docs/quick_start_guide/1.txt File Reference

Detailed Description

1) Compile and Run HARM (using latest git version)
Version 26 Created by Jonathan M. at 7:52pm. Previous Version

1) *Be in Linux*

1a) Install emacs and other packages necessary along the way or now.

1b) Install vis5d+, HDF, etc.

**See new notebook for vis5dPlus installation instructions**

2) *Create directory for git code tree:* Command: "mkdir harm ; cd harm"

2b) Copy ssh public key from your linux into unfuddle for your user:

ssh-keygen [hit enter if any questions]

2c) Copy that the contents of the public key (e.g. ~/.ssh/id_rsa.pub) to unfuddle in your personal settings.

3) *Get Code:* Command: "git clone git@harm.unfuddle.com:harm/harmgit.git"

cd harmgit

4) *Setup links to desired simulation model initializations and boundary condition files:* Command (E.g.):

ln -s initboundcode/init.fishmon.c init.c

ln -s initboundcode/init.fishmon.h init.h

ln -s initboundcode/bounds.fishmon.c bounds.c

5) Pre-compile stuff: (do this if icc not already installed and not calling source command given below in .bashrc or .profile)

5a) *Source any libraries:* E.g. Command: "source /opt/intel/mkl/10.0.3.020/tools/environment/mklvarsem64t.sh"

If no icc, then download:

e.g. http://software.intel.com/en-us/non-commercial-software-development and choose the one with both Intel and Fortran compilers (e.g. Intel® Parallel Studio XE 2013 for Linux)

If you don't want to get icc (Intel compiler), then set USEICCINTEL=0 and USEGCC=1 in makehead.inc

If no lapack, then set USELAPACK=0 and USELAPACKNEW=0 in makehead.inc

If no MPI, set USEMPI=0 (for first setting which is a choice) in makehead.inc

If no OpenMP (or problems compiling on MAC), set USEOPENMP=0 in makehead.inc

5b) Install packages like hdf4 (several things for ubuntu packages, including dev stuff) (if root, install, else ask)

e.g. in ubuntu: sudo aptitude install libhdf4g-dev libhdf4g-doc libhdf4-0 libhdf4-dev libhdf4-doc hdf4-tools

Also in makefile, search for "bin2txt" and either choose block of code for "system" type installation or "user" type installation.
In bin2txt.c, choose same case for how hdf.h and mfhdf.h are included, but sometimes just "hdf\<all>" is correct.

5c) Also ensure you have installed vis5d+ as in other guide before bin2txt will compile.

5d) To get MPI, goto: http://www.mpich.org/downloads/ and Get the "mpich-3.0.2 (stable release)" version to install from source.  Look at the README, follow "bash" versions of "configure" "make" "make install" with your username instead of <USERNAME>

6) *Compile Codes:*

6a) # CAREFUL! (do this if have root access)
sudo bash
cd /bin
rm -f sh
ln -s bash sh
exit  # to get back to your user

6b) Command: "make superclean ; make prepsmcalc ; make smcalc ; cp smcalc ~/bin/"

6c) Command: "make superclean ; make prepiinterp ; make iinterp ; cp iinterp ~/bin/"

Edit makefile and do 2 things:

i) search -lv5d .  Before that, add "-L /home/<username>/lib"  without quotes and with <username> replaced by your user name.
ii) Also, add "-I /home/<username>/include"  (-I is a capital i and not a capital l) to the end of that same line.

6d) Command: "make superclean ; make prepbin2txt ; make bin2txt ; cp bin2txt ~/bin/"

6e) Command: "make superclean ; make prep ; make"

**NOTE**: If have N cores, can vastly speed-up compile by doing:

6d(e.g. 16 cores)) Command: "make superclean ; make prep ; make -j 16"

**NOTE**: Default compiler is typical ICC using USEICC=1 in the file "makefile".  See bottom of this document for notes on changing this for other machines.

7) *Make directory for run code:* Command: "mkdir run ; cp grmhd run ; cd run"

8) *If OpenMP and MPI, then Run Code with 4 OpemMP threads per node in 1x1x1 MPI matrix:* "nohup ./grmhd 4 1 1 1 &"

*If turned off MPI and OPENMP, do: "nohup ./grmhd &"*

9a) *Look at results with SM (Supermongo) using SM project.*

9b) Or use vis5d+

10) IF YOU ARE ON A REMOTE COMPUTER:  *Standard permissions on many servers is that anyone can read your files.  Wherever you place the *code* or move it to (e.g. some supercomputer or other server), PLEASE change the permissions of that directory so noone else can access (i.e. copy) the code.  I don't want just anybody being able to copy HARM.  Please do this for each and every machine you place the code onto.  The command you should run is:*

chmod -R og-rwx <dir>

*For example, do:*

a) mkdir harmcode

b) chmod -R og-rwx harmcode

*Again, do this no matter where you copy the code to.*

11) Finally, this is not a shared code.  Only you are allowed access to this code.  Do not share it or share your access to this site.  Thank you for understanding!

-Jonathan McKinney

Definition in file 1.txt.