Icarus 1.0 Quick Start: Difference between revisions

(3 intermediate revisions by the same user not shown)

Line 15:

Port 22223

That's it. Progress is not needed unless you specifically know you need it. It won't hurt to add it, but at present it isn't needed. Also, you'll need to generate RSA ~~and/~~or ~~DSA~~ keys and upload them (this is mentioned in the quick start page above) to https://progress.nccs.nasa.gov/keyupload/.

That's it. Progress is not needed unless you specifically know you need it. It won't hurt to add it, but at present it isn't needed. Also, you'll need to generate RSA or ED25519 keys and upload them (this is mentioned in the quick start page above) to https://progress.nccs.nasa.gov/keyupload/. (NOTE: DSA keys are not recommended as some sites, e.g., NAS, have started disallowing them.)

The commands below assume that your shell is <code>csh</code>. Since the scripts to build and run GEOS-5 tend to be written in the same, you shouldn't bother trying to import too much into an alternative shell. If you prefer a different shell, it is easiest just to open a <code>csh</code> process to build the model and your experiment.

Line 31:

This should check out the latest stable version of the model from the repository and create a directory called <code>GEOSagcm</code>.

==== CVS Errors ====

If the CVS checkout doesn't work for you, there are many possibilities. If the error says something about "keyupload", then the key upload either hasn't taken hold yet (can take 5-10 minutes to work after uploading the key), or, perhaps, the wrong key was uploaded.

If you see something like "access denied for this host", then your best bet is to contact NCCS. Per a response from NCCS to a user that had something similar happen, they need to add the CVS hosts to an LDAP entry.

=== Compiling the Model ===

Line 58:

Line 64:

4) other/comp/gcc-4.6.3-sp1

5) other/SIVO-PyD/spd_1.20.0_gcc-4.6.3-sp1_mkl-15.0.0.090

If this all worked, then type:

Line 65:

Line 70:

This will build the model. It will take about 30 minutes. If this works, it should create a directory under <code>GEOSagcm</code> called <code>Linux/bin</code>. In here you should find the executable: <code>GEOSgcm.x</code> .

GEOS-5 has moved to using SGI MPT by default at NCCS. This means the model '''CANNOT be built on Dali'''. You can build the model on any Discover head node or any Haswell compute node.

== Setting up a Run ==

=== Passwordless Logins ===

First of all, to run jobs on the cluster you will need to set up passwordless <code>ssh</code> (which operates within the cluster, between the nodes running the job). To do so, run the following from your '''discover''' home directory:

cd .ssh

ssh-keygen -t ~~dsa~~

ssh-keygen -t rsa

cat ~~id_dsa~~.pub >> authorized_keys

cat id_rsa.pub >> authorized_keys

Similarly, transferring the daily output files (in monthly tarballs) requires passwordless authentication from '''discover''' to '''dirac'''. While in <code>~/.ssh</code> on '''discover''', run

ssh-keygen -t ~~dsa~~

ssh-keygen -t rsa

Then, log into '''dirac''' and cut and paste the contents of the <code>id_rsa.pub</code> file on '''discover''' into the <code>~/.ssh/authorized_keys</code> file on '''dirac'''. Problems with <code>ssh</code> should be referred to NCCS support.

==== DSA Keys ====

Note: Due to evolution of security, it is recommended to not use DSA keys. NAS currently doesn't not allow them, and RSA and ED25519 keys are considered "better" anyway.

Then, log into '''dirac''' and cut and paste the contents of the <code>id_rsa.pub</code> and <code>id_dsa.pub</code> files on '''discover''' into the <code>~/.ssh/authorized_keys</code> file on '''dirac'''. Problems with <code>ssh</code> should be referred to NCCS support.

=== Setting up a model run ===

To set the model up to run, cd to <code>GEOSagcm/src/Applications/GEOSgcm_App</code> and run:

@@ Line 15: / Line 15: @@
       Port 22223
-That's it. Progress is not needed unless you specifically know you need it. It won't hurt to add it, but at present it isn't needed. Also, you'll need to generate RSA and/or DSA keys and upload them (this is mentioned in the quick start page above) to https://progress.nccs.nasa.gov/keyupload/.
+That's it. Progress is not needed unless you specifically know you need it. It won't hurt to add it, but at present it isn't needed. Also, you'll need to generate RSA or ED25519 keys and upload them (this is mentioned in the quick start page above) to https://progress.nccs.nasa.gov/keyupload/. (NOTE: DSA keys are not recommended as some sites, e.g., NAS, have started disallowing them.)
 The commands below assume that your shell is <code>csh</code>.  Since the scripts to build and run GEOS-5  tend to be written in the same, you shouldn't bother trying to import too much into an alternative shell.  If you prefer a different shell, it is easiest just to open a <code>csh</code> process to build the model and your experiment.
@@ Line 31: / Line 31: @@
 This should check out the latest stable version of the model from the repository and create a directory called <code>GEOSagcm</code>.
+==== CVS Errors ====
+If the CVS checkout doesn't work for you, there are many possibilities. If the error says something about "keyupload", then the key upload either hasn't taken hold yet (can take 5-10 minutes to work after uploading the key), or, perhaps, the wrong key was uploaded.
+If you see something like "access denied for this host", then your best bet is to contact NCCS. Per a response from NCCS to a user that had something similar happen, they need to add the CVS hosts to an LDAP entry.
 === Compiling the Model ===
@@ Line 58: / Line 64: @@
 ) other/comp/gcc-4.6.3-sp1
 ) other/SIVO-PyD/spd_1.20.0_gcc-4.6.3-sp1_mkl-15.0.0.090
 If this all worked, then type:
@@ Line 65: / Line 70: @@
 This will build the model.  It will take about 30 minutes.  If this works, it should create a directory under <code>GEOSagcm</code> called <code>Linux/bin</code>.  In here you should find the executable: <code>GEOSgcm.x</code> .
+<span style="color:red">NOTE NOTE NOTE NOTE NOTE NOTE NOTE NOTE NOTE NOTE NOTE NOTE NOTE NOTE NOTE NOTE NOTE</span>
+GEOS-5 has moved to using SGI MPT by default at NCCS. This means the model '''CANNOT be built on Dali'''. You can build the model on any Discover head node or any Haswell compute node.
 == Setting up a Run ==
+=== Passwordless Logins ===
 First of all, to run jobs on the cluster you will need to set up passwordless <code>ssh</code> (which operates within the cluster, between the nodes running the job).  To do so, run the following from your '''discover''' home directory:
   cd .ssh
-  ssh-keygen -t dsa
+  ssh-keygen -t rsa
-  cat id_dsa.pub >>  authorized_keys
+  cat id_rsa.pub >>  authorized_keys
 Similarly, transferring the daily output files (in monthly tarballs) requires passwordless authentication from '''discover''' to '''dirac'''.  While in <code>~/.ssh</code> on '''discover''', run
-   ssh-keygen -t dsa
+   ssh-keygen -t rsa
+Then, log into  '''dirac''' and cut and paste the contents of the <code>id_rsa.pub</code> file on '''discover''' into the  <code>~/.ssh/authorized_keys</code> file on   '''dirac'''.  Problems with <code>ssh</code> should be referred to NCCS support.
+==== DSA Keys ====
+Note: Due to evolution of security, it is recommended to not use DSA keys. NAS currently doesn't not allow them, and RSA and ED25519 keys are considered "better" anyway.
-Then, log into  '''dirac''' and cut and paste the contents of the <code>id_rsa.pub</code> and <code>id_dsa.pub</code> files on '''discover''' into the  <code>~/.ssh/authorized_keys</code> file on   '''dirac'''.  Problems with <code>ssh</code> should be referred to NCCS support.
+=== Setting up a model run ===
 To set the model up to run, cd to <code>GEOSagcm/src/Applications/GEOSgcm_App</code> and run: