my build paths - Revision history

Robertson at 18:14, 5 May 2025

2025-05-05T18:14:15Z

← Older revision		Revision as of 18:14, 5 May 2025
Line 29:		Line 29:
	Below is an excerpt from the custom library section.		Below is an excerpt from the custom library section.

	:<div class="box">setenv MPI_SOFT ""<br /><br />switch ($FORT)<br /><br /># Intel Compiler:<br /><br /> case "ifort"<br /> setenv ESMF_COMPILER intelgcc<br /> if ($?USE_DEBUG) then<br /> setenv ESMF_BOPT g<br /> else<br /> setenv ESMF_BOPT O<br /> endif<br /><br /> setenv ESMF_ABI 64<br /> setenv ESMF_COMM ${which_MPI}<br /> setenv ESMF_SITE default<br /><br /> setenv ARPACK_LIBDIR /opt/intelsoft/serial/ARPACK<br /><br /> if ($?USE_MPI) then<br /> if ($which_MPI == "mpich" ) then<br /> setenv MPI_SOFT /opt/intelsoft/mpich<br /> else if ($which_MPI == "mpich2" ) then<br /> setenv MPI_SOFT /opt/intelsoft/mpich2<br /> else if ($which_MPI == "openmpi" ) then<br /> setenv MPI_SOFT /opt/intelsoft/openmpi<br /> else if ($which_MPI == "mvapich2" ) then<br /> setenv MPI_SOFT /opt/intelsoft/mvapich2<br /> endif<br /><br /> setenv MCT_INCDIR ${MPI_SOFT}/mct/include<br /> setenv MCT_LIBDIR ${MPI_SOFT}/mct/lib<br /> setenv PARPACK_LIBDIR ${MPI_SOFT}/PARPACK<br /> endif<br /><br /> if ($?USE_NETCDF4) then<br /> if ($?USE_PARALLEL_IO && $?USE_MPI) then<br /> setenv ESMF_DIR ${MPI_SOFT}/esmf_nc4<br /> setenv NETCDF ${MPI_SOFT}/netcdf4<br /> setenv NF_CONFIG ${NETCDF}/bin/nf-config<br /> setenv NETCDF_INCDIR ${NETCDF}/include<br /> setenv NETCDF4 1<br /> else<br /> setenv ESMF_DIR ${MPI_SOFT}/esmf_nc4<br /> setenv NETCDF /opt/intelsoft/serial/netcdf4<br /> setenv NF_CONFIG ${NETCDF}/bin/nf-config<br /> setenv NETCDF_INCDIR ${NETCDF}/include<br /> setenv NETCDF4 1<br /> endif<br /> else<br /> setenv ESMF_DIR ${MPI_SOFT}/esmf_nc3<br /> setenv NETCDF /opt/intelsoft/serial/netcdf3<br /> setenv NETCDF_INCDIR ${NETCDF}/include<br /> setenv NETCDF_LIBDIR ${NETCDF}/lib<br /> endif<br /><br /> if ($?USE_PIO) then<br /> setenv PIO ${MPI_SOFT}/pio<br /> setenv PIO_LIBDIR ${PIO}/lib<br /> setenv PIO_INCDIR ${PIO}/include<br /> setenv PNETCDF ${MPI_SOFT}/pnetcdf<br /> setenv PNETCDF_LIBDIR ${PNETCDF}/lib<br /> setenv PNETCDF_INCDIR ${PNETCDF}/include<br /> endif<br /><br /> if ($?USE_SCORPIO) then<br /> setenv SCORPIO ${MPI_SOFT}/scorpio<br /> setenv PIO_LIBDIR ${SCORPIO}/lib<br /> setenv PIO_INCDIR ${SCORPIO}/include<br /> setenv PNETCDF ${MPI_SOFT}/pnetcdf<br /> setenv PNETCDF_LIBDIR ${PNETCDF}/lib<br /> setenv PNETCDF_INCDIR ${PNETCDF}/include<br /> endif<br /><br /> if ($?USE_HDF5) then<br /> if ($?USE_PARALLEL_IO && $?USE_MPI) then<br /> setenv HDF5 ${MPI_SOFT}/hdf5<br /> setenv HDF5_LIBDIR ${HDF5}/lib<br /> setenv HDF5_INCDIR ${HDF5}/include<br /> else<br /> setenv HDF5 /opt/intelsoft/serial/hdf5<br /> setenv HDF5_LIBDIR ${HDF5}/lib<br /> setenv HDF5_INCDIR ${HDF5}/include<br /> endif<br /> endif<br /><br /> . . .<br /><br /> breaksw</div>		:<div class="box">setenv MPI_SOFT ""<br /><br />switch ($FORT)<br /><br /># Intel Compiler:<br /><br /> case "ifort"<br /> setenv ESMF_COMPILER intelgcc<br /> if ($?USE_DEBUG) then<br /> setenv ESMF_BOPT g<br /> else<br /> setenv ESMF_BOPT O<br /> endif<br /><br /> setenv ESMF_ABI 64<br /> setenv ESMF_COMM ${which_MPI}<br /> setenv ESMF_SITE default<br /><br /> setenv ARPACK_LIBDIR /opt/intelsoft/serial/ARPACK<br /><br /> if ($?USE_MPI) then<br /> if ($which_MPI == "mpich" ) then<br /> setenv MPI_SOFT /opt/intelsoft/mpich<br /> else if ($which_MPI == "mpich2" ) then<br /> setenv MPI_SOFT /opt/intelsoft/mpich2<br /> else if ($which_MPI == "openmpi" ) then<br /> setenv MPI_SOFT /opt/intelsoft/openmpi<br /> else if ($which_MPI == "mvapich2" ) then<br /> setenv MPI_SOFT /opt/intelsoft/mvapich2<br /> endif<br /><br /> setenv MCT_INCDIR ${MPI_SOFT}/mct/include<br /> setenv MCT_LIBDIR ${MPI_SOFT}/mct/lib<br /> setenv PARPACK_LIBDIR ${MPI_SOFT}/PARPACK<br /> endif<br /><br /> if ($?USE_NETCDF4) then<br /> if ($?USE_PARALLEL_IO && $?USE_MPI) then<br /> setenv ESMF_DIR ${MPI_SOFT}/esmf_nc4<br /> setenv NETCDF ${MPI_SOFT}/netcdf4<br /> setenv NF_CONFIG ${NETCDF}/bin/nf-config<br /> setenv NETCDF_INCDIR ${NETCDF}/include<br /> setenv NETCDF4 1<br /> else<br /> setenv ESMF_DIR ${MPI_SOFT}/esmf_nc4<br /> setenv NETCDF /opt/intelsoft/serial/netcdf4<br /> setenv NF_CONFIG ${NETCDF}/bin/nf-config<br /> setenv NETCDF_INCDIR ${NETCDF}/include<br /> setenv NETCDF4 1<br /> endif<br /> else<br /> setenv ESMF_DIR ${MPI_SOFT}/esmf_nc3<br /> setenv NETCDF /opt/intelsoft/serial/netcdf3<br /> setenv NETCDF_INCDIR ${NETCDF}/include<br /> setenv NETCDF_LIBDIR ${NETCDF}/lib<br /> endif<br /><br /> if ($?USE_PIO) then<br /> setenv PIO ${MPI_SOFT}/pio<br /> setenv PIO_LIBDIR ${PIO}/lib<br /> setenv PIO_INCDIR ${PIO}/include<br /> setenv PNETCDF ${MPI_SOFT}/pnetcdf<br /> setenv PNETCDF_LIBDIR ${PNETCDF}/lib<br /> setenv PNETCDF_INCDIR ${PNETCDF}/include<br /> endif<br /><br /> if ($?USE_HDF5) then<br /> if ($?USE_PARALLEL_IO && $?USE_MPI) then<br /> setenv HDF5 ${MPI_SOFT}/hdf5<br /> setenv HDF5_LIBDIR ${HDF5}/lib<br /> setenv HDF5_INCDIR ${HDF5}/include<br /> else<br /> setenv HDF5 /opt/intelsoft/serial/hdf5<br /> setenv HDF5_LIBDIR ${HDF5}/lib<br /> setenv HDF5_INCDIR ${HDF5}/include<br /> endif<br /> endif<br /><br /> . . .<br /><br /> breaksw</div>

Robertson at 16:53, 24 May 2021

2021-05-24T16:53:02Z

← Older revision		Revision as of 16:53, 24 May 2021
Line 3:		Line 3:
	{{note}}'''Note:''' in SVN revision 933 (January 26, 2019) the custom libraries section was removed from the ROMS [[build_roms\|build script]] and placed in <span class="red">Compilers/my_build_paths.csh</span> and <span class="red">Compilers/my_build_paths.sh</span> to both streamline the ROMS build script and make setting up new applications less tedious. More information can be found in ROMS [https://www.myroms.org/projects/src/ticket/794 Trac ticket #794]. Prior to ROMS release 933, the paths mentioned below were included in the ROMS build script.		{{note}}'''Note:''' in SVN revision 933 (January 26, 2019) the custom libraries section was removed from the ROMS [[build_roms\|build script]] and placed in <span class="red">Compilers/my_build_paths.csh</span> and <span class="red">Compilers/my_build_paths.sh</span> to both streamline the ROMS build script and make setting up new applications less tedious. More information can be found in ROMS [https://www.myroms.org/projects/src/ticket/794 Trac ticket #794]. Prior to ROMS release 933, the paths mentioned below were included in the ROMS build script.


			Rather than editing files released with ROMS and possibly creating conflicts during updates, we suggest that you copy the appropriate '''my_build_paths''' file to another folder (we recommend <span class="red">~/Compilers/ROMS</span>) and set [[MY_PATHS]] to the full path to your '''my_build_paths''' file (i.e. ~/Compilers/ROMS/my_build_paths.csh).

	The path of the libraries and MPI implementations required by ROMS can be set using environment variables which take precedence over the values specified in the makefile macro definitions file ('''Compilers/*.mk'''). To activate custom paths set in <span class="red">my_build_paths</span>, set [[USE_MY_LIBS]] to '''yes''' and make sure [[MY_PATHS]] is properly set in the ROMS [[build_roms\|build script]].		The path of the libraries and MPI implementations required by ROMS can be set using environment variables which take precedence over the values specified in the makefile macro definitions file ('''Compilers/*.mk'''). To activate custom paths set in <span class="red">my_build_paths</span>, set [[USE_MY_LIBS]] to '''yes''' and make sure [[MY_PATHS]] is properly set in the ROMS [[build_roms\|build script]].

Robertson: Created page with "
Library and Executable Paths - my_build_paths.csh, my_build_paths.sh
{{note}}'''Note:''' in SVN revision 933 (January 26, 20..."

2021-05-24T16:40:14Z

Created page with "<div class="title">Library and Executable Paths - my_build_paths.csh, my_build_paths.sh</div> {{note}}'''Note:''' in SVN revision 933 (January 26, 20..."

New page

<div class="title">Library and Executable Paths - my_build_paths.csh, my_build_paths.sh</div>

{{note}}'''Note:''' in SVN revision 933 (January 26, 2019) the custom libraries section was removed from the ROMS [[build_roms|build script]] and placed in Compilers/my_build_paths.csh and Compilers/my_build_paths.sh to both streamline the ROMS build script and make setting up new applications less tedious. More information can be found in ROMS [https://www.myroms.org/projects/src/ticket/794 Trac ticket #794]. Prior to ROMS release 933, the paths mentioned below were included in the ROMS build script.

The path of the libraries and MPI implementations required by ROMS can be set using environment variables which take precedence over the values specified in the makefile macro definitions file ('''Compilers/*.mk'''). To activate custom paths set in my_build_paths, set [[USE_MY_LIBS]] to '''yes''' and make sure [[MY_PATHS]] is properly set in the ROMS [[build_roms|build script]].

==Compiler and MPI Implementation==

There is a section (the one from my_build_paths.csh is shown below) in the [[MY_PATHS]] file to make it easier to switch between different compilers and '''MPI''' implementations. This will only apply to '''MPI''' implementations that use the mpif90 style wrapper script ('''MPICH''', '''MPICH2''', '''OpenMPI''', etc.).

:<div class="box">if ($?USE_MPIF90) then switch ($FORT) case "ifort" if ($which_MPI == "mpich" ) then setenv MPI_ROOT /opt/intelsoft/mpich else if ($which_MPI == "mpich2" ) then setenv MPI_ROOT /opt/intelsoft/mpich2 else if ($which_MPI == "openmpi" ) then setenv MPI_ROOT /opt/intelsoft/openmpi else if ($which_MPI == "mvapich2" ) then setenv MPI_ROOT /opt/intelsoft/mvapich2 endif setenv PATH ${MPI_ROOT}/bin:$PATH setenv MPI_INCDIR ${MPI_ROOT}/include breaksw case "pgi" if ($which_MPI == "mpich" ) then setenv MPI_ROOT /opt/pgisoft/mpich else if ($which_MPI == "mpich2" ) then setenv MPI_ROOT /opt/pgisoft/mpich2 else if ($which_MPI == "openmpi" ) then setenv MPI_ROOT /opt/pgisoft/openmpi else if ($which_MPI == "mvapich2" ) then setenv MPI_ROOT /opt/pgisoft/mvapich2 endif setenv PATH ${MPI_ROOT}/bin:$PATH setenv MPI_INCDIR ${MPI_ROOT}/include breaksw case "gfortran" if ($which_MPI == "mpich2" ) then setenv MPI_ROOT /opt/gfortransoft/mpich2 else if ($which_MPI == "openmpi" ) then setenv MPI_ROOT /opt/gfortransoft/openmpi else if ($which_MPI == "mvapich2" ) then setenv MPI_ROOT /opt/gfortransoft/mvapich2 endif setenv PATH ${MPI_ROOT}/bin:$PATH setenv MPI_INCDIR ${MPI_ROOT}/include breaksw endsw endif</div>

{{note}}Keep in mind that you need to adjust the paths to your '''MPI''' implementations for your particular system. You must also set '''USE_MPIF90''' to on.

==External Library Paths==

For information about required and optional external libraries visit the [[External Libraries]] page.

For most applications, only the location of the '''NetCDF''' library ('''NETCDF_LIBDIR''') and include directory ('''NETCDF_INCDIR''') are needed. Notice that when the [[#USE_NETCDF4|USE_NETCDF4]] macro is activated, we need the serial or parallel version of the '''NetCDF-4/HDF5''' library. The configuration script '''NF_CONFIG''' (available since NetCDF 4.2) is used to set up all the required libraries according to the installed options ('''OPeNDAP''', '''NetCDF4/HDF5''' file format). The parallel library uses the '''MPI-I/O''' layer (available in most modern MPI implementation) requiring compiling with the selected '''MPI''' library.

In ROMS distributed-memory applications, you may use either the serial or parallel version of the '''NetCDF-4/HDF5''' library. The parallel version is required when parallel I/O is activated (ROMS cpp option [[Options#PARALLEL_IO|PARALLEL_IO]] and [[Options#HDF5|HDF5]]). For more I/O options see the [[IO|ROMS I/O page]].

However, in serial or shared-memory ROMS applications, we need to use the serial version of the '''NetCDF-4/HDF5''' to avoid conflicts with the compiler. We cannot activate '''MPI''' constructs in serial or shared-memory ROMS code. Hybrid parallelism is not possible.

Below is an excerpt from the custom library section.

:<div class="box">setenv MPI_SOFT "" switch ($FORT) # Intel Compiler: case "ifort" setenv ESMF_COMPILER intelgcc if ($?USE_DEBUG) then setenv ESMF_BOPT g else setenv ESMF_BOPT O endif setenv ESMF_ABI 64 setenv ESMF_COMM ${which_MPI} setenv ESMF_SITE default setenv ARPACK_LIBDIR /opt/intelsoft/serial/ARPACK if ($?USE_MPI) then if ($which_MPI == "mpich" ) then setenv MPI_SOFT /opt/intelsoft/mpich else if ($which_MPI == "mpich2" ) then setenv MPI_SOFT /opt/intelsoft/mpich2 else if ($which_MPI == "openmpi" ) then setenv MPI_SOFT /opt/intelsoft/openmpi else if ($which_MPI == "mvapich2" ) then setenv MPI_SOFT /opt/intelsoft/mvapich2 endif setenv MCT_INCDIR ${MPI_SOFT}/mct/include setenv MCT_LIBDIR ${MPI_SOFT}/mct/lib setenv PARPACK_LIBDIR ${MPI_SOFT}/PARPACK endif if ($?USE_NETCDF4) then if ($?USE_PARALLEL_IO && $?USE_MPI) then setenv ESMF_DIR ${MPI_SOFT}/esmf_nc4 setenv NETCDF ${MPI_SOFT}/netcdf4 setenv NF_CONFIG ${NETCDF}/bin/nf-config setenv NETCDF_INCDIR ${NETCDF}/include setenv NETCDF4 1 else setenv ESMF_DIR ${MPI_SOFT}/esmf_nc4 setenv NETCDF /opt/intelsoft/serial/netcdf4 setenv NF_CONFIG ${NETCDF}/bin/nf-config setenv NETCDF_INCDIR ${NETCDF}/include setenv NETCDF4 1 endif else setenv ESMF_DIR ${MPI_SOFT}/esmf_nc3 setenv NETCDF /opt/intelsoft/serial/netcdf3 setenv NETCDF_INCDIR ${NETCDF}/include setenv NETCDF_LIBDIR ${NETCDF}/lib endif if ($?USE_PIO) then setenv PIO ${MPI_SOFT}/pio setenv PIO_LIBDIR ${PIO}/lib setenv PIO_INCDIR ${PIO}/include setenv PNETCDF ${MPI_SOFT}/pnetcdf setenv PNETCDF_LIBDIR ${PNETCDF}/lib setenv PNETCDF_INCDIR ${PNETCDF}/include endif if ($?USE_SCORPIO) then setenv SCORPIO ${MPI_SOFT}/scorpio setenv PIO_LIBDIR ${SCORPIO}/lib setenv PIO_INCDIR ${SCORPIO}/include setenv PNETCDF ${MPI_SOFT}/pnetcdf setenv PNETCDF_LIBDIR ${PNETCDF}/lib setenv PNETCDF_INCDIR ${PNETCDF}/include endif if ($?USE_HDF5) then if ($?USE_PARALLEL_IO && $?USE_MPI) then setenv HDF5 ${MPI_SOFT}/hdf5 setenv HDF5_LIBDIR ${HDF5}/lib setenv HDF5_INCDIR ${HDF5}/include else setenv HDF5 /opt/intelsoft/serial/hdf5 setenv HDF5_LIBDIR ${HDF5}/lib setenv HDF5_INCDIR ${HDF5}/include endif endif . . . breaksw</div>

my build paths - Revision history

Robertson at 18:14, 5 May 2025

Robertson at 16:53, 24 May 2021

Robertson: Created page with "Library and Executable Paths - my_build_paths.csh, my_build_paths.sh {{note}}'''Note:''' in SVN revision 933 (January 26, 20..."

Robertson: Created page with "
Library and Executable Paths - my_build_paths.csh, my_build_paths.sh
{{note}}'''Note:''' in SVN revision 933 (January 26, 20..."