Changes between Version 2 and Version 3 of camhpc

Timestamp:

10/19/16 13:10:38 (8 years ago)

Author:

Mathieu Morlighem

Comment:

--

camhpc

@@ +1 @@
+== Getting an account ==
 
-~/.ssh/config
+Talk to Neil...
 
-Do the rss key thing on both citadel and login.hpc.cam.ac.uk
+== ssh configuration ==
 
-From outside campus:
-
+You can add the following lines to `~/.ssh/config` on your local machine if you are running ISSM from outside campus:
+{{{
+#!sh
 Host camhpc darwin login.hpc.cam.ac.uk
   HostName login.hpc.cam.ac.uk
-  User nsa12
-  ProxyCommand ssh nsa12@citadel.ch.cam.ac.uk nc %h %p 2> /dev/null
+  User YOURHPCUSERNAME
+  ProxyCommand ssh YOURUSERNAME@citadel.ch.cam.ac.uk nc %h %p 2> /dev/null
   HostKeyAlias login.hpc.cam.ac.uk
-
-from campus:
-
+}}}
+If you can ssh to hoc directly (from campus), you don't need to go through citadel and you can log in directly:
+{{{
+#!sh
 Host camhpc darwin login.hpc.cam.ac.uk
   HostName login.hpc.cam.ac.uk
-  User nsa12
+  User YOURHPCUSERNAME
+}}}
+and replace `YOURHPCUSERNAME` by your hoc username.
 
+Once this is done, you can ssh to HPC by simply doing:
+
+{{{
+#!sh
+ssh camhpc
+}}}
+
+== 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 already have one, you can skip their creation described below. 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
+$your_localhost% ssh-keygen -t rsa
+Generating public/private rsa key pair.
+Enter file in which to save the key (/Users/username/.ssh/id_rsa):RETURN
+Enter passphrase (empty for no passphrase):RETURN
+Enter same passphrase again:RETURN
+Your identification has been saved in /Users/username/.ssh/id_rsa.
+Your public key has been saved in /Users/username/.ssh/id_rsa.pub.
+}}}
+
+Two files were created: your private key `/Users/username/.ssh/id_rsa`, and the public key `/Users/username/.ssh/id_rsa.pub`. The private key is read-only and only for you, it is used to decrypt all correspondence encrypted with the public key. The contents of the public key need to be copied to `~/.ssh/authorized_keys` on your greenplanet account:
+
+{{{
+#!sh
+$your_localhost%scp ~/.ssh/id_rsa.pub username@your_remotehost:~
+}}}
+
+Now on '''Greenplanet''', copy the content of id_rsa.pub:
+
+{{{
+#!sh
+$your_remotehost%cat ~/id_rsa.pub >> ~/.ssh/authorized_keys
+$your_remotehost%rm ~/id_rsa.pub
+}}}
+
+== Environment ==
+
+On HPC, add the following lines to `~/.bashrc`:
+{{{
+#!sh
+export ISSM_DIR=PATHTOTRUNK
+source $ISSM_DIR/etc/environment.sh
+module load petsc/3.6.4
+}}}
+
+''Log out and log back in'' to apply this change.
+
+== Installing ISSM on Greenplanet ==
+
+Greenplanet will ''only'' be used to run the code, you will use your local machine for pre and post processing, you will never use Greenplanet's matlab. You can check out ISSM and install the following packages:
+ - automake (the one provided by default is too old)
+ - m1qn3
+
+Use the following configuration script (adapt to your needs):
+
+{{{
+#!sh
+./configure \
+   --prefix=$ISSM_DIR \
+   --with-wrappers=no \
+   --with-kml=no \
+   --with-bamg=no \
+   --with-metis-dir="/usr/local/Cluster-Apps/petsc/3.6.4/intel12.1-impi/" \
+   --with-petsc-dir="/usr/local/Cluster-Apps/petsc/3.6.4/intel12.1-impi/" \
+   --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
+   --with-mpi-include="/usr/local/Cluster-Apps/intel/impi/4.1.3.045/include64/" \
+   --with-mpi-libflags="-L/usr/local/Cluster-Apps/intel/impi/4.1.3.045/lib64 -lmpi" \
+   --with-mkl-libflags="-L/usr/local/Cluster-Apps/intel/mkl/10.3.10.319/composer_xe_2011_sp1.10.319/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm" \
+   --with-mumps-dir="/usr/local/Cluster-Apps/petsc/3.6.4/intel12.1-impi/" \
+   --with-cxxoptflags="-DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX "
+}}}
+== camhpc_settings.m ==
+
+You have to add a file in `$ISSM_DIR/src/m` entitled `camhpc_settings.m` with your personal settings:
+
+{{{
+#!m
+cluster.login='nsa12';
+cluster.partition='sandybridge';
+cluster.project='ARNOLD-SL3';
+cluster.port=0;
+cluster.codepath='/home/nsa12/trunk-jpl/bin';
+cluster.executionpath='/home/nsa12/trunk-jpl/execution/';
+cluster.numnodes=1;
+cluster.cpuspernode=3;
+cluster.time=2;
+}}}
+
+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=camhpc()`
+
+== Running jobs on HPC ==
+
+On HPC, you can use up to XX cores per node. The more nodes and the longer the requested time, the more you will have to wait in the queue. Per job you can only request up to XXXGB of RAM. So choose your settings wisely:
+
+ {{{
+#!m
+md.cluster=camhpc('numnodes',1,'cpuspernode',8);
+md.cluster.time=10;
+}}}
+
+to have a maximum job time of 10 minutes and 8 cores on one node. 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, type in:
+
+ {{{
+#!sh
+squeue -u username
+}}}
+
+You can delete your job manually by typing:
+
+{{{
+#!sh
+scancel JOBID
+}}}
+
+where JOBID is the ID of your job (indicated in the Matlab session). Matlab indicates too the directory of your job where you can find the files `JOBNAME.outlog` and `JOBNAME.errlog`. The outlog file contains the informations that would appear if you were running your job on your local machine and the errlog file contains the error information in case the job encounters an error. 
+
+If you want to load results from the cluster manually (for example if you have an error due to an internet interruption), you find in the informations Matlab gave you `$ISSM_DIR/execution/LAUNCHSTRING/JOBNAME.lock `, you copy the LAUNCHSTRING and you type in Matlab:
+
+{{{
+#!m
+md=loadresultsfromcluster(md,'LAUNCHSTRING');
+}}}
+
+== slurm ==
+
+A comparision of PBS to slurm commands can be found here: http://slurm.schedmd.com/rosetta.pdf 
+
+Useful commands:
+
+Graphical overview over greenplanet usage:
+{{{
+sview
+}}}
+
+Get number of idle nodes:
+{{{
+sinfo --states=idle
+}}}
+
+See jobs of <username>:
+{{{
+squeue -u <username>
+}}}
+
+Get more information on jobs of user:
+{{{
+sacct -u <username> --format=User,JobID,account,Timelimit,elapsed,ReqMem,MaxRss,ExitCode
+}}}
+
+Get information on partition (here c6145):
+{{{
+scontrol show partition=c6145
+}}}
+
+Get sorted list of users on partition:
+{{{
+squeue  | grep -i c6145 | awk '{print $4}' | sort | uniq -c | sort -rn
+}}}