Build HPC commonly-used Tools using LLVM Flang

[PeixinQiao]

Export Environment variables

$ mkdir install-llvm-flang install-hpc-tools # prepare the installation path
$ export optflags="-O3"
$ export installLLVMFlangPath=/path-to-install-llvm-flang
$ export installHPCToolsPath=/path-to-install-hpc-tools
$ export PATH=$installLLVMFlangPath/bin:$installHPCToolsPath/bin:$PATH
$ export LD_LIBRARY_PATH=$installLLVMFlangPath/lib:$installHPCToolsPath/lib:$LD_LIBRARY_PATH

Build LLVM Flang

$ git clone https://github.com/llvm/llvm-project.git
$ cd llvm-project
$ mkdir build-f18 && cd build-f18
$ cmake -G Ninja -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$installLLVMFlangPath -DLLVM_TARGETS_TO_BUILD="X86" -DLLVM_ENABLE_PROJECTS="clang;flang;mlir;openmp" ../llvm-project/llvm
$ ninja -j
$ ninja install

Build OpenMPI

$ wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz
$ tar xf openmpi-4.0.3.tar.gz
$ cd openmpi-4.0.3
$ mkdir build-f18 && cd build-f18
$ CC=clang CXX=clang++ FC="flang-new -flang-experimental-exec" CFLAGS=$optflags CXXFLAGS=$optflags FCFLAGS=$optflags ../configure --prefix=$installHPCToolsPath --without-knem --without-ucx --enable-pretty-print-stacktrace --enable-orterun-prefix-by-default --enable-mpi1-compatibility
$ cat ../../mpi-libtool.patch
diff --git a/libtool b/libtool
index 8052fda..bf63042 100755
--- a/libtool
+++ b/libtool
@@ -11841,7 +11841,7 @@ no_builtin_flag=""
 pic_flag=""
 
 # How to pass a linker flag through the compiler.
-wl=""
+wl="-Wl,"
 
 # Compiler flag to prevent dynamic linking.
 link_static_flag=""
$ patch -p1 < ../../mpi-libtool.patch
$ make -j
$ make install

Test:

$ cat test.f90 
program hello_world
  use mpi
  !include 'mpif.h'
  integer ierr, num_procs, my_id
  call MPI_INIT ( ierr )
  ! find out my process ID, and how many processes were started.
  call MPI_COMM_RANK (MPI_COMM_WORLD, my_id, ierr)
  call MPI_COMM_SIZE (MPI_COMM_WORLD, num_procs, ierr)
  print *, "Hello world! I'm process ", my_id, " out of ", num_procs, " processes."
  call MPI_FINALIZE ( ierr )
  !stop
end program hello_world
$ mpif90 test.f90 
$ mpirun -n 4 ./a.out
 Hello world! I'm process  0 out of  4 processes.
 Hello world! I'm process  2 out of  4 processes.
 Hello world! I'm process  3 out of  4 processes.
 Hello world! I'm process  1 out of  4 processes.

[PeixinQiao]

Build HDF5

$ wget https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-1_12_1.tar.gz
$ tar -xf hdf5-hdf5-1_12_1.tar.gz
$ cd hdf5-hdf5-1_12_1
$ cat ../disable-real-2and3.patch 
diff --git a/m4/aclocal_fc.f90 b/m4/aclocal_fc.f90
index e9a11c0..f5bd5aa 100644
--- a/m4/aclocal_fc.f90
+++ b/m4/aclocal_fc.f90
@@ -112,7 +112,7 @@ PROGRAM FC_AVAIL_KINDS
       ENDDO
 
       ! Find real KINDs
-      list_rkinds(num_rkinds)=SELECTED_REAL_KIND(1)
+      list_rkinds(num_rkinds)=4!SELECTED_REAL_KIND(1)
       max_decimal_prec = 1
       prev_rkind=list_rkinds(num_rkinds)
 
@@ -120,7 +120,7 @@ PROGRAM FC_AVAIL_KINDS
          exp: DO jk = 1, 700
             k = SELECTED_REAL_KIND(ik,jk)
             IF(k.LT.0) EXIT exp
-            IF(k.NE.prev_rkind)THEN
+            IF(k.NE.prev_rkind .AND. k.NE.2 .AND. k.NE.3)THEN
                ! Check if we aleady have that kind
                new_kind = .TRUE.
                DO kk = 1, num_rkinds
$ patch -p1 < ../disable-real-2and3.patch
$ mkdir build-f18 && cd build-f18
$ CC=mpicc CXX=mpicxx FC=mpif90 CFLAGS=$optflags CXXFLAGS=$optflags FCFLAGS=$optflags ../configure --prefix=$installHPCToolsPath --enable-shared --enable-static --enable-fortran --enable-parallel --enable-optimization=high
$ cat ../../hdf5-1_12_1-libtool.patch
diff --git a/libtool b/libtool
index 3b86358..e8ca993 100755
--- a/libtool
+++ b/libtool
@@ -11832,7 +11832,7 @@ no_builtin_flag=""
 pic_flag=""
 
 # How to pass a linker flag through the compiler.
-wl=""
+wl="-Wl,"
 
 # Compiler flag to prevent dynamic linking.
 link_static_flag=""
$ patch -p1 < ../../hdf5-1_12_1-libtool.patch
$ make -j
$ make install

[PeixinQiao]

Build PNetCDF

$ wget https://parallel-netcdf.github.io/Release/pnetcdf-1.11.2.tar.gz
$ tar -xf pnetcdf-1.11.2.tar.gz
$ cd pnetcdf-1.11.2
$ mkdir build-f18 && cd build-f18
$ CC=mpicc CXX=mpicxx FC=mpif90 CFLAGS=$optflags CXXFLAGS=$optflags FCFLAGS=$optflags FFLAGS=$optflags ../configure --prefix=$installHPCToolsPath --enable-shared --enable-static --enable-fortran --enable-large-file-test
$ make -j
$ make install

[PeixinQiao]

Build NetCDF-C

$ wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.7.3.tar.gz
$ tar -xf netcdf-c-4.7.3.tar.gz
$ cd netcdf-c-4.7.3
$ mkdir build-f18 && cd build-f18
$ CC=mpicc CFLAGS="$optflags -I$installHPCToolsPath/include" LDFLAGS="$ldflags -L$installLLVMFlangPath/lib -L$installHPCToolsPath/lib" ../configure --prefix=$installHPCToolsPath --build=aarch64-linux --enable-static --enable-shared --with-pic --enable-parallel-tests --enable-pnetcdf --enable-largefile --enable-large-file-tests --disable-dap
$ make -j
$ make install

[PeixinQiao]

Build NetCDF-Fortran

$ wget https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.4.5.tar.gz
$ tar -xf netcdf-fortran-4.4.5.tar.gz
$ cd netcdf-fortran-4.4.5
$ mkdir build-f18 && cd build-f18
$ CC=mpicc CFLAGS="$optflags -I$installHPCToolsPath/include" FC=mpif90 FCFLAGS="$optflags -fPIC -I$installHPCToolsPath/include" LDFLAGS="$ldflags -L$installLLVMFlangPath/lib -L$installHPCToolsPath/lib" ../configure --prefix=$installHPCToolsPath --enable-static --enable-shared --with-pic --enable-parallel-tests --enable-largefile --enable-large-file-tests
$ cat ../../netcdf-fortran-libtool.patch 
diff --git a/libtool b/libtool
index 6593284..70d26a6 100755
--- a/libtool
+++ b/libtool
@@ -11691,7 +11691,7 @@ no_builtin_flag=""
 pic_flag=""
 
 # How to pass a linker flag through the compiler.
-wl=""
+wl="-Wl,"
 
 # Compiler flag to prevent dynamic linking.
 link_static_flag=""
@@ -11843,7 +11843,7 @@ no_builtin_flag=""
 pic_flag=""
 
 # How to pass a linker flag through the compiler.
-wl=""
+wl="-Wl,"
 
 # Compiler flag to prevent dynamic linking.
 link_static_flag=""
$ patch -p1 < ../../netcdf-fortran-libtool.patch
$ make -j
$ make install