merged 11 commits into from
Jul 20, 2023
Merged

Update AMReX, E3SM, and OpenPMD submodules #104

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b30597d
update AMReX, E3SM, and OpenPMD submodules
jeanbez Jun 14, 2023
5020091
Merge branch 'master' into update-dependencies
jeanbez Jul 11, 2023
f71c933
bump OpenPMD version
jeanbez Jul 17, 2023
a934a13
update OpenPMD library
jeanbez Jul 18, 2023
0b8dce5
update OpenPMD integration with library installation
jeanbez Jul 18, 2023
ac69016
Merge branch 'master' into update-dependencies
jeanbez Jul 18, 2023
5bc71f0
update library path configuration
jeanbez Jul 18, 2023
4c09693
update CI
jeanbez Jul 18, 2023
cc578af
update path
jeanbez Jul 19, 2023
58b803c
ensure sufficient permissions
jeanbez Jul 19, 2023
af4cc3f
ensure enough permission is given
jeanbez Jul 19, 2023
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1 change: 1 addition & 0 deletions .github/workflows/h5bench-hdf5-1.10.4.yml
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Expand Up @@ -40,6 +40,7 @@ jobs:
-DH5BENCH_ALL=ON
make -j 2
make install
ldconfig

- name: Test h5bench SYNC write/read
run: |
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1 change: 1 addition & 0 deletions .github/workflows/h5bench-hdf5-1.10.7.yml
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Expand Up @@ -40,6 +40,7 @@ jobs:
-DH5BENCH_ALL=ON
make -j 2
make install
ldconfig

- name: Test h5bench SYNC write/read
run: |
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1 change: 1 addition & 0 deletions .github/workflows/h5bench-hdf5-1.10.8.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@ jobs:
-DH5BENCH_ALL=ON
make -j 2
make install
ldconfig

- name: Test h5bench SYNC write/read
run: |
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1 change: 1 addition & 0 deletions .github/workflows/h5bench-hdf5-1.12.0.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@ jobs:
-DH5BENCH_ALL=ON
make -j 2
make install
ldconfig

- name: Test h5bench SYNC write/read
run: |
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6 changes: 4 additions & 2 deletions .github/workflows/h5bench-hdf5-1.14.0.yml
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Expand Up @@ -87,7 +87,8 @@ jobs:
cmake .. \
-DH5BENCH_ALL=ON
make -j 2
make install
sudo make install
ldconfig

- name: Build h5bench ASYNC
run: |
Expand All @@ -105,7 +106,8 @@ jobs:
-DCMAKE_C_FLAGS="-I$ASYNC_HOME/include -L$ASYNC_HOME/lib" \
-DH5BENCH_ALL=ON
make -j 2
make install
sudo make install
ldconfig

- name: Test h5bench SYNC write/read
run: |
Expand Down
7 changes: 5 additions & 2 deletions .github/workflows/h5bench-hdf5-1.14.1.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,8 @@ jobs:
cmake .. \
-DH5BENCH_ALL=ON
make -j 2
make install
sudo make install
ldconfig

- name: Build h5bench ASYNC
run: |
Expand All @@ -105,7 +106,9 @@ jobs:
-DCMAKE_C_FLAGS="-I$ASYNC_HOME/include -L$ASYNC_HOME/lib" \
-DH5BENCH_ALL=ON
make -j 2
make install
sudo make install
ldconfig

- name: Test h5bench SYNC write/read
run: |
export LD_LIBRARY_PATH=/opt/hdf5/lib:$LD_LIBRARY_PATH
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2 changes: 2 additions & 0 deletions .github/workflows/h5bench-hdf5-develop-test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -104,6 +104,7 @@ jobs:
-DH5BENCH_ALL=ON
make -j 2
sudo make install
sudo ldconfig

- name: Build h5bench ASYNC
run: |
Expand All @@ -122,6 +123,7 @@ jobs:
-DH5BENCH_ALL=ON
make -j 2
sudo make install
sudo ldconfig

- name: Test h5bench SYNC
run: |
Expand Down
2 changes: 2 additions & 0 deletions .github/workflows/h5bench-hdf5-develop.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -102,6 +102,7 @@ jobs:
-DH5BENCH_ALL=ON
make -j 2
sudo make install
sudo ldconfig

- name: Build h5bench ASYNC
run: |
Expand All @@ -122,6 +123,7 @@ jobs:
-DH5BENCH_ALL=ON
make -j 2
sudo make install
sudo ldconfig

- name: Test h5bench SYNC write/read
run: |
Expand Down
9 changes: 8 additions & 1 deletion CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -244,7 +244,7 @@ if(H5BENCH_OPENPMD)
set(openPMD_USE_ADIOS2 OFF)
set(openPMD_USE_JSON OFF)
set(openPMD_USE_PYTHON OFF)
set(openPMD_INSTALL OFF)
set(openPMD_INSTALL ON)
set(openPMD_BUILD_TESTING OFF)
set(openPMD_BUILD_EXAMPLES OFF)
set(openPMD_BUILD_CLI_TOOLS OFF)
Expand Down Expand Up @@ -370,6 +370,13 @@ if(H5BENCH_METADATA)
endif()

if(H5BENCH_OPENPMD)
install(
TARGETS
openPMD
LIBRARY
DESTINATION lib
)

install(
TARGETS
h5bench_openpmd_write
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2 changes: 1 addition & 1 deletion amrex
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Submodule amrex updated 1028 files
2 changes: 1 addition & 1 deletion e3sm
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Submodule e3sm updated 47 files
+249 −0 .github/workflows/cache_async_vol.yml
+39 −30 .github/workflows/logvol_master.yml
+41 −32 .github/workflows/mpich_static.yml
+43 −32 .github/workflows/ubuntu_ompi.yml
+2 −1 Makefile.am
+93 −35 README.md
+6 −0 cache.cfg
+74 −43 configure.ac
+5 −1 datasets/README.md
+ − datasets/map_i_case_16p.bp
+ − datasets/map_i_case_16p.h5
+ − datasets/map_i_case_16p.nc
+ − datasets/map_i_case_16p.nc4
+5 −5 docs/BLOB_IO.md
+139 −105 docs/INSTALL.md
+ − docs/cori_07192022.jpg
+ − docs/summit_09_2022.jpg
+36 −1 docs/variables.md
+18 −19 src/Makefile.am
+2 −2 src/cases/e3sm_io_case.cpp
+1 −0 src/cases/e3sm_io_case.hpp
+16 −3 src/cases/header_def_F_case.cpp
+2 −2 src/cases/header_def_G_case.cpp
+2 −2 src/cases/header_def_I_case.cpp
+14 −8 src/cases/report_timing.cpp
+57 −34 src/cases/scorpio_wrapper.cpp
+19 −4 src/cases/var_wr_case.cpp
+5 −5 src/drivers/e3sm_io_driver_adios2.cpp
+8 −16 src/drivers/e3sm_io_driver_h5blob.cpp
+2 −1 src/drivers/e3sm_io_driver_h5blob.hpp
+197 −94 src/drivers/e3sm_io_driver_hdf5.cpp
+1 −1 src/drivers/e3sm_io_driver_hdf5.hpp
+78 −14 src/drivers/e3sm_io_driver_hdf5_log.cpp
+18 −21 src/drivers/e3sm_io_driver_hdf5_md.cpp
+156 −59 src/e3sm_io.c
+6 −0 src/e3sm_io.h
+60 −36 src/e3sm_io_profile.m4
+10 −0 src/e3sm_io_profile.m4h
+5 −0 src/e3sm_io_profile_timers.m4
+26 −10 src/read_decomp.cpp
+53 −16 test.sh
+101 −0 tests/select_or.c
+8 −2 utils/Makefile.am
+14 −14 utils/README.md
+17 −108 utils/bpstat.cpp
+180 −0 utils/map_stat.c
+2 −2 utils/wrap_runs.sh
2 changes: 1 addition & 1 deletion openpmd
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Submodule openpmd updated 358 files