Shell Programming and Scripting

When I put set -x in there properly as you say, it gives the following for the lines where I specify the path and try to execute nwchem:
+ path=.:/opt/local/bin/x86_64:/opt/gridengine/bin/lx26-amd64:/opt/intel/impi/3.1/bin64:/usr/kerberos/bin:/usr/java/jdk1.5.0_10/bin:/opt/intel/itac/7.1/bin:/opt/intel/fce/10.1.011/bin:/opt/intel/idbe/10.1.011/bin:/opt/intel/cce/10.1.011/bin:/opt/globus/bin:/opt/globus/sbin:/opt/intel/clck/1.1:/usr/local/bin:/bin:/usr/bin:/opt/Bio/ncbi/bin:/opt/Bio/mpiblast/bin/:/opt/Bio/EMBOSS/bin:/opt/Bio/clustalw/bin:/opt/Bio/t_coffee/bin:/opt/Bio/phylip/exe:/opt/Bio/mrbayes:/opt/Bio/fasta:/opt/Bio/glimmer/bin:/opt/Bio/glimmer/scripts:/opt/Bio/gromacs/bin/:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/maven/bin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/usr/X11R6/bin:/usr/local/dislin/bin:/opt/local/share/nwchem/nwchem
+ nwchem SDDbeckehandh3_spin.nw
./nw_chem_DIMERscript.sh: line 152: nwchem: command not found


Also, when I submit the script by hand, the following message is given:
nwchem SDDBPW911_spin.nw
# of processors not specified. Defaulting to 1
Submitting NWCHEM job SDDBPW911_spin ....

Your job 4675247 ("SDDBPW911_spin.19706.script") has been submitted
The job number is just the number that it has going into the queue, but the number between spin. and .script corresponds to something else. I'm not sure what. Does this fact that it's going to a queuing system matter here? It's still executed from the shell with just the simple nwchem command after all...

---------- Post updated at 08:57 AM ---------- Previous update was at 08:54 AM ----------

I added the path as you said. Here is what the ./bash_profile looks like now:
# .bash_profile

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi

# User specific environment and startup programs

PATH=$PATH:$HOME/bin
path=$PATH:/opt/local/share/nwchem/nwchem
export PATH
unset USERNAME

Is this correct? I tried it as is and it didn't change anything.

Does anyone have any other ideas about where I might look for answers to this question? I had always assumed that the problem would end here and that someone on this board would know the answer...

Earlier you said you added this to your .sh script:
If "which nwchem" returns "/opt/local/share/nwchem/nwchem", this means nwchem is in "/opt/local/share/nwchem" -- so if you want to add this directory to the PATH, that section should read as follows:

Code:

PATH=$PATH:/opt/local/share/nwchem
nwchem $basis_name$func_name$spin_name".nw"

Have you tried simply putting the full path in your bash script rather than changing the $PATH variable?
What I mean is, inside your script that creates the folders and such write

Code:

... make folders ...
/opt/local/share/nwchem/nwchem
... other stuff ...

This works fine for me. Below is a script named script that makes a directory and a file, and then runs nwchem. nwchem for me simply prints out "This is nwchem". Note that nwchem is called by its full path (~ is just a shortform for /Users/****/).

Code:

  1 #!/bin/bash
  2 mkdir newdir
  3 touch newdir/file1
  4 ~/Documents/nwchem/nwchem

output as follows

Code:

dhcp23:nwchem ******n$ ./script
This is nwchem
dhcp23:nwchem *****$ ls -l
total 40
drwxr-xr-x  3 ****  staff   102  4 Aug 12:20 newdir
-rwxr-xr-x  1 *****  staff  9560  4 Aug 12:17 nwchem
-rw-r--r--  1 ***** staff    81  4 Aug 12:17 nwchem.cxx
-rwxrwxrwx  1 *****  staff    71  4 Aug 12:18 script

nwchem is run and the directory and file inside it is created.
You may also want to check that you have execute permissions for nwchem.
If not, change it with chmod, chmod 744 nwchem will give you read write and execute permissions and others only read.

That worked! Thanks so much! You've made my job 1000% easier.

Cheers,
EMF

lol, the easy way is the best way.