Update README.md

Author: houjun

README.md

@@ -1,98 +1,45 @@
-# Installation Instructions for Cori Machines
+# Installation Instructions
 
-## Install libfabric
-```
-0. wget https://github.com/ofiwg/libfabric/archive/v1.11.2.tar.gz
-1. tar xvzf v1.11.2.tar.gz
-2. cd libfabric-1.11.2
-3. mkdir install
-4. export LIBFABRIC_DIR=$(pwd)/install
-5. ./autogen.sh
-6. ./configure --prefix=$LIBFABRIC_DIR CC=cc CFLAG="-O2"
-7. make -j8
-8. make install
-9. export LD_LIBRARY_PATH="$LIBFABRIC_DIR/lib:$LD_LIBRARY_PATH"
-10. export PATH="$LIBFABRIC_DIR/include:$LIBFABRIC_DIR/lib:$PATH"
-```
+## Install PDC and its dependent libraries
+
+Please follow the instructions in the [PDC documentation website](https://pdc.readthedocs.io/en/latest/getting_started.html#installing-pdc-from-source-code) to install libfabric, mercury, and PDC. We recommend using the PDC develop branch.
 
-## Install Mercury
-Make sure the ctest passes. PDC may not work without passing all the tests of Mercury.
 
-Step 2 in the following is not required. It is a stable commit that has been used to test when these these instructions were written. One may skip it to use the current master branch of Mercury.
-```
-0. git clone https://github.com/mercury-hpc/mercury.git
-1. cd mercury
-2. git checkout e741051fbe6347087171f33119d57c48cb438438
-3. git submodule update --init
-4. export MERCURY_DIR=$(pwd)/install
-5. mkdir install
-6. cd install
-7. cmake ../ -DCMAKE_INSTALL_PREFIX=$MERCURY_DIR -DCMAKE_C_COMPILER=cc -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=ON -DNA_USE_OFI=ON -DNA_USE_SM=OFF -DCMAKE_C_FLAGS="-dynamic" -DCMAKE_CXX_FLAGS="-dynamic"
-8. make
-9. make install
-10. ctest -DMPI_RUN_CMD=srun
-11. export LD_LIBRARY_PATH="$MERCURY_DIR/lib:$LD_LIBRARY_PATH"
-12. export PATH="$MERCURY_DIR/include:$MERCURY_DIR/lib:$PATH"
-```
-## Install PDC
-ctest contains both sequential and MPI tests for the PDC settings. These can be used to perform regression tests.
-```
-0. git clone https://github.com/hpc-io/pdc.git
-1. cd pdc
-2. git checkout stable
-3. cd src
-4. mkdir install
-5. cd install
-6. export PDC_DIR=$(pwd)
-7. cmake ../ -DBUILD_MPI_TESTING=ON -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=ON -DCMAKE_INSTALL_PREFIX=$PDC_DIR -DPDC_ENABLE_MPI=ON -DMERCURY_DIR=$MERCURY_DIR -DCMAKE_C_COMPILER=cc -DCMAKE_C_FLAGS="-dynamic"
-8. make -j8
-9. ctest -DMPI_RUN_CMD=srun 
-```
 ## Environmental variables
-During installation, we have set some environmental variables. These variables may disappear after the close the current session ends.
-We recommend adding the following lines to ~/.bashrc. (One may also execute them manually after logging in).
-The MERCURY_DIR and LIBFABRIC_DIR variables should be identical to the values that were set during the installation of Mercury and libfabric.
-The install path is the path containing bin and lib directory, instead of the one containing the source code.
+The following  environment variables should be set before continuing.
 ```
-export PDC_DIR="where/you/installed/your/pdc"
-export MERCURY_DIR="where/you/installed/your/mercury"
-export LIBFABRIC_DIR="where/you/installed/your/libfabric"
+export PDC_DIR="where/you/install/your/pdc"
+export VOL_DIR="where/you/install/your/vol-pdc"
+export HDF5_DIR="where/you/install/your/hdf5"
+export MERCURY_DIR="where/you/install/your/mercury"
+export LIBFABRIC_DIR="where/you/install/your/libfabric"
 export LD_LIBRARY_PATH="$LIBFABRIC_DIR/lib:$MERCURY_DIR/lib:$LD_LIBRARY_PATH"
 export PATH="$LIBFABRIC_DIR/include:$LIBFABRIC_DIR/lib:$MERCURY_DIR/include:$MERCURY_DIR/lib:$PATH"
 ```
 
 ## Install HDF5
 ```
-0. wget "https://www.hdfgroup.org/package/hdf5-1-12-1-tar-gz/?wpdmdl=15727&refresh=612559667d6521629837670"
-1. mv index.html?wpdmdl=15727&refresh=612559667d6521629837670 hdf5-1.12.1.tar.gz
-2. tar zxf hdf5-1.12.1.tar.gz
-3. cd hdf5-1.12.1
-4. ./configure --prefix=/global/homes/../<username>/hdf5
-5. make
-6. make check
-7. make install
-8. make check-install
+git clone https://github.com/HDFGroup/hdf5.git
+cd hdf5
+git checkout hdf5-1_14_1-2
+export HDF5_LIBTOOL=/usr/bin/libtoolize
+./autogen.sh
+./configure CC=mpicc --prefix=$HDF5_DIR --enable-parallel --disable-tests --disable-hl --disable-fortran 
+make && make install
 ```
 
 ## Building vol-pdc
-CMakeLists.txt seem to be heavily adapted from the [mercury](https://github.com/mercury-hpc/mercury) git repo. Building should be very similar.
 ```
-0. git clone https://github.com/hpc-io/vol-pdc.git
-1. cd vol-pdc
-2. mkdir build
-3. cd build
-4. ccmake ..
-5. set BUILD_SHARED_LIBS to ON (default OFF)
-6. set HDF5_DIR to where HDF5 is installed
-7. set HDF5_INCLUDE_DIR to the include directory in the HDF5 package
-8. set HDF5_LIBRARY to the lib directory in the HDF5 package
-9. press [c] to configure then exit
-10. cmake .. 
+git clone https://github.com/hpc-io/vol-pdc.git
+cd vol-pdc
+mkdir build
+cd build
+cmake ../ -DCMAKE_INSTALL_PREFIX=$VOL_DIR -DBUILD_SHARED_LIBS=ON -DHDF5_DIR=$HDF5_DIR -DPDC_DIR=$PDC_DIR/share/cmake/pdc -DBUILD_EXAMPLES=ON
 ```
 
 # Notes
 
-The following functions have yet to be implemented and are either currently do nothing, or don't do anything relevant to the VOL:
+The following functions have yet to be implemented and either currently do nothing, or don't do anything relevant to the VOL:
 
 - H5VL_pdc_attr_get
 - H5VL_pdc_attr_close