After I got the tests to run, I started working my way through the tutorial. Specifically, I am trying part 4. I managed to get to step 18 before I ran into problems. In step 18, we are trying to generate the inital conditions for NewtonX to use. To do this you run a line of code:
$NX/initcond.pl >initcond.log &
This line of code immediately spits out a message which is a number in brackets followed by another number. The numbers change each time. It then prints a message saying initcond.pl is dying now. At this point, the console freezes and does not respond until you abort with ctrl-c. It then spits out an exit code, “Exit 255.” (Which I have been unable to find more information on).
To try to figure out what was wrong, I examined the initcond.log file. So far I have gotten two different messages which seem to alternate with no real reason. The first occurs early in the run and says:
Cheking input files
Cheking geometry lines
Searching for qvector...
qvector does not exist
Creating qvector...
It appears to die while trying to make the missing qvector. The qvector it is referring to used to be a file in version 1.1 that contained the quantum vibrational number, but it isn’t referenced at all in 1.4.
The second error happens later in the run and says:
Starting run_g09_initcond.pl at Tue Nov 22 08:21:30 PST 2016
Vertical energies with Gaussian 09
Starting . $g09root/g09/bsd/g09.profile;$g09root/g09/g09 gaussian.com at Tue Nov 22 08:21:30 PST 2016
Finished . $g09root/g09/bsd/g09.profile;$g09root/g09/g09 gaussian.com with ERROR at Tue Nov 22 08:21:30 PST 2016
Finished run_g09_initcond.pl with ERROR at Tue Nov 22 08:21:30 PST 2016
This error seems to be referring to the same issue with NewtonX inserting an extra /g09/ which we were seeing earlier. However, when I tried using the same set of variable definitions which worked in the tests, it did not change anything. Also, I poked around in the file and found the same qvector error as earlier but instead of crashing after creating the qvector, it continued successfully. So it seems like that error is one that it can sometimes get past.
So far I haven’t been able to figure out when one error occurs versus the other. There doesn’t seem to be any particular logic to it.
-Kristine
I have some progress to report here.
I was likewise able to successfully do the Tutorial 1.4 Chapter 4 as you have, up to Step 18. I made sure I had g09root=/share/apps/compute/gaussian/09.E.01
After running: $NX/initcond.pl >initcond.log &
and immediately seeing the error message “initcond.pl is dying now”
I poked around for a log file, and found one in HIOPHENE_TDDFT_SPEC/IC-TDDFT/DEBUG/runnx.error
The message in there said that memory could not be allocated to gaussian. This sounded suspiciously like something wrong with the %mem= line in the gaussian.com input file the Tutorial has you write. I simply deleted that line from the gaussian.com file in the JOB_AD directory and tried Step 18 again. And it works! However it is a rather lengthy step and we should properly submit this job to the batch queue to run it. This will take some work to get going, though Newton-X says there are some useful templates in the /NX-1.4.0-2/batch directory (files called pini and pini-ew)
Now that we have this working, it will be useful to make a new post, and make a link from this post, about finishing Tutorial 4 and what kind of output you get (the spectrum, show a plot of your results, etc) And perhaps a separate post with your SLURM batch file. Make sure to categorize/tag your posts as appropriate. (There’s no end to my control freaking!)