Changes between Version 31 and Version 32 of pleiadesbash

Timestamp:

01/12/22 13:58:20 (3 years ago)

Author:

schlegel

Comment:

--

pleiadesbash

@@ -26 +26 @@
 
 #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
 }}}
 
@@ -37 +37 @@
 '''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:
  - m1qn3
- - PETSc (use `install-3.13-pleiades.sh` or newer)
+ - PETSc (use `install-3.15-pleiades.sh` or newer)
 
 For documentation of pleiades, see here: http://www.nas.nasa.gov/hecc/support/kb/
@@ -71 +71 @@
 == Installing ISSM on Pleiades with Dakota ==
 
-For Dakota to run, you you will still need to make PETSc, and m1qn3.
-
-In addition, will need to build the external packages:
+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 your `~/.cshrc`, add the following lines:
+
+{{{
+#Set compilers
+setenv CC mpicc
+setenv CXX mpicxx
+setenv F77 mpif77
+}}}
+
+And change your loaded packages to (note the removal of the pkgsrc):
+
+{{{
+#Packages
+module load comp-intel/2018.3.222
+module load mpi-intel/2018.3.222
+}}}
+
+Then ''log out and log 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: 
+ - gsl, install-pleiades.sh
+ - boost, install-1.55-pleiades.sh
  - dakota, install-6.2-pleiades.sh
 
-Finally, you will need to make with mpi compilers by using the configuration script:
-
-{{{
-#!sh
-export F77=mpif77
-export FC=mpif90
-
+Finally, you will need to use the following configuration script:
+
+{{{
+#!sh
 ./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
 }}}
+
+Remember, you will need to run the following command before configuring ISSM:
+
+{{{
+cd $ISSM_DIR
+autoreconf -ivf
+}}}
+
+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`:
+
+{{{
+#Packages
+module load pkgsrc/2020Q4
+}}}
+
 
 == Installing ISSM on Pleiades with CoDiPack ==
@@ -138 +174 @@
 
 You will get a lot of warnings while compiling (like ''warning #2196: routine is both "inline" and "noinline"''), just ignore them.
+
 == pfe_settings.m ==
 
@@ -152 +189 @@
 }}}
 
-use your username for the `login` and enter your code path and execution path. Be sure to create the final execution directory (mkdir) within the nobackup folder. These settings will be picked up automatically by matlab when you do `md.cluster=pfe()`. To determine your `grouplist`, on Pleiades run: 
+use your username for the `login` and enter your code path and execution path. Be sure to create the final execution directory (mkdir) within the nobackup folder. These settings will be picked up automatically by matlab when you do `md.cluster=pfe()`. 
+
+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'};
+}}}
+
+To determine your `grouplist`, on Pleiades run: 
 
 {{{
@@ -158 +204 @@
 }}}
 
-Make sure your module list includes pkgsrc, comp-intel/2016.2.181, and mpi-sgi/mpt .
 
 == Running jobs on Pleiades ==
@@ -166 +211 @@
  {{{
 #!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: