Changes between Version 2 and Version 3 of hexagon


Ignore:
Timestamp:
03/22/16 09:45:36 (9 years ago)
Author:
bdef
Comment:

Changing info to the real ones for the install on Hexagon

Legend:

Unmodified
Added
Removed
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  • hexagon

    v2 v3  
    11== Getting an account ==
    22
    3 First, you need to send an email to XXX (email: xxx [at] iomail.org) and request an account.
     3First, you need to get an account from NOTUR, the webpage for you request is : https://www.metacenter.no/user/application/form/notur/.
    44
    55== ssh configuration ==
    … …  
    88{{{
    99#!sh
    10 Host hexagon hexagon.uib.xxxx
    11   HostName gplogin1.ps.uci.edu
    12   User YOURHEXAGONUSERNAME
    13   HostKeyAlias gplogin1.ps.uci.edu
    14   HostbasedAuthentication no
     10Host hexagon hexagon.hpc.uib.no
     11    HostName hexagon.hpc.uib.no
     12    User YOURHEXAGONUSERNAME
    1513}}}
    1614and replace `YOURHEXAGONUSERNAME` by your hexagon username.
    1715
    18 Once this is done, you can ssh green planet by simply doing:
     16Once this is done, you can ssh hexagon by simply doing:
    1917
    2018{{{
    … …  
    5957#!sh
    6058export ISSM_DIR=PATHTOTRUNK
    61 source $ISSM_DIR/etc/environment.sh
    6259export CRAYPE_LINK_TYPE=dynamic
    6360#
    … …  
    6764module load craype-barcelona
    6865module load automake
    69 module load boost/1.60.0
    70 module load gdal
    71 module load proj
    72 module load gmt
    73 module load cmake
    7466module load cray-petsc
    7567module load cray-tpsl
    7668module load cray-mpich
    77 module load cray-hdf5
    78 module load cray-netcdf
    79 module load ncview
    8069module load gsl
    81 module load python
    82 module load git
    83 module load sqlite
    84 module load swig
    8570}}}
    8671
    … …  
    8974== Installing ISSM on Hexagon ==
    9075
    91 You can check out ISSM and install the following packages (most packages are preinstalled and loaded through ''model load'' commands in your ''~/.bashrc''):
    92  - autotools
    93  - PETSc (use the hexagon script and ``follow`` the instructions, you will need to submit a job and compile PETSc manually, do not make test, it will not work on the cluster)
    94  - m1qn3
     76You can check out ISSM and install m1qn3. This is the only package we will install, the module loaded from your bashrc are taking care of the rest.
    9577
    96 Use the following configuration script (adapt to your needs):
    97 
     78Copy the Hexagon configuration script from the configs directory and rename it:
    9879{{{
    9980#!sh
    100 ./configure \
    101  --prefix=$ISSM_DIR \
    102  --with-wrappers=no \
    103  --with-kml=no \
    104  --with-bamg=no \
    105  --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
    106  --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
    107  --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
    108  --with-mpi-include="/sopt/mpi/openmpi-1.8.3/intel_15.0.0/include" \
    109  --with-mpi-libflags="-L/sopt/mpi/openmpi-1.8.3/intel_15.0.0/lib -lmpi" \
    110  --with-mkl-dir="/sopt/Intel/composer_xe_2015.0.090/mkl/lib/intel64" \
    111  --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
    112  --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
    113  --with-cxxoptflags="-O3" \
    114  --with-petsc-libflags="-L$PETSC_ROOT/lib -lcraypetsc_gnu_real -lmetis"
     81cp configs/config-linux64-hexagon.sh configure.sh
     82}}}
    11583
     84When running autotools you may run into the following error message :
     85{{{
     86#!sh
     87src/c/Makefile.am:9: Libtool library used but `LIBTOOL' is undefined
     88src/c/Makefile.am:9:   The usual way to define `LIBTOOL' is to add `LT_INIT'
     89src/c/Makefile.am:9:   to `configure.ac' and run `aclocal' and `autoconf' again.
     90src/c/Makefile.am:9:   If `LT_INIT' is in `configure.ac', make sure
     91src/c/Makefile.am:9:   its definition is in aclocal's search path.
     92}}}
     93running libtoolize should solve this issue.
     94
     95
     96Due to the fact that the autotool on this machine is getting old you should comment the following line in  `src/c/main/EnvironmentInit.cpp `:
     97{{{
     98#!sh
     99if(!my_rank) printf("(website: %s contact: %s)\n",PACKAGE_URL,PACKAGE_BUGREPORT);
    116100}}}
    117101== hexagon_settings.m ==
    118102
    119 You have to add a file in `$ISSM_DIR/src/m` entitled `hexagon_settings.m` with your personal settings:
    120 
    121 {{{
    122 #!m
    123 cluster.login='mmorligh';
    124 cluster.queue='c6145';
    125 cluster.codepath='/home/mmorligh/trunk-jpl/bin/';
    126 cluster.executionpath='/home/mmorligh/trunk-jpl/execution/';
    127 }}}
    128 
    129 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=hexagon()`
     103TO BE DONE function of hexagon.py
    130104
    131105== Running jobs on Hexagon ==
     106TO BE UPDATED
    132107
    133108On Hexagon, you can use up to 30 cores per node. The more nodes and the longer the requested time, the more you will have to wait in the queue. So choose your settings wisely: