Changes between Initial Version and Version 1 of Stallo

Timestamp:

08/23/17 23:34:14 (7 years ago)

Author:

bdef

Comment:

--

Stallo

@@ +1 @@
+== Getting an account ==
+
+First, you need to get an account from NOTUR, the webpage for you request is : https://www.metacenter.no/user/application/form/notur/.
+
+== ssh configuration ==
+
+You can add the following lines to `~/.ssh/config` on your local machine:
+{{{
+#!sh
+Host stallo stallo.uit.no
+    HostName stallo.uit.no
+    User YOURSTALLOUSERNAME
+}}}
+and replace `YOURSTALLOUSERNAME` by your stallo username.
+
+Once this is done, you can ssh stallo by simply doing:
+
+{{{
+#!sh
+ssh stallo
+}}}
+
+== Password-less ssh ==
+
+Once you have the account, you can setup a public key authentification in order to avoid having to input your password for each run. 
+You need to have a SSH public/private key pair. If you do not, you can create a SSH public/private key pair by typing the following command and following the prompts (no passphrase necessary):
+{{{
+#!sh
+$your_localhost% ssh-keygen -t rsa
+Generating public/private rsa key pair.
+Enter file in which to save the key (/Users/username/.ssh/id_rsa):RETURN
+Enter passphrase (empty for no passphrase):RETURN
+Enter same passphrase again:RETURN
+Your identification has been saved in /Users/username/.ssh/id_rsa.
+Your public key has been saved in /Users/username/.ssh/id_rsa.pub.
+}}}
+
+Two files were created: your private key `/Users/username/.ssh/id_rsa`, and the public key `/Users/username/.ssh/id_rsa.pub`. The private key is read-only and only for you, it is used to decrypt all correspondence encrypted with the public key. The contents of the public key need to be copied to `~/.ssh/authorized_keys` on your stallo account:
+
+{{{
+#!sh
+$your_localhost%scp ~/.ssh/id_rsa.pub username@your_remosthost:~
+}}}
+
+Now on '''Stallo''', copy the content of id_rsa.pub:
+
+{{{
+#!sh
+$your_remosthost%cat ~/id_rsa.pub >> ~/.ssh/authorized_keys
+$your_remosthost%rm ~/id_rsa.pub
+}}}
+
+== Environment ==
+
+On Stallo, add the following lines to `~/.bashrc`:
+{{{
+#!sh
+#Module loading                                                                                           
+module load Automake/1.15-intel-2016a
+module load libtool/2.4.6-intel-2016a
+module load CMake/3.5.2-intel-2016a
+module load intel/2016a
+module load ParMETIS/4.0.3-intel-2016a
+module load MUMPS/5.1.1-intel-2016a-parmetis
+module load PETSc/3.7.2-intel-2016a-Python-2.7.11
+module load FFTW/3.3.4-intel-2016a
+module load OpenSSL/1.0.1s-intel-2016a
+#ISSM                                                                                                     
+export ISSM_DIR=PATHTOISSM
+}}}
+
+''Log out and log back in'' or source you .bashrc to apply this change.
+
+== Installing ISSM on Vilje ==
+
+The only package from external packages that you may require (if you need to run some inversion) is m1qn3. Install it from external packages
+{{{
+cd externalpackages/m1qn3
+./install.sh
+}}}
+
+Once this is done in ISSM_DIR do:
+{{{
+run ./scripts/automakererun.sh
+}}}
+
+Use the following configuration script:
+
+{{{
+#!/bin/sh
+./configure \
+    --prefix=$ISSM_DIR \
+    --without-kriging \
+    --with-wrappers=no \
+    --with-petsc-dir="/global/hds/software/cpu/eb3/PETSc/3.7.2-intel-2016a-Python-2.7.11" \
+    --with-mpi-include="/global/hds/software/cpu/eb3/impi/5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25/include64" \
+    --with-mpi-libflags="-L/global/hds/software/cpu/eb3/impi/5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25/lib64 -lmpich -lmpichf90 -lmpichcxx -lmpl" \
+    --with-metis-dir="/global/hds/software/cpu/eb3/ParMETIS/4.0.3-intel-2016a/include" \
+    --with-mumps-dir="/global/hds/software/cpu/eb3/MUMPS/5.1.1-intel-2016a-parmetis" \
+    --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
+    --with-hypre-dir="/global/hds/software/cpu/eb3/Hypre/2.11.1-intel-2016a" \
+    --with-mkl-libflags="-L/global/hds/software/cpu/eb3/imkl/11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25/mkl/lib/intel64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lmkl_scalapack_lp64 -L/global/hds/software/cpu/eb3/FFTW/3.3.4-intel-2016a/lib/ -lfftw3_mpi -L/global/hds/software/cpu/eb3/SuiteSparse/4.5.3-intel-2016a-ParMETIS-4.0.3/lib -lklu -lamd -lamd -lbtf -lsuitesparseconfig -lumfpack -lcholmod -L/global/hds/software/cpu/eb3/ifort/2016.1.150-GCC-4.9.3-2.25/lib/intel64 -lifcore -lifport -L/global/hds/software/cpu/eb3/OpenSSL/1.0.1s-intel-2016a/lib -lssl -L/global/hds/software/cpu/eb3/SCOTCH/6.0.4-intel-2016a/lib -lesmumps -lptesmumps  -lptscotch  -lptscotcherr  -lptscotcherrexit -lscotch -lscotcherr -lscotcherrexit -lscotch_group" \
+    --enable-development
+}}}
+
+You can then make your configuration file executable (if it is not already) execute it and install ISSM:
+{{{
+chmod +x configure.sh
+./configure
+make install
+}}}
+
+== stallo_settings.py ==
+
+{{{
+def stallo_settings(md):                                                                                                                     
+    md.login='YOURNOTURLOGIN'
+    md.queue='normal'
+    md.codepath='YOURCODEPATH'#home is fne
+    md.executionpath='YOUREXECPATH'#should be in /global/work/username to avoid flooding your home
+    md.accountname='nn4659k'#this is for ice2ice
+    md.numnodes=1
+    md.numprocess=16
+    return md
+}}}
+== stallo_settings.m ==
+
+The use of the Python version of the code is encouraged at Uib but you are welcome to clone the python settings.