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Merge branch 'master' into jedwards/cmake_piolibsettings
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@edwardhartnett
edwardhartnett authored Jul 29, 2020
2 parents 1c70406 + 72186bb commit 047e557
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Showing 6 changed files with 120 additions and 75 deletions.
4 changes: 0 additions & 4 deletions .github/workflows/autotools.yml
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Expand Up @@ -40,9 +40,5 @@ jobs:
run: autoreconf -i
- name: configure
run: ./configure
- name: make
run: make
- name: make check
run: make check
- name: make distcheck
run: make distcheck
46 changes: 46 additions & 0 deletions .github/workflows/strict_autotools.yml
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@@ -0,0 +1,46 @@
name: strict_autotools

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

jobs:
build:

runs-on: ubuntu-latest

env:
CC: mpicc
FC: mpifort
CPPFLAGS: "-I/usr/include -I/usr/local/include"
DISTCHECK_CONFIGURE_FLAGS: "--enable-fortran"

steps:
- uses: actions/checkout@v2
- name: Installs
run: |
sudo apt-get install netcdf-bin libnetcdf-dev doxygen graphviz wget gfortran libjpeg-dev libz-dev openmpi-bin libopenmpi-dev
- name: pnetcdf build
run: |
wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz
tar -xzvf pnetcdf-1.12.1.tar.gz
ls -l
pushd pnetcdf-1.12.1
./configure --prefix=/usr --enable-shared
make
sudo make install
popd
- name: autoreconf
run: autoreconf -i
- name: configure
run: ./configure
env:
CFLAGS: "-std=c99 -fsanitize=address -fno-omit-frame-pointer -Werror"
# FFLAGS: "-fsanitize=address -fno-omit-frame-pointer"
# FCFLAGS: "-fsanitize=address -fno-omit-frame-pointer -Werror"
- name: make -j distcheck
run: make -j distcheck
2 changes: 1 addition & 1 deletion src/clib/pio_msg.c
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Expand Up @@ -779,7 +779,7 @@ int put_vars_handler(iosystem_desc_t *ios)
if (start_present)
if ((mpierr = MPI_Bcast(start, ndims, MPI_OFFSET, 0, ios->intercomm)))
return check_mpi(ios, NULL, mpierr, __FILE__, __LINE__);
PLOG((1, "put_vars_handler getting start[0] = %d ndims = %d", start[0], ndims));
/* PLOG((1, "put_vars_handler getting start[0] = %d ndims = %d", start[0], ndims)); */
if ((mpierr = MPI_Bcast(&count_present, 1, MPI_CHAR, 0, ios->intercomm)))
return check_mpi(ios, NULL, mpierr, __FILE__, __LINE__);
if (count_present)
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8 changes: 4 additions & 4 deletions tests/cunit/CMakeLists.txt
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Expand Up @@ -259,10 +259,10 @@ else ()
EXECUTABLE ${CMAKE_CURRENT_BINARY_DIR}/test_darray_multivar2
NUMPROCS ${AT_LEAST_FOUR_TASKS}
TIMEOUT ${DEFAULT_TEST_TIMEOUT})
add_mpi_test(test_darray_multivar3
EXECUTABLE ${CMAKE_CURRENT_BINARY_DIR}/test_darray_multivar3
NUMPROCS ${AT_LEAST_FOUR_TASKS}
TIMEOUT ${DEFAULT_TEST_TIMEOUT})
# add_mpi_test(test_darray_multivar3
# EXECUTABLE ${CMAKE_CURRENT_BINARY_DIR}/test_darray_multivar3
# NUMPROCS ${AT_LEAST_FOUR_TASKS}
# TIMEOUT ${DEFAULT_TEST_TIMEOUT})
add_mpi_test(test_darray_1d
EXECUTABLE ${CMAKE_CURRENT_BINARY_DIR}/test_darray_1d
NUMPROCS ${AT_LEAST_FOUR_TASKS}
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3 changes: 2 additions & 1 deletion tests/cunit/run_tests.sh
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Expand Up @@ -10,11 +10,12 @@ trap exit INT TERM

printf 'running PIO tests...\n'

# test_darray_multivar3
PIO_TESTS='test_intercomm2 test_async_mpi test_spmd test_rearr test_async_simple '\
'test_async_3proc test_async_4proc test_iosystem2_simple test_iosystem2_simple2 '\
'test_iosystem2 test_iosystem3_simple test_iosystem3_simple2 test_iosystem3 test_pioc '\
'test_pioc_unlim test_pioc_putget test_pioc_fill test_darray test_darray_multi '\
'test_darray_multivar test_darray_multivar2 test_darray_multivar3 test_darray_1d '\
'test_darray_multivar test_darray_multivar2 test_darray_1d '\
'test_darray_3d test_decomp_uneven test_decomps test_darray_async_simple '\
'test_darray_async test_darray_async_many test_darray_2sync test_async_multicomp '\
'test_darray_fill test_darray_vard test_async_1d test_darray_append'
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132 changes: 67 additions & 65 deletions tests/cunit/test_darray_multivar3.c
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Expand Up @@ -78,21 +78,22 @@ int test_multivar_darray(int iosysid, int ioid, int num_flavors, int *flavor,
int custom_fillvalue_int = -TEST_VAL_42;
float custom_fillvalue_float = -42.5;
int test_data_int[arraylen];
float test_data_float[arraylen];
/* float test_data_float[arraylen]; */
int ret; /* Return code. */

/* Initialize some data. */
for (int f = 0; f < arraylen; f++)
{
test_data_int[f] = my_rank * 10 + f;
test_data_float[f] = my_rank * 10 + f + 0.5;
/* test_data_float[f] = my_rank * 10 + f + 0.5; */
}

/* Use PIO to create the example file in each of the four
* available ways. */
for (int fmt = 0; fmt < num_flavors; fmt++)
{
for (int use_fv = 0; use_fv < NUM_FV_TESTS; use_fv++)
/* for (int use_fv = 0; use_fv < NUM_FV_TESTS; use_fv++) */
for (int use_fv = 0; use_fv < 1; use_fv++)
{
/* Create the filename. */
sprintf(filename, "data_%s_iotype_%d_use_fv_%d.nc", TEST_NAME, flavor[fmt], use_fv);
Expand Down Expand Up @@ -150,78 +151,79 @@ int test_multivar_darray(int iosysid, int ioid, int num_flavors, int *flavor,

/* This should not work since we cannot mix record and not
* record vars. */
int frame[NUM_VAR] = {0, 0, 0};
/* int frame[NUM_VAR] = {0, 0, 0}; */

if (PIOc_write_darray_multi(ncid, varid, ioid, NUM_VAR, arraylen * NUM_VAR, test_data_float,
frame, NULL, 0) != PIO_EVARDIMMISMATCH)
ERR(ERR_WRONG);
/* if (PIOc_write_darray_multi(ncid, varid, ioid, NUM_VAR, arraylen * NUM_VAR, test_data_float, */
/* frame, NULL, 0) != PIO_EVARDIMMISMATCH) */
/* ERR(ERR_WRONG); */

/* This should work since int and float are the same size
* and both are record vars. */
if ((ret = PIOc_write_darray_multi(ncid, varid+1, ioid, NUM_VAR-1, arraylen * (NUM_VAR-1), test_data_float,
frame, NULL, 0)))
ERR(ret);
/* if ((ret = PIOc_write_darray_multi(ncid, varid+1, ioid, NUM_VAR-1, arraylen * (NUM_VAR-1), test_data_float, */
/* frame, NULL, 0))) */
/* ERR(ret); */

/* Close the netCDF file. */
if ((ret = PIOc_closefile(ncid)))
ERR(ret);

/* Check the file contents. */
/* { */
/* int ncid2; /\* The ncid of the re-opened netCDF file. *\/ */
/* int test_data_int_in[arraylen]; */
/* /\* float test_data_float_in[arraylen]; *\/ */

/* /\* Reopen the file. *\/ */
/* if ((ret = PIOc_openfile(iosysid, &ncid2, &flavor[fmt], filename, PIO_NOWRITE))) */
/* ERR(ret); */

/* /\* Read the var data with read_darray(). *\/ */
/* for (int v = 0; v < NUM_VAR; v++) */
/* { */
/* if (v < NUM_VAR - 1) */
/* { */
/* if ((ret = PIOc_setframe(ncid2, varid[v], 0))) */
/* ERR(ret); */

/* /\* Read the data. *\/ */
/* if ((ret = PIOc_read_darray(ncid2, varid[v], ioid, arraylen, test_data_int_in))) */
/* ERR(ret); */

/* /\* Check the results. *\/ */
/* for (int f = 0; f < arraylen; f++) */
/* if (test_data_int_in[f] != test_data_int[f]) */
/* return ERR_WRONG; */
/* } */
/* } /\* next var *\/ */

/* /\* Now read the fill values. *\/ */
/* PIO_Offset idx[NDIM] = {0, 0, 3}; */
/* int file_fv_int; */
/* float file_fv_float; */

/* /\* Check an int fill value. *\/ */
/* if ((ret = PIOc_get_var1_int(ncid2, 1, idx, &file_fv_int))) */
/* return ret; */
/* if (use_fv) */
/* { */
/* if (file_fv_int != custom_fillvalue_int) */
/* return ERR_WRONG; */
/* } */

/* /\* Check the float fill value. *\/ */
/* if ((ret = PIOc_get_var1_float(ncid2, 2, idx, &file_fv_float))) */
/* return ret; */
/* /\* if (use_fv) *\/ */
/* /\* { *\/ */
/* /\* if (file_fv_float != custom_fillvalue_float) *\/ */
/* /\* return ERR_WRONG; *\/ */
/* /\* } *\/ */

/* /\* Close the netCDF file. *\/ */
/* if ((ret = PIOc_closefile(ncid2))) */
/* ERR(ret); */
/* } */
{
int ncid2; /* The ncid of the re-opened netCDF file. */
/* float test_data_float_in[arraylen]; */

/* Reopen the file. */
if ((ret = PIOc_openfile(iosysid, &ncid2, &flavor[fmt], filename, PIO_NOWRITE)))
ERR(ret);

/* Read the var data with read_darray(). */
for (int v = 0; v < NUM_VAR; v++)
{
if (v < NUM_VAR - 1)
{
int test_data_int_in[arraylen];

if ((ret = PIOc_setframe(ncid2, varid[v], 0)))
ERR(ret);

/* Read the data. */
if ((ret = PIOc_read_darray(ncid2, varid[v], ioid, arraylen, test_data_int_in)))
ERR(ret);

/* /\* Check the results. *\/ */
/* for (int f = 0; f < arraylen; f++) */
/* if (test_data_int_in[f] != test_data_int[f]) */
/* return ERR_WRONG; */
}
} /* next var */

/* /\* Now read the fill values. *\/ */
/* PIO_Offset idx[NDIM] = {0, 0, 3}; */
/* int file_fv_int; */
/* float file_fv_float; */

/* /\* Check an int fill value. *\/ */
/* if ((ret = PIOc_get_var1_int(ncid2, 1, idx, &file_fv_int))) */
/* return ret; */
/* if (use_fv) */
/* { */
/* if (file_fv_int != custom_fillvalue_int) */
/* return ERR_WRONG; */
/* } */

/* /\* Check the float fill value. *\/ */
/* if ((ret = PIOc_get_var1_float(ncid2, 2, idx, &file_fv_float))) */
/* return ret; */
/* if (use_fv) */
/* { */
/* if (file_fv_float != custom_fillvalue_float) */
/* return ERR_WRONG; */
/* } */

/* Close the netCDF file. */
if ((ret = PIOc_closefile(ncid2)))
ERR(ret);
}
}
}

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