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enable netcdf4 only if NetCDF 4.9.0 and later #134

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enable netcdf4 only if NetCDF 4.9.0 and later #134

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9cf8c6f
NetCDF-C version 4.9.0 is required
wkliao Mar 25, 2022
ba61a2f
add h5ldump to check output file kind
wkliao Mar 26, 2022
7759be9
check if NC_NODIMSCALE_ATTACH is defined
wkliao Mar 26, 2022
b194130
dump all log files when fail
wkliao Mar 26, 2022
6e6003d
update HDF5 log vol to use 1.2.0
wkliao Mar 27, 2022
207dd2c
github actions: requires netcdf-c 4.9.0
wkliao Mar 28, 2022
125f838
use PnetCDF 1.12.3
wkliao Mar 28, 2022
248b95c
reduce make outputs from dependent libraries
wkliao Mar 28, 2022
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53 changes: 29 additions & 24 deletions .github/workflows/ubuntu_mpich.yml
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Expand Up @@ -33,19 +33,20 @@ jobs:
- name: Install PnetCDF
run: |
WORKDIR=$(pwd)
rm -rf pnetcdf-1.12.3.tar.gz pnetcdf-1.12.3
rm -rf pnetcdf-1.12.3.tar.gz pnetcdf-1.12.3 qout
wget -cq https://parallel-netcdf.github.io/Release/pnetcdf-1.12.3.tar.gz
tar -zxf pnetcdf-1.12.3.tar.gz
cd pnetcdf-1.12.3
./configure --prefix=${WORKDIR}/.local/pnc/1.12.3 \
--disable-fortran \
--disable-cxx
make -j 4 install
make -j 4 install > qout 2>&1
cd ..
- name: Install HDF5
if: ${{ success() }}
run: |
WORKDIR=$(pwd)
rm -rf hdf5-1.13.0.tar.gz hdf5-1.13.0
rm -rf hdf5-1.13.0.tar.gz hdf5-1.13.0 qout
wget -cq https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.0/src/hdf5-1.13.0.tar.gz
tar -zxf hdf5-1.13.0.tar.gz
cd hdf5-1.13.0
Expand All @@ -60,16 +61,17 @@ jobs:
--disable-tools \
--disable-tests \
CC=mpicc
make -j 4 install
make -j 4 install > qout 2>&1
cd ..
- name: Install NetCDF-C
if: ${{ success() }}
run: |
WORKDIR=$(pwd)
rm -rf v4.8.1.tar.gz netcdf-c-4.8.1
wget -cq https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.8.1.tar.gz
tar -zxf v4.8.1.tar.gz
cd netcdf-c-4.8.1
./configure --prefix=${WORKDIR}/.local/netcdf/4.8.1 \
rm -rf v4.9.0.tar.gz netcdf-c-4.9.0 qout
wget -cq https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.0.tar.gz
tar -zxf v4.9.0.tar.gz
cd netcdf-c-4.9.0
./configure --prefix=${WORKDIR}/.local/netcdf/4.9.0 \
--disable-dap \
--disable-nczarr \
--disable-nczarr-filters \
Expand All @@ -78,12 +80,13 @@ jobs:
CPPFLAGS="-I${WORKDIR}/.local/hdf5/1.13.0/include" \
LDFLAGS="-L${WORKDIR}/.local/hdf5/1.13.0/lib" \
LIBS="-lhdf5"
make -j 4 install
make -j 4 install > qout 2>&1
cd ..
- name: Install ADIOS2
if: ${{ success() }}
run: |
WORKDIR=$(pwd)
rm -rf v2.7.1.tar.gz ADIOS2-2.7.1 adios2_build
rm -rf v2.7.1.tar.gz ADIOS2-2.7.1 adios2_build qout
wget -cq https://github.com/ornladios/ADIOS2/archive/refs/tags/v2.7.1.tar.gz
tar -zxf v2.7.1.tar.gz
mkdir adios2_build
Expand All @@ -104,20 +107,21 @@ jobs:
-DADIOS2_BUILD_EXAMPLES=OFF \
-DBUILD_TESTING=OFF \
../ADIOS2-2.7.1
make -j 4
make -j 4 install
make -j 4 install > qout 2>&1
cd ..
- name: Install log VOL
if: ${{ success() }}
run: |
WORKDIR=$(pwd)
rm -rf logvol.1.1.0.tar.gz vol-log-based-logvol.1.1.0
wget -cq https://github.com/DataLib-ECP/vol-log-based/archive/refs/tags/logvol.1.1.0.tar.gz
tar -zxf logvol.1.1.0.tar.gz
cd vol-log-based-logvol.1.1.0
rm -rf logvol.1.2.0.tar.gz vol-log-based-logvol.1.2.0 qout
wget -cq https://github.com/DataLib-ECP/vol-log-based/archive/refs/tags/logvol.1.2.0.tar.gz
tar -zxf logvol.1.2.0.tar.gz
cd vol-log-based-logvol.1.2.0
autoreconf -i
./configure --prefix=${WORKDIR}/.local/logvol/1.1.0 \
./configure --prefix=${WORKDIR}/.local/logvol/1.2.0 \
--with-hdf5=${WORKDIR}/.local/hdf5/1.13.0
make -j 4 install
make -j 4 install > qout 2>&1
cd ..
- name: Build E3SM_IO with PnetCDF only
if: ${{ success() }}
run: |
Expand Down Expand Up @@ -150,7 +154,7 @@ jobs:
WORKDIR=$(pwd)
./configure --with-pnetcdf=${WORKDIR}/.local/pnc/1.12.3 \
--with-hdf5=${WORKDIR}/.local/hdf5/1.13.0 \
--with-logvol=${WORKDIR}/.local/logvol/1.1.0 \
--with-logvol=${WORKDIR}/.local/logvol/1.2.0 \
CC=mpicc CXX=mpicxx \
CFLAGS=-fno-var-tracking-assignments \
CXXFLAGS=-fno-var-tracking-assignments
Expand All @@ -163,7 +167,7 @@ jobs:
run: |
WORKDIR=$(pwd)
./configure --with-pnetcdf=${WORKDIR}/.local/pnc/1.12.3 \
--with-netcdf4=${WORKDIR}/.local/netcdf/4.8.1 \
--with-netcdf4=${WORKDIR}/.local/netcdf/4.9.0 \
CC=mpicc CXX=mpicxx \
CFLAGS=-fno-var-tracking-assignments \
CXXFLAGS=-fno-var-tracking-assignments
Expand All @@ -190,8 +194,8 @@ jobs:
WORKDIR=$(pwd)
./configure --with-pnetcdf=${WORKDIR}/.local/pnc/1.12.3 \
--with-hdf5=${WORKDIR}/.local/hdf5/1.13.0 \
--with-netcdf4=${WORKDIR}/.local/netcdf/4.8.1 \
--with-logvol=${WORKDIR}/.local/logvol/1.1.0 \
--with-netcdf4=${WORKDIR}/.local/netcdf/4.9.0 \
--with-logvol=${WORKDIR}/.local/logvol/1.2.0 \
--with-adios2=${WORKDIR}/.local/adios2/2.7.1 \
CC=mpicc CXX=mpicxx \
CFLAGS=-fno-var-tracking-assignments \
Expand All @@ -201,6 +205,7 @@ jobs:
if: ${{ failure() }}
run: |
cat config.log
cat test.sh.log utils/*.log
- name: Test E3SM_IO all APIs -- parallel runs
if: ${{ success() }}
run: |
Expand All @@ -209,6 +214,6 @@ jobs:
if: ${{ success() }}
run: |
WORKDIR=$(pwd)
make distcheck DISTCHECK_CONFIGURE_FLAGS="--with-pnetcdf=${WORKDIR}/.local/pnc/1.12.3 --with-hdf5=${WORKDIR}/.local/hdf5/1.13.0 --with-netcdf4=${WORKDIR}/.local/netcdf/4.8.1 --with-logvol=${WORKDIR}/.local/logvol/1.1.0 --with-adios2=${WORKDIR}/.local/adios2/2.7.1 CC=mpicc CXX=mpicxx CFLAGS=-fno-var-tracking-assignments CXXFLAGS=-fno-var-tracking-assignments"
make distcheck DISTCHECK_CONFIGURE_FLAGS="--with-pnetcdf=${WORKDIR}/.local/pnc/1.12.3 --with-hdf5=${WORKDIR}/.local/hdf5/1.13.0 --with-netcdf4=${WORKDIR}/.local/netcdf/4.9.0 --with-logvol=${WORKDIR}/.local/logvol/1.2.0 --with-adios2=${WORKDIR}/.local/adios2/2.7.1 CC=mpicc CXX=mpicxx CFLAGS=-fno-var-tracking-assignments CXXFLAGS=-fno-var-tracking-assignments"
make distclean

49 changes: 25 additions & 24 deletions INSTALL.md
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Expand Up @@ -8,14 +8,14 @@
+ m4 1.4.18
* MPI C and C++ compilers
+ Configured with a std 11 C++ compiler (supporting constant initializer)
* (Optional) [PnetCDF 1.12.2](https://parallel-netcdf.github.io/Release/pnetcdf-1.12.2.tar.gz)
* (Optional) [PnetCDF 1.12.3](https://parallel-netcdf.github.io/Release/pnetcdf-1.12.3.tar.gz)
* (Optional) [HDF5 1.13.0](https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.0/src/hdf5-1.13.0.tar.gz)
+ Configured with parallel I/O support (configured with `--enable-parallel` is required)
* (Optional) [HDF5 Log-based VOL](https://github.com/DataLib-ECP/vol-log-based.git)
+ Experimental software developed as part of the Datalib project
* (Optional) [ADIOS 2.7.1](https://github.com/ornladios/ADIOS2/archive/refs/tags/v2.7.1.tar.gz)
+ Configured with parallel I/O support (cmake with `-DADIOS2_USE_MPI=ON` is required)
* (Optional) [NetCDF-C 4.8.1](https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.8.1.tar.gz)
* (Optional) [NetCDF-C 4.9.0](https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.0.tar.gz)
+ Configured with parallel HDF5 support (i.e. `--enable-netcdf4`)
+ Note currently this option fails to run due to a
[bug](https://github.com/Unidata/netcdf-c/issues/2251) in NetCDF-C.
Expand All @@ -26,12 +26,12 @@
+ Configure PnetCDF with MPI C compiler
+ Run `make install`
+ Example build commands are given below. This example will install
the PnetCDF library under folder `${HOME}/PnetCDF/1.12.2`.
the PnetCDF library under folder `${HOME}/PnetCDF/1.12.3`.
```
% wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.2.tar.gz
% tar -zxf pnetcdf-1.12.2.tar.gz
% cd pnetcdf-1.12.2
% ./configure --prefix=${HOME}/PnetCDF/1.12.2 CC=mpicc
% wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.3.tar.gz
% tar -zxf pnetcdf-1.12.3.tar.gz
% cd pnetcdf-1.12.3
% ./configure --prefix=${HOME}/PnetCDF/1.12.3 CC=mpicc
% make -j 4 install
```
* Build HDF5 with parallel I/O support
Expand All @@ -54,10 +54,10 @@
+ Compile with zlib library to enable metadata compression (--enable-zlib)
+ Example commands are given below.
```
% wget https://github.com/DataLib-ECP/vol-log-based/archive/refs/tags/logvol.1.1.0.tar.gz
% tar -zxf logvol.1.1.0.tar.gz
% cd vol-log-based-logvol.1.1.0
% ./configure --prefix=${HOME}/Log_VOL/1.1.0 --with-hdf5=${HOME}/HDF5/1.13.0 --enable-shared CC=mpicc
% wget https://github.com/DataLib-ECP/vol-log-based/archive/refs/tags/logvol.1.2.0.tar.gz
% tar -zxf logvol.1.2.0.tar.gz
% cd vol-log-based-logvol.1.2.0
% ./configure --prefix=${HOME}/Log_VOL/1.2.0 --with-hdf5=${HOME}/HDF5/1.13.0 --enable-shared CC=mpicc
% make -j 4 install
```
* Build ADIOS with parallel I/O support
Expand All @@ -79,12 +79,12 @@
+ Configure NetCDF-C with parallel HDF5 I/O enabled.
+ Run `make install`
+ Example build commands are given below. This example will install
the NetCDF library under the folder `${HOME}/NetCDF/4.8.1`.
the NetCDF library under the folder `${HOME}/NetCDF/4.9.0`.
```
% wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.8.1.tar.gz
% tar -zxf v4.8.1.tar.gz
% cd netcdf-c-4.8.1
% ./configure --prefix=${HOME}/NetCDF/4.8.1 \
% wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.0.tar.gz
% tar -zxf v4.9.0.tar.gz
% cd netcdf-c-4.9.0
% ./configure --prefix=${HOME}/NetCDF/4.9.0 \
CC=mpicc \
CPPFLAGS=-I${HOME}/HDF5/1.13.0/include \
LDFLAGS=-L${HOME}/HDF5/1.13.0/lib \
Expand Down Expand Up @@ -117,10 +117,11 @@
% git clone https://github.com/Parallel-NetCDF/E3SM-IO.git
% cd E3SM-IO
% autoreconf -i
% ./configure --with-pnetcdf=${HOME}/PnetCDF/1.12.2 \
% ./configure --with-pnetcdf=${HOME}/PnetCDF/1.12.3 \
--with-hdf5=${HOME}/HDF5/1.13.0 \
--with-logvol=${HOME}/Log_VOL/1.1.0 \
--with-logvol=${HOME}/Log_VOL/1.2.0 \
--with-adios2=${HOME}/ADIOS2/2.7.1 \
--with-netcdf4=${HOME}/NetCDF/4.9.0 \
CC=mpicc CXX=mpicxx
% make
```
Expand Down Expand Up @@ -208,13 +209,13 @@

### Current supported APIs (option `-a`) and I/O strategies (option `-x`)
+ Table below lists the supported combinations.
| | pnetcdf | hdf5 | hdf5_log | netcdf4 | adios |
|-----------|:-------:|:----:|:--------:|:-------:|:-----:|
| canonical | yes | yes | no | yes | no |
| log | no | yes | yes | yes* | no |
| blob | yes | yes | no | no | yes |
| | pnetcdf | hdf5 | hdf5_log | netcdf4* | adios |
|-----------|:-------:|:----:|:--------:|:--------:|:-----:|
| canonical | yes | yes | no | yes | no |
| log | no | yes | yes | yes | no |
| blob | yes | yes | no | no | yes |

`*` Requires setting of 2 VOL environment variables. See description below.
`*` NetCDF-C version 4.9.0 or newer is required.

+ **-a pnetcdf -x canonical**
* A single NetCDF file in the classic CDF5 format will be created. All
Expand Down
3 changes: 2 additions & 1 deletion Makefile.am
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Expand Up @@ -25,6 +25,7 @@ endif
if ENABLE_LOGVOL
TESTS_ENVIRONMENT += export ENABLE_LOGVOL=1;
TESTS_ENVIRONMENT += export LOGVOL_LIB_PATH="@LOGVOL_LIB_PATH@";
TESTS_ENVIRONMENT += export H5LDUMP="@H5LDUMP@";
endif

TESTS = test.sh
Expand All @@ -40,7 +41,7 @@ EXTRA_DIST = test.sh \
AUTHORS \
slurm.knl

ptest: $(check_PROGRAMS)
ptest: src/e3sm_io
@echo "==========================================================="
@echo " Parallel testing on 16 MPI processes"
@echo "==========================================================="
Expand Down
63 changes: 53 additions & 10 deletions configure.ac
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Expand Up @@ -330,7 +330,7 @@ AM_CONDITIONAL(ENABLE_PNC, [test "x$have_pnc" = xyes])
have_hdf5=no
have_multi_dset=no
AC_ARG_WITH([hdf5],
[AS_HELP_STRING([--with-hdf5@<:@=INC,LIB | =DIR@:>@],
[AS_HELP_STRING([--with-hdf5@<:@=INC,LIB | =DIR@:>@],
[Enable HDF5 feature and provide the HDF5 installation path(s):
--with-hdf5=INC,LIB for include and lib paths separated by a comma.
--with-hdf5=DIR for the path containing include/ and lib/ subdirectories.
Expand Down Expand Up @@ -420,7 +420,7 @@ AC_ARG_WITH([netcdf4],
if test -n "$withval"; then
netcdf4_inc="$withval/include"
netcdf4_lib="$withval/lib"
netcdf4_bindir="$NETCDF4_INSTALL/bin"
netcdf4_bindir="$withval/bin"
fi
;;
esac
Expand All @@ -433,6 +433,7 @@ AC_ARG_WITH([netcdf4],
if test "x$netcdf4_config" != x ; then
netcdf4_cflags=`$netcdf4_config --cflags`
netcdf4_lflags=`$netcdf4_config --libs`
netcdf4_version=`$netcdf4_config --version | cut -d' ' -f2 | cut -d'-' -f1`
else
netcdf4_cflags="-I$netcdf4_inc"
netcdf4_lflags="-L$netcdf4_lib"
Expand All @@ -453,17 +454,48 @@ AC_ARG_WITH([netcdf4],
LDFLAGS="$LDFLAGS $netcdf4_lflags"
fi
fi
AC_CHECK_HEADER([netcdf.h], [have_netcdf4=yes], [have_netcdf4=no])
AC_CHECK_HEADERS([netcdf.h netcdf_meta.h], [have_netcdf4=yes], [have_netcdf4=no])
if test "x$have_netcdf4" = xno ; then
AC_MSG_WARN([
-----------------------------------------------------------------------
Missing NetCDF-header files 'netcdf4_c.h' required to build E3SM_IO. Use
configure command-line option --with-netcdf4=/path/to/implementation
to specify the location of NetCDF installation. Disable NetCDF 4 support.
Missing NetCDF-header files 'netcdf.h' or 'netcdf_meta.h' which are
required to build E3SM_IO. Use configure command-line option
--with-netcdf4=/path/to/implementation to specify the location of
NetCDF-4 installation. Disable NetCDF-4 support.
-----------------------------------------------------------------------])
fi

AC_MSG_CHECKING([if NetCDF $netcdf_version is configured with parallel I/O enabled])
if test "x$have_netcdf4" = xyes ; then
AC_MSG_CHECKING([NetCDF-C version])
if test "x$netcdf4_version" = x ; then
nc_version_major=`${EGREP} NC_VERSION_MAJOR $netcdf4_inc/netcdf_meta.h| head -1 | cut -d' ' -f3`
nc_version_minor=`${EGREP} NC_VERSION_MINOR $netcdf4_inc/netcdf_meta.h| head -1 | cut -d' ' -f3`
nc_version_patch=`${EGREP} NC_VERSION_PATCH $netcdf4_inc/netcdf_meta.h| head -1 | cut -d' ' -f3`
netcdf4_version="${nc_version_major}.${nc_version_minor}.${nc_version_patch}"
fi
AC_MSG_RESULT([$netcdf4_version])

dnl Check if NetCDF version is 4.9.0 or later
AC_MSG_CHECKING([whether NetCDF-C version is 4.9.0 or later])
AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
#include <netcdf_meta.h>
#define VER_NUM (NC_VERSION_MAJOR*1000000 + NC_VERSION_MINOR*1000 + NC_VERSION_PATCH)
#if (VER_NUM < 4009000)
#error NetCDF version is older than 4.9.0
#endif
]])], [netcdf_ge_4_9_0=yes], [netcdf_ge_4_9_0=no])
AC_MSG_RESULT([$netcdf_ge_4_9_0])

if test "x${netcdf_ge_4_9_0}" = xno; then
AC_MSG_ERROR([
------------------------------------------------------------
Supplied NetCDF-4 version is $netcdf4_version, but 4.9.0 or later
is required. Abort.
------------------------------------------------------------])
fi
fi

AC_MSG_CHECKING([if NetCDF-4 is configured with parallel I/O enabled])
if test "x$netcdf4_config" != x ; then
netcdf4_has_par=`$netcdf4_config --has-parallel4`
else
Expand All @@ -474,7 +506,7 @@ AC_ARG_WITH([netcdf4],
AC_MSG_WARN([
------------------------------------------------------------
NetCDF was not built with parallel NetCDF 4 support.
Disable NetCDF4.
Disable NetCDF4.
------------------------------------------------------------])
have_netcdf4 = no
elif test "x$netcdf4_lib" != x ; then
Expand Down Expand Up @@ -503,11 +535,13 @@ AC_ARG_WITH([logvol],
*,*)
logvol_inc="`echo $withval |cut -f1 -d,`"
logvol_lib="`echo $withval |cut -f2 -d, -s`"
logvol_bindir="$logvol_inc/../bin"
;;
*)
if test -n "$withval"; then
logvol_inc="$withval/include"
logvol_lib="$withval/lib"
logvol_bindir="$withval/bin"
fi
;;
esac
Expand Down Expand Up @@ -539,6 +573,15 @@ AC_ARG_WITH([logvol],
if test "x$have_logvol" = xyes ; then
AC_SUBST(LOGVOL_LIB_PATH, [$logvol_lib])
fi
if test "x$logvol_bindir" != x ; then
AC_PATH_PROG([h5ldump],[h5ldump],,[$logvol_bindir])
else
dnl Check h5ldump under $PATH
AC_PATH_PROG([h5ldump],[h5ldump])
fi
if test "x$h5ldump" != x ; then
AC_SUBST(H5LDUMP, [$h5ldump])
fi
])
AM_CONDITIONAL(ENABLE_LOGVOL, [test "x$have_logvol" = xyes])

Expand Down Expand Up @@ -618,9 +661,9 @@ if test "x${have_pnc}" = xno && test "x${have_nc4}" = xno && test "x${have_hdf5}
-----------------------------------------------------------------------
At least one API driver must be enabled.
Use configure command-line option --with-pnetcdf=/path/to/implementation
to specify the location of PnetCDF installation.
to specify the location of PnetCDF installation.
Use configure command-line option --with-netcdf4=/path/to/implementation
to specify the location of NetCDF installation.
to specify the location of NetCDF installation.
Use configure command-line option --with-hdf5=/path/to/implementation
to specify the location of HDF5 installation.
Use configure command-line option --with-adios2=/path/to/implementation
Expand Down
2 changes: 1 addition & 1 deletion src/drivers/e3sm_io_driver_nc4.cpp
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Expand Up @@ -73,7 +73,7 @@ int e3sm_io_driver_nc4::create (std::string path, MPI_Comm comm, MPI_Info info,
E3SM_IO_TIMER_START (E3SM_IO_TIMER_NC4)
E3SM_IO_TIMER_START (E3SM_IO_TIMER_NC4_OPEN)

err = nc_create_par (path.c_str (), NC_CLOBBER | NC_NETCDF4, comm, info, fid);
err = nc_create_par (path.c_str (), NC_CLOBBER | NC_NETCDF4 | NC_NODIMSCALE_ATTACH, comm, info, fid);
CHECK_NCERR

/* turn off fill mode for the entire file */
Expand Down
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