Changes between Version 7 and Version 8 of pleiadescsh

Timestamp:

01/12/22 13:27:47 (3 years ago)

Author:

schlegel

Comment:

--

pleiadescsh

@@ -29 +29 @@
 
 #Packages
-module load pkgsrc
+module load pkgsrc/2020Q4
 module load comp-intel/2016.2.181
-module load mpi-sgi/mpt
+module load mpi-hpe/mpt
 }}}
 
@@ -39 +39 @@
 
 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:
- - PETSc (use the pleiades script install-3.13-pleiades.sh or newer)
+ - PETSc (use the pleiades script install-3.13-pleiades.sh)
  - m1qn3
 
@@ -59 +59 @@
  --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \
  --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \
- --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
+ --with-scalapack-lib="-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64/libmkl_scalapack_lp64.so" \
  --with-cxxoptflags="-O3 -axAVX" \
  --with-fortran-lib="-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64/ -lifcore -lifport" \
@@ -68 +68 @@
 == Installing ISSM on Pleiades with Dakota ==
 
-For Dakota to run, you you will still need to make cmake, PETSc, and m1qn3.
+For Dakota to run, you you will still need to make PETSc and m1qn3, but you will need to make sure you are using the intel mpi and that the externalpackages are built with the mpi compilers. 
 
-In addition, will need to build the external package:
+In your `~/.cshrc`, add the following lines:
+
+{{{
+setenv CC mpicc
+setenv CXX mpicxx
+setenv F77 mpif77
+}}}
+
+And change your loaded packages to (no the removal of the pkgsrc):
+
+{{{
+#Packages
+module load comp-intel/2018.3.222
+module load mpi-intel/2018.3.222
+}}}
+
+Then log out and back in, and reinstall the following packages:
+ - PETSc (use the pleiades script install-3.14-pleiades.sh)
+ - m1qn3
+ 
+In addition, will need to build the external package: 
+ - boost, install-1.55-pleiades.sh
  - dakota, install-6.2-pleiades.sh
 
-Finally, you will need to make with mpi compilers by using the following configuration script:
+Finally, you will need to use the following configuration script:
 
 {{{
 #!/bin/csh
 
-export F77=mpif77
-export FC=mpif90
-
 ./configure \
  --prefix=$ISSM_DIR \
+ --enable-standalone-libraries \
  --with-wrappers=no \
- --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \
- --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
- --with-boost-dir=/nasa/pkgsrc/sles12/2018Q3/ \
+ --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
+ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+ --with-metis-dir=$PETSC_ROOT \
+ --with-petsc-dir=$PETSC_ROOT \
+ --with-scalapack-lib="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/libmkl_scalapack_lp64.so" \
+ --with-boost-dir=$ISSM_DIR/externalpackages/boost/install \
  --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
- --with-gsl-dir=/nasa/pkgsrc/sles12/2018Q3/ \
  --with-mpi-include=" " \
  --with-mpi-libflags=" -lmpi" \
- --with-mkl-libflags="-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -limf -lsvml -lirc" \
- --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \
- --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \
- --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
- --with-graphics-lib="/usr/lib64/libX11.so" \
- --with-fortran-lib="-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64/ -lifcore -lifport" \
+ --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" \
+ --with-mumps-dir=$PETSC_ROOT \
+ --with-fortran-lib="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64_lin/ -lifcore -lifport -lgfortran" \
+ --with-cxxoptflags="-O3 " \
  --with-vendor="intel-pleiades-mpi" \
  --enable-development
 }}}
+
+Note, if you would like the capabilities of pkgsrc/2020Q4, including updated svn, make sure that you build dakota without that package loaded.  Once you have ISSM compiled and installed with dakota, feel free to add back in to your `~/.cshrc`:
+
+{{
+module load pkgsrc/2020Q4
+}}
 
 == pfe_settings.m ==
@@ -116 +141 @@
 use your username for the `login` and enter your code path and execution path. These settings will be picked up automatically by matlab when you do `md.cluster=pfe()`
 
-Make sure your module list includes pkgsrc, comp-intel/2016.2.181, and mpi-sgi/mpt .
+Without dakota, make sure your module list includes scicon/app-tools, comp-intel/2016.2.181, and mpi-hpe/mpt.
+With dakota, make sure your module list includes scicon/app-tools, comp-intel/2018.3.222, and mpi-intel/2018.3.222. You can specify your own list of modules by adding to `pfe_settings.m`, for example,:
+
+{{
+cluster.modules = {'comp-intel/2018.3.222' 'mpi-intel/2018.3.222' 'scicon/app-tools'};
+}}
+
 
 == Running jobs on Pleiades ==
@@ -124 +155 @@
  {{{
 #!m
-md.cluster=pfe('numnodes',8,'time',30,'processor','wes','queue','devel');
+md.cluster=pfe('numnodes',8,'time',30,'processor','bro','queue','devel');
 md.cluster.time=10;
 }}}
 
-to have a maximum job time of 10 minutes and 8 westmere nodes. If the run lasts longer than 10 minutes, it will be killed and you will not be able to retrieve your results.
+to have a maximum job time of 10 minutes and 8 broadwell nodes. If the run lasts longer than 10 minutes, it will be killed and you will not be able to retrieve your results.
 
 Now if you want to check the status of your job and the queue you are using, use this command: