Running interactive job with SLURM

The following command is useful for submitting an interactive job on a cluster running SLURM
srun --ntasks=32 --ntasks-per-node=16 --time=00:30:00 --partition=express --pty bash

Profiling Code on Mac

Today I found Instruments, a program available on the Mac OS for performing many code assessments including profiling.  I found it very easy to use.  Below are steps to profile a code.

1. With the gnu compile suite, compile your code with the -g flag (this isn't necessary but provides a better profiling experience and you get timing down to individual lines of code)
2. Open Instruments
3. Select Time Profiler
   
4. At the top by the red circle and pause button, select Choose target and select your code.  Provide a working directory and inputs as desired/needed.
   
5. Click the red circle to begin profiling.
6. At the bottom you should see the Call Tree filing up
   
7. Double click on any item in the Call Tree to get more information
   

Compiling VisIt on Cluster

I needed to build visit on a cluster to read silo files and successfully completed the build with the following command.

./build_visit2_12_3 --hdf5 --szip --silo --parallel --qt5 --console --prefix /home/msu/mowkes/opt/visit2_7_2 

The build_visit script is available from https://wci.llnl.gov/codes/visit/source.html. Additional options are provided by running ./build_visit -h or visiting http://www.visitusers.org/index.php?title=Build_visit_overview

Improving workflow: Zotero & Latex

I use Zotero as my reference manager. I've tried others including the popular Mendeley program but find Zotero's import feature the easiest to use and Zotero meets my needs well.

There are a couple of add-ons that I recently added to Zotero to improve my workflow when adding and using references in Latex documents. The first keeps the bibtex file automatically updated whenever changes are made to your Zotero library. To do this install Zotero automatic export from rokdd.de/permanent:zotero-autoexporting

The second allows for cite-keys (e.g. \cite{smith_fluids_1987}) to be either copied and pasted or dragged and dropped directly into your favorite text editor. To do this I followed directions from this forum by Kramer. The add-on works by adding an additional export format to Zotero.

Copy the code from http://pastebin.com/GXmCJevn and save it in a file called BibtexCiteKeyOnly.js within the translators folder in your zotero. If you don't know where your zotero folder is you can find it by going to Zotero Preferences, Advanced, and clicking on Show Data Directory. Once you restart Zotero (or Firefox) enable the export mode by going to Zotero Preferences, Export, and choosing BibTeX-CITEP. You should now be able to drag a reference (or multiple references) into your text editor and get the citekey. Or you can copy the citekey using Cmd+Shift+C and paste it using Cmd+V.

Start iPython notebook with inline plotting

I recently found iPython notebook which is a tool that allows you to use python interactively to make plots and perform analysis on data. To start a iPython notebook session with inline plots run ipython notebook --pylab inline

Mount filesystem using ssh

It is very easy to mount a filesystem that lives on a remote computer using sshfs. Simply run, mkdir mountpoint
sshfs -o follow_symlinks hostname: mountpoint/ where hostname is what you use to ssh into the remote computer (e.g. name@computer.gov)

Compliing and using LLNL Silo on Mac OS X and linking Fortran program

Download hdf5, uncompress, and then install using ./configure --prefix=/opt/hdf5
make
make install
Download szip, uncompress and then install using ./configure --prefix=/opt/szip
make
make install
Download (silo), uncompress, then install using ./configure --enable-fortran --with-hdf5=/opt/hdf5/include/,/opt/hdf5/lib --with-szlib=/opt/szip/ --prefix=/opt/silo/ --disable-silex
make
make install
You should find the silo libraries in /opt/silo/lib. To make sure you have the fortran routines you can run in /opt/silo/lib nm libsiloh5.a | grep dbcreate which should show 00000000000039f0 T _dbcreate_ <==== this shows you have the fortran routines
0000000000019078 S _dbcreate_.eh
To compile a program that uses silo.h run a command similar to gfortran -I /opt/silo/include/ -L /opt/silo/lib/ -L /opt/hdf5/lib/ -L /opt/szip/lib/ -o fbasic fbasic.f -lsiloh5 -lhdf5 -lsz -lz -lstdc++ that compiles fbasic.f, which is an example program provided by LLNL (see below)

fbasic.f c-----------------------------------------------------------------------------
c
c Copyright (c) 2000 - 2008, Lawrence Livermore National Security, LLC
c Produced at the Lawrence Livermore National Laboratory
c LLNL-CODE-400142
c All rights reserved.
c
c This file is  part of VisIt. For  details, see https://visit.llnl.gov/.  The
c full copyright notice is contained in the file COPYRIGHT located at the root
c of the VisIt distribution or at http://www.llnl.gov/visit/copyright.html.
c
c Redistribution  and  use  in  source  and  binary  forms,  with  or  without
c modification, are permitted provided that the following conditions are met:
c
c  - Redistributions of  source code must  retain the above  copyright notice,
c    this list of conditions and the disclaimer below.
c  - Redistributions in binary form must reproduce the above copyright notice,
c    this  list of  conditions  and  the  disclaimer (as noted below)  in  the
c    documentation and/or other materials provided with the distribution.
c  - Neither the name of  the LLNS/LLNL nor the names of  its contributors may
c    be used to endorse or promote products derived from this software without
c    specific prior written permission.
c
c THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT  HOLDERS AND CONTRIBUTORS "AS IS"
c AND ANY EXPRESS OR  IMPLIED WARRANTIES, INCLUDING,  BUT NOT  LIMITED TO, THE
c IMPLIED WARRANTIES OF MERCHANTABILITY AND  FITNESS FOR A PARTICULAR  PURPOSE
c ARE  DISCLAIMED. IN  NO EVENT  SHALL LAWRENCE  LIVERMORE NATIONAL  SECURITY,
c LLC, THE  U.S.  DEPARTMENT OF  ENERGY  OR  CONTRIBUTORS BE  LIABLE  FOR  ANY
c DIRECT,  INDIRECT,   INCIDENTAL,   SPECIAL,   EXEMPLARY,  OR   CONSEQUENTIAL
c DAMAGES (INCLUDING, BUT NOT  LIMITED TO, PROCUREMENT OF  SUBSTITUTE GOODS OR
c SERVICES; LOSS OF  USE, DATA, OR PROFITS; OR  BUSINESS INTERRUPTION) HOWEVER
c CAUSED  AND  ON  ANY  THEORY  OF  LIABILITY,  WHETHER  IN  CONTRACT,  STRICT
c LIABILITY, OR TORT  (INCLUDING NEGLIGENCE OR OTHERWISE)  ARISING IN ANY  WAY
c OUT OF THE  USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
c DAMAGE.
c
c-----------------------------------------------------------------------------

      program main
      implicit none
      include "silo.inc"
      integer dbfile, ierr

c The 11 and 22 arguments represent the lengths of strings
      ierr = dbcreate("fbasic.silo", 11, DB_CLOBBER, DB_LOCAL,
     . "Comment about the data", 22, DB_HDF5, dbfile)

      if(dbfile.eq.-1) then
          write (6,*) 'Could not create Silo file!\n'
          goto 10000
      endif

c Add other Silo calls here.

c Close the Silo file.
      ierr = dbclose(dbfile)
10000 stop
      end