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Squashed 'src/externals/pio2/' changes from 7309b9b60..c77a30d95
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c77a30d95 Merge pull request ESMCI#1855 from jedwards4b/create_logfile_only_if_loglevel
983bd8e66 only create log files if log level > 0
989e026f5 Merge pull request ESMCI#1854 from jedwards4b/redef_from_def_test
7df2e2afe remove this test, no longer valid
360a360ac Merge pull request ESMCI#1852 from NCAR/ejh_readme
af9b0733a commented out test_async_1d
ca842d15a commented out test_async_1d
66132141f updating readme
5206ff4c5 updating readme
c6fd1755c updating readme
47f466fd1 updating readme
8b2f798a4 Merge pull request ESMCI#1851 from NCAR/ejh_cmake
4ea3f9362 turning on netcdf integration in cmake build
304b7296e Merge pull request ESMCI#1850 from NCAR/ejh_next_1
2123df499 turned test code back on
40d9637c2 Merge pull request ESMCI#1849 from NCAR/ejh_next
582d6f7b6 turned test code back off
0a41fbf89 turned test code back off
d7eb8207b turned test code back on
41ac8bc7f turned test code back on
2f90688c7 turned test code back on
9f6b1b5c9 fixed type size in async code
16b469d00 turning test code back on
268c69929 Merge pull request ESMCI#1848 from NCAR/ejh_preprocessor
558f24000 cleanup of automake and pre-processor symbols
e8a87005b removed pre-processor symbol USE_NETCDF4
77a31b1bc Merge pull request ESMCI#1844 from NCAR/ejh_no_pnetcdf_build
818eead20 commented out part of tst_async_multi
7b0b78b16 commented out part of tst_async_multi
41ea01e99 commented out part of tst_pio_async
388681f92 commented out part of test_async_1d
34f6b99db fixed no-pnetcdf workflow, renamed ubuntu latest workflow
463e37d4e adding new workflow
dddf14773 Merge pull request ESMCI#1843 from NCAR/ejh_warn
c95152b6e fixed warnings and netcdf-integration build without pnetcdf
2d0c61c2e Merge pull request ESMCI#1840 from NCAR/ejh_cmake_again_3
444c30dc4 fixing cmake workflow
b43e67e44 fixing cmake workflow
42366fb63 Merge pull request ESMCI#1836 from NCAR/ejh_cmake_again
dcaba92f8 changed test timeout in cmake
19570c281 fixed code warning, removed print statements from test
f632317cd make configure search for netcdf-fortran if --enable-fortran and --enable-netcdf-integration are used
57446873a debug test
9b5964267 add fortran build
c6912419b fix paths
3705bbdf2 adding fortran
f65e972e4 adding fortran
d914a8353 adding cmake build
9accccb00 Merge pull request ESMCI#1835 from NCAR/ejh_cmake_fortran_workflow
27d20a3be try a different cmake?
ee9fe1b61 giving up on cmake build for now
ebfb0e503 adding another cmake build
8fd204e80 adding another cmake build
219d72fb9 adding another cmake build
ed0304884 turned off fortran in cmake build
b56162ef1 fixed fortran test
5c34c279f turning on fortran build in cmake workflow
ee329568b Merge pull request ESMCI#1833 from NCAR/ejh_ncint_test_2
85f50f29d more testing
da6015c2c Merge pull request ESMCI#1831 from NCAR/ejh_ncint_test
11959c931 fixing ncint test for 4.7.4 by commenting out code
8dbde41a0 fixed comment
ccbb2302f fix test_darray_multivar3.c
7172df901 turning on netcdf integration in workflow
e53623410 Merge pull request ESMCI#1826 from NCAR/ejh_test_more
1eb5a219d working on workflows
40ce8ea26 switching to pnetcdf-1.12.2
593e85371 adding testing
0f0558ffe adding testing
0f3502fa0 adding testing
862538461 Merge pull request ESMCI#1823 from NCAR/ejh_more_tests
71a695cba working on asan build
70066f238 working on asan build
b5801cd8b working on asan build
8fd651963 working on asan build
a679c5bd5 adding testing with hdf5-1.10.7
3308d5e93 renamed workflow files to reduce confusion
f34ef23a9 merged master
0887324d4 fixed warnings, trying to get asan workflow to build
6947e3114 Merge branch 'master' into ejh_more_tests
d862880a7 added asan testing
e341609e3 Merge pull request ESMCI#1821 from NCAR/ejh_test_on
1464bf0a4 Merge branch 'master' into ejh_test_on
ef34338ae fixed test_darray_multivar3.c
2d6de331b fixed test_darray_multivar3.c
1ef9493f0 Merge pull request ESMCI#1820 from NCAR/ejh_default_blocksize
9e492a483 changed default blocksize
36eba03fa Merge pull request ESMCI#1817 from NCAR/ejh_docs
c7b3010cc documentation improvements
082fc0f32 documentation improvements
cacb65e7b documentation improvements
9548daac5 fixed warnings in code
4200f55a1 Merge pull request ESMCI#1809 from NCAR/ejh_perf_more
ce23930d6 now setting chunksizes for netcdf4 performance runs
f59373773 whitespace cleanup
6f7a1dcdf fixed mpe problem in test_simple.c
9a669de89 modification to perf program output
9abd0ca71 Merge pull request ESMCI#1806 from NCAR/ejh_perf
329ef8f2d cleanup
9f912f859 merged master
be3b13f22 fixes to test_perf2.c
84511247c Merge pull request ESMCI#1805 from NCAR/ejh_fix_test
5df3c5dc6 whitespace cleanup
118e44a76 better async error handling in tests
57c03b9c3 whitespace cleanup
379983a92 more fixes for async test error handling
9bdf340a2 more work on async error handling
25d5bf4f0 more work on async error handling
3b550c794 more work on async error handling
f83540176 more work on async error handling
bb6adea7f fixed comment
b44d3237c better handling for test failure in async tests
40da636a3 added AERR() macro for errors on async tests
d8ec81a98 fixed comment
9cec790f1 fixed whitespace issues in pio_error.h
d14471895 fix printing of some incorrect error codes in cunit tests
9dad4e97a Merge pull request ESMCI#1802 from jedwards4b/avoid_msg_starving
e6fc3e00b clean up test
90f497c14 change waitany to waitsome to avoid message starving
53bdadcbf Merge pull request ESMCI#1800 from NCAR/ejh_docs_2
dd1b8d038 updated documentation and cleaned unneeded preprocessor symbols from test_perf2 and test_async_perf
5d0f8a5b0 Merge pull request ESMCI#1799 from NCAR/ejh_t1
eec9e0b50 stop running test_async_perf with other CMakeList.txt tests
c254d12f0 turned off logging in test
e86c55cb6 try reducing the size of this test
358e71917 document new error code
b51b8324c move large allocate from stack
4f01bc28b fix test
570abae1e add error for rearranger mismatch in async mode
564a15116 fix async_perf test
860f6f99f Merge branch 'more_async_tests' of github.com:jedwards4b/ParallelIO into more_async_tests
a8493e337 add test_async_perf to cmake build
66564a550 Merge branch 'master' into more_async_tests
5852d9093 Merge pull request ESMCI#1765 from t-brown/master
40da5e29c add SUBSET rearranger
d741f3700 Merge branch 'master' into master
1a3fa8630 Merge pull request ESMCI#1794 from NCAR/ejh_fix_perf
2184073b0 Merge branch 'master' into master
2a2a08dad turned off subset rearrarger in test_async_perf
b51f6768c more improvements to performance programs
6a29e16eb merged master
f0a9c0ad1 fixing test_async_perf
5ca0b5586 Merge pull request ESMCI#1791 from jedwards4b/async_subset
6b08ffb66 now test both rearrangers in tst_perf2
d956b7904 added commas to output
7e385d133 fix test
bbe58daf7 add tests
c8f91fbca subset working in async
744b73163 Merge pull request ESMCI#1790 from jedwards4b/add_nf_pio
bbb9ed716 remove need for netcdf or pnetcdf fortran libs
53d652ed8 add netcdf fortran build
5d1ca6791 add nf_pio, netcdf now defines cdf5 format
8a0cb4f84 Merge pull request ESMCI#1786 from jedwards4b/sort_only_on_compute
3d49f3008 array sort should only happen on compute tasks
7f28489f5 Merge pull request ESMCI#1784 from jedwards4b/add_async_get_att_test
4b79b0203 add new function to include file
15921d6ff fix documentation biff
d937cc331 add global_set_log_level, fix issue
5cd85396f add async test for get_att - test currently timesout
38d9acda5 Merge pull request ESMCI#1782 from jedwards4b/async_fixes
ffe4098c1 move malloc to correct location
e05d8f2b0 remove unneeded change
7806081b4 changes for async interface
7e242f78b Merge pull request ESMCI#1781 from jedwards4b/with_pnetcdf_cmake
6c4d85875 use WITH_PNETCDF in CMake build
f960b3799 Merge branch 'master' into master
1d0dabdf3 Merge pull request ESMCI#1778 from jedwards4b/add_pio_init_async_from_comms
1de5ded13 Merge branch 'add_pio_init_async_from_comms' of github.com:jedwards4b/ParallelIO into add_pio_init_async_from_comms
7a52d1d9d try this
875966b5b fix mem issue
60f9f17f3 fix documentation
f63773317 remove .f90.in from gitignore file, add tests
cf09cd22d remove unused var
7f28e28cf fix Makefile.am
8af4d74d9 try again
2d3cb219a fix test generation issue
4a012a898 add test to autoconf
155c11dee fix line length issue
01e9e31dd add async test from fortran
bcc711331 remove set_log_level from test
8f10a32a2 remove debug print
ea404f6b3 add PIOc_init_async_from_comms and test
53c5a2c23 Merge pull request ESMCI#1776 from jedwards4b/update_f_examples
0f5da9dc3 Merge branch 'master' into update_f_examples
a8acfd49d more doc cleanup
cad018af7 more documentation and refinment
4fd48cfce add some documentation
9e999911c correct ranks in async
0f65ecc0d cleanup
a27009b57 working example from fortran
81c778517 Merge pull request ESMCI#1774 from jedwards4b/unique_name_err_buffer
e079cb408 make example resultlen distinct names from that in pio_error.h
c30ff49c5 make example err_buffers distinct names from that in pio_error.h
e26c200c2 work on async interface
092a618ee begin work on fortran async interface
66449308c Merge branch 'master' into master
364a445bf Adding an autoconf check for C99.

git-subtree-dir: src/externals/pio2
git-subtree-split: c77a30d95d4814470f569b332cadeb0dea32414f
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jedwards4b committed Feb 17, 2021
1 parent 4d93f87 commit 80c0b75
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2 changes: 1 addition & 1 deletion .github/workflows/cmake.yml
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ jobs:
sudo apt-spy2 fix --commit
# after selecting a specific mirror, we need to run 'apt-get update'
sudo apt-get update
sudo apt-get install netcdf-bin libnetcdf-dev doxygen graphviz wget gfortran libjpeg-dev libz-dev openmpi-bin libopenmpi-dev
sudo apt-get install netcdf-bin libnetcdf-dev doxygen graphviz wget gfortran libjpeg-dev libz-dev openmpi-bin libopenmpi-dev cmake
- name: cache-pnetcdf
id: cache-pnetcdf
Expand Down
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@@ -0,0 +1,135 @@
name: cmake_netcdf-4.7.4_hdf5-1.10.7_pnetcdf-12.1_ncint_mpich-3.3

on:
push:
branches: [ master ]
pull_request:
branches: [ master ]

jobs:
build:

runs-on: ubuntu-latest

env:
CPPFLAGS: "-I/home/runner/mpich/include -I/home/runner/hdf5/include -I/home/runner/netcdf-c/include -I/home/runner/netcdf-fortran/include -I/home/runner/pnetcdf/include"
LDFLAGS: "-L/home/runner/mpich/lib -L/home/runner/hdf5/lib -L/home/runner/netcdf-c/lib -L/home/runner/netcdf-fortran/lib -L/home/runner/pnetcdf/lib"

steps:
- uses: actions/checkout@v2
- name: Installs
run: |
sudo apt-get install doxygen graphviz wget gfortran libjpeg-dev libz-dev cmake gfortran
- name: cache-mpich
id: cache-mpich
uses: actions/cache@v2
with:
path: ~/mpich
key: mpich-${{ runner.os }}-3.3.2

- name: build-mpich
if: steps.cache-mpich.outputs.cache-hit != 'true'
run: |
wget http://www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz &> /dev/null
tar -xzf mpich-3.3.2.tar.gz
pushd mpich-3.3.2
./configure --prefix=/home/runner/mpich
make
sudo make install
popd
- name: cache-hdf5
id: cache-hdf5
uses: actions/cache@v2
with:
path: ~/hdf5
key: hdf5-${{ runner.os }}-1.10.7-mpich-3.3.2

- name: build-hdf5
if: steps.cache-hdf5.outputs.cache-hit != 'true'
run: |
set -x
export PATH="/home/runner/mpich/bin:$PATH"
export CC=/home/runner/mpich/bin/mpicc
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.7/src/hdf5-1.10.7.tar.gz &> /dev/null
tar -xzf hdf5-1.10.7.tar.gz
pushd hdf5-1.10.7
./configure --prefix=/home/runner/hdf5 --enable-parallel --disable-tools --disable-fortran --disable-cxx --enable-parallel-tests
make
sudo make install
popd
- name: cache-netcdf-c
id: cache-netcdf-c
uses: actions/cache@v2
with:
path: ~/netcdf-c
key: netcdf-c-${{ runner.os }}-4.7.4-mpich-3.3.2-2

- name: build-netcdf-c
if: steps.cache-netcdf-c.outputs.cache-hit != 'true'
run: |
set -x
export PATH="/home/runner/mpich/bin:$PATH"
export CC=/home/runner/mpich/bin/mpicc
wget https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-c-4.7.4.tar.gz &> /dev/null
tar -xzf netcdf-c-4.7.4.tar.gz
pushd netcdf-c-4.7.4
./configure --prefix=/home/runner/netcdf-c --disable-dap --disable-utilities
make -j
sudo make install
popd
- name: cache-netcdf-fortran
id: cache-netcdf-fortran
uses: actions/cache@v2
with:
path: ~/netcdf-fortran
key: netcdf-fortran-${{ runner.os }}-4.5.3-mpich-3.3.2-2

- name: build-netcdf-fortran
if: steps.cache-netcdf-fortran.outputs.cache-hit != 'true'
run: |
set -x
export PATH="/home/runner/mpich/bin:$PATH"
export CC=/home/runner/mpich/bin/mpicc
wget https://github.com/Unidata/netcdf-fortran/archive/v4.5.3.tar.gz &> /dev/null
tar -xzf v4.5.3.tar.gz
pushd netcdf-fortran-4.5.3
./configure --prefix=/home/runner/netcdf-fortran
make -j
sudo make install
popd
- name: cache-pnetcdf
id: cache-pnetcdf
uses: actions/cache@v2
with:
path: ~/pnetcdf
key: pnetcdf-${{ runner.os }}-1.12.1-mpich-3.3.2

- name: build-pnetcdf
if: steps.cache-pnetcdf.outputs.cache-hit != 'true'
run: |
set -x
export PATH="/home/runner/mpich/bin:$PATH"
export CC=/home/runner/mpich/bin/mpicc
wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz &> /dev/null
tar -xzf pnetcdf-1.12.1.tar.gz
pushd pnetcdf-1.12.1
./configure --prefix=/home/runner/pnetcdf --enable-shared --disable-cxx
make
sudo make install
popd
- name: cmake build
run: |
set -x
ls -l
echo 'export PATH=/home/runner/mpich/bin:$PATH' > .bashrc
source .bashrc
export CC=/home/runner/mpich/bin/mpicc
export FC=/home/runner/mpich/bin/mpifort
export LD_LIBRARY_PATH=/home/runner/netcdf-c/lib:/home/runner/pnetcdf/lib:$LD_LIBRARY_PATH
rm -rf b1
mkdir b1
cd b1
cmake -Wno-dev -DPIO_ENABLE_NETCDF_INTEGRATION=On -DNetCDF_C_LIBRARY=/home/runner/netcdf-c/lib/libnetcdf.so -DNetCDF_C_INCLUDE_DIR=/home/runner/netcdf-c/include -DPnetCDF_PATH=/home/runner/pnetcdf -DPIO_ENABLE_FORTRAN=On -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off -DNetCDF_Fortran_LIBRARY=/home/runner/netcdf-fortran/lib/libnetcdff.so -DNetCDF_Fortran_INCLUDE_DIR=/home/runner/netcdf-fortran/include ..
make VERBOSE=1
make tests VERBOSE=1
ctest -VV
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@@ -0,0 +1,149 @@
name: netcdf-4.7.4_hdf5-1.10.7_pnetcdf-12.1_ncint_mpich-3.3_asan

on:
push:
branches: [ master ]
pull_request:
branches: [ master ]

jobs:
build:

runs-on: ubuntu-latest

env:
CPPFLAGS: "-I/home/runner/mpich/include -I/home/runner/hdf5/include -I/home/runner/netcdf-c/include -I/home/runner/netcdf-fortran/include -I/home/runner/pnetcdf/include"
LDFLAGS: "-L/home/runner/mpich/lib -L/home/runner/hdf5/lib -L/home/runner/netcdf-c/lib -L/home/runner/netcdf-fortran/lib -L/home/runner/pnetcdf/lib"

steps:
- uses: actions/checkout@v2
- name: Installs
run: |
sudo apt-get install doxygen graphviz wget gfortran libjpeg-dev libz-dev
- name: cache-mpich
id: cache-mpich
uses: actions/cache@v2
with:
path: ~/mpich
key: mpich-${{ runner.os }}-3.3.2

- name: build-mpich
if: steps.cache-mpich.outputs.cache-hit != 'true'
run: |
wget http://www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz &> /dev/null
tar -xzf mpich-3.3.2.tar.gz
pushd mpich-3.3.2
./configure --prefix=/home/runner/mpich
make
sudo make install
popd
- name: cache-hdf5
id: cache-hdf5
uses: actions/cache@v2
with:
path: ~/hdf5
key: hdf5-${{ runner.os }}-1.10.7-mpich-3.3.2

- name: build-hdf5
if: steps.cache-hdf5.outputs.cache-hit != 'true'
run: |
set -x
export PATH="/home/runner/mpich/bin:$PATH"
export CC=/home/runner/mpich/bin/mpicc
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.7/src/hdf5-1.10.7.tar.gz &> /dev/null
tar -xzf hdf5-1.10.7.tar.gz
pushd hdf5-1.10.7
./configure --prefix=/home/runner/hdf5 --enable-parallel --disable-tools --disable-fortran --disable-cxx --enable-parallel-tests
make
sudo make install
popd
- name: cache-netcdf-c
id: cache-netcdf-c
uses: actions/cache@v2
with:
path: ~/netcdf-c
key: netcdf-c-${{ runner.os }}-4.7.4-mpich-3.3.2-2

- name: build-netcdf-c
if: steps.cache-netcdf-c.outputs.cache-hit != 'true'
run: |
set -x
export PATH="/home/runner/mpich/bin:$PATH"
export CC=/home/runner/mpich/bin/mpicc
wget https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-c-4.7.4.tar.gz &> /dev/null
tar -xzf netcdf-c-4.7.4.tar.gz
pushd netcdf-c-4.7.4
./configure --prefix=/home/runner/netcdf-c --disable-dap --disable-utilities
make -j
sudo make install
popd
- name: cache-netcdf-fortran
id: cache-netcdf-fortran
uses: actions/cache@v2
with:
path: ~/netcdf-fortran
key: netcdf-fortran-${{ runner.os }}-4.5.3-mpich-3.3.2-2

- name: build-netcdf-fortran
if: steps.cache-netcdf-fortran.outputs.cache-hit != 'true'
run: |
set -x
export PATH="/home/runner/mpich/bin:$PATH"
export CC=/home/runner/mpich/bin/mpicc
wget https://github.com/Unidata/netcdf-fortran/archive/v4.5.3.tar.gz &> /dev/null
tar -xzf v4.5.3.tar.gz
pushd netcdf-fortran-4.5.3
./configure --prefix=/home/runner/netcdf-fortran
make -j
sudo make install
popd
- name: cache-pnetcdf
id: cache-pnetcdf
uses: actions/cache@v2
with:
path: ~/pnetcdf
key: pnetcdf-${{ runner.os }}-1.12.1-mpich-3.3.2

- name: build-pnetcdf
if: steps.cache-pnetcdf.outputs.cache-hit != 'true'
run: |
set -x
export PATH="/home/runner/mpich/bin:$PATH"
export CC=/home/runner/mpich/bin/mpicc
wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz &> /dev/null
tar -xzf pnetcdf-1.12.1.tar.gz
pushd pnetcdf-1.12.1
./configure --prefix=/home/runner/pnetcdf --enable-shared --disable-cxx
make
sudo make install
popd
- name: cmake build
run: |
set -x
gcc --version
echo 'export PATH=/home/runner/mpich/bin:$PATH' > .bashrc
source .bashrc
export CC=/home/runner/mpich/bin/mpicc
export FC=/home/runner/mpich/bin/mpifort
export LD_LIBRARY_PATH="/home/runner/netcdf-c/lib:/home/runner/mpich/lib:/home/runner/hdf5/lib:/home/runner/netcdf-fortran/lib:/home/runner/pnetcdf/lib:$LD_LIBRARY_PATH"
mkdir build
cd build
cmake -Wno-dev -DNetCDF_C_LIBRARY=/home/runner/netcdf-c/lib/libnetcdf.so -DNetCDF_C_INCLUDE_DIR=/home/runner/netcdf-c/include -DPnetCDF_PATH='/home/runner/pnetcdf' -DPIO_ENABLE_FORTRAN=Off -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off .. || (cat CMakeFiles/CMakeOutput.log && cat CMakeFiles/CMakeError.log)
make VERBOSE=1
make tests VERBOSE=1
# ctest -VV
- name: autotools build
run: |
set -x
gcc --version
echo 'export PATH=/home/runner/mpich/bin:$PATH' > .bashrc
source .bashrc
export CC=/home/runner/mpich/bin/mpicc
export FC=/home/runner/mpich/bin/mpifort
export CFLAGS="-fsanitize=address -fno-omit-frame-pointer"
export FCFLAGS="-fsanitize=address -fno-omit-frame-pointer"
autoreconf -i
./configure --enable-fortran --enable-netcdf-integration
make -j check
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