Changes between Version 38 and Version 39 of pleiadesbash


Ignore:
Timestamp:
05/16/22 11:29:54 (3 years ago)
Author:
jdquinn
Comment:

Added solid earth configuration

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  • pleiadesbash

    v38 v39  
    4141== Installing ISSM on Pleiades ==
    4242
    43 '''Do NOT install mpich'''. We have to use the one provided by NAS. Pleiades will ''only'' be used to run the code, you will use your local machine for pre and post processing, you will never use Pleiades' matlab. You can check out ISSM and install the following packages:
     43'''Do NOT install mpich'''. We have to use the one provided by NAS. Pleiades will ''only'' be used to run the code, you will use your local machine for pre- and post- processing, you will never use Pleiades' copy of MATLAB. You can check out ISSM and install the following packages:
    4444 - m1qn3
    4545 - PETSc (use `install-3.14-pleiades.sh` or newer)
    4646
    47 For documentation of pleiades, see here: http://www.nas.nasa.gov/hecc/support/kb/
     47For documentation on the Pleiades cluster, see here: http://www.nas.nasa.gov/hecc/support/kb/
    4848
    4949You will need to run the following command before configuring ISSM:
    … …  
    7878== Installing ISSM on Pleiades with Dakota ==
    7979
    80 For Dakota to run, you will not need to remake PETSc and m1qn3, as long as you made them using the intel mpi and the mpi compilers, as described above.
    81 
    82 In your `~/.bashrc`, change your loaded packages to remove the pkgsrc. Since pkgsrc loads an incompatible boost, it needs to be removed to build dakota:
     80You will not need to remake PETSc and m1qn3, as long as you made them using the Intel MPI libraries and compilers, as described above.
     81
     82In `~/.bashrc`, change your loaded packages to remove pkgsrc (it loads an incompatible copy of Boost and needs to be removed in order to build Dakota):
    8383
    8484{{{
    … …  
    8888}}}
    8989
    90 Then ''log out and log back in'', and build the external packages:
     90Then, ''log out and log back in'' and build the following external packages:
    9191 - gsl, install-pleiades.sh
    9292 - boost, install-1.55-pleiades.sh
    … …  
    9696
    9797{{{
    98 #!sh
     98#/
    9999./configure \
    100100 --prefix=$ISSM_DIR \
    … …  
    131131}}}
    132132
     133NOTE: Refer to jenkins/pleiades-dakota for external packages and configuration updates that may not yet be listed here.
     134
     135== Installing ISSM on Pleiades with Solid Earth Capabilities ==
     136
     137The required external packages and configuration of ISSM with Solid Earth capabilities is similar to building ISSM with Dakota. You will not need to remake PETSc and m1qn3, as long as you made them using the Intel MPI libraries and compilers, as described above.
     138
     139In `~/.bashrc`, change your loaded packages to remove pkgsrc (it loads an incompatible copy of Boost and needs to be removed in order to build Dakota):
     140
     141#Packages
     142module load comp-intel/2018.3.222
     143module load mpi-intel/2018.3.222
     144}}}
     145
     146Then, ''log out and log back in'' and build the following external packages:
     147 - zlib, install-1.sh
     148 - hdf5, install-1-parallel.sh
     149 - gsl, install-pleiades.sh
     150 - boost, install-1.55-pleiades.sh
     151 - dakota, install-6.2-pleiades.sh
     152 - curl, install-7-linux.sh
     153 - netcdf, install-4.7-parallel.sh
     154 - sqlite, install.sh
     155 - proj, install-6.sh
     156 - gdal, install-3.sh
     157 - gshhg, install.sh
     158 - gmt, install-6-linux.sh
     159 - gmsh, install-4.sh
     160
     161Finally, you will need to use the following configuration script (i.e. adding the "with" lines for Dakota and Boost):
     162
     163{{{
     164#!sh
     165./configure \
     166--prefix=$ISSM_DIR \
     167--enable-development \
     168--enable-standalone-libraries \
     169--with-wrappers=no \
     170--with-vendor="intel-pleiades-mpi" \
     171--with-cxxoptflags="-O3 " \
     172--with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \
     173--with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
     174--with-boost-dir="${ISSM_DIR}/externalpackages/boost/install" \
     175--with-dakota-dir="${ISSM_DIR}/externalpackages/dakota/install" \
     176--with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \
     177--with-mpi-include=" " \
     178--with-mpi-libflags=" -lmpi" \
     179--with-mkl-libflags="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm" \
     180--with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
     181--with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \
     182--with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
     183--with-scalapack-lib="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/libmkl_scalapack_lp64.so" \
     184--with-graphics-lib="/usr/lib64/libX11.so" \
     185--with-fortran-lib="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64_lin/ -lifcore -lifport -lgfortran" \
     186}}}
     187
     188Again, you will need to run the following command before configuring ISSM:
     189
     190{{{
     191cd $ISSM_DIR
     192autoreconf -ivf
     193}}}
     194
     195NOTE: Refer to jenkins/pleiades-solid_earth for external packages and configuration updates that may not yet be listed here.
    133196
    134197== Installing ISSM on Pleiades with CoDiPack ==
    … …  
    139202 - codipack, install.sh
    140203
    141 Your configuration script should look like that:
     204Your configuration script should look like this:
    142205
    143206{{{
    … …  
    168231 --enable-development
    169232
    170 #NB: The following is the old flag list, which does not work with the mpi compiler
     233#NOTE: The following is the old flag list, which does not work with the mpi compiler
    171234#--with-cxxoptflags="-g -O3 -diag-disable=2196 -axCORE-AVX2,AVX -xSSE4.2 " \
    172235}}}
    173236
    174 You will get a lot of warnings while compiling (like ''warning #2196: routine is both "inline" and "noinline"''), just ignore them.
     237You will get a lot of warnings while compiling (i.e. ''warning #2196: routine is both "inline" and "noinline"''), which can be ignored.
    175238
    176239== pfe_settings.m ==
    177240
    178 You have to add a file in `$ISSM_DIR/src/m` entitled `pfe_settings.m` (on the machine you wish to access Pleiades) with your personal settings:
     241You have to add a file in `$ISSM_DIR/src/m` titled `pfe_settings.m` (on the machine you wish to access Pleiades) with your personal settings:
    179242
    180243{{{
    … …  
    204267
    205268== Running jobs on Pleiades ==
    206 
    207269On Pleiades, the more nodes and the longer the requested time, the more you will have to wait in the queue. So choose your settings wisely:
    208270