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Clicked A Few Times

5:32:53 AM PDT - Wed, Oct 17th 2012
Dear all, I installed ECCE in my CentOS6 machine, where I had already got a mpi compiled version of nwchem installed. Initially I followed Lindqvist's blog trying to do a test run of md prepare. ECCE seems to create a folder ecce_user under my /tmp folder. Inside that folder, there are some temporary files marking the log files of the previous runs. A job folder inside the ecce_user folder holds many subfolders. In these subfolders, I was able to locate a folder I created for the test run. Inside this folder, there are files like the followings [user@localhost shortpep_prep]$ l total 52 drwxrwxr-x. 2 user user 4096 Oct 17 18:10 . drwxrwxr-x. 3 user user 4096 Oct 17 18:10 .. -rw-rw-r--. 1 user user 445 Oct 17 18:10 ecce.out -rw-rw-r--. 1 user user 141 Oct 17 18:10 ecceSession.cmd -rw-rw-r--. 1 user user 3214 Oct 17 18:10 ecceSession.db -rw-rw-r--. 1 user user 390 Oct 17 18:10 ecceSession.nam -rw-rw-r--. 1 user user 2430 Oct 17 18:10 ecceSession.pdb -rw-rw-r--. 1 user user 2 Oct 17 18:10 .ecce.status -rw-rw-r--. 1 user user 270 Oct 17 18:10 nwch.nw -rw-rw-r--. 1 user user 7007 Oct 17 18:10 nwch.nwout -rw-rw-r--. 1 user user 2542 Oct 17 18:10 RC_M.frg_TMP -rwxr--r--. 1 user user 3658 Oct 17 18:10 submit__shortpep_prep The test run went fine until I ran optimize job. During the test run, I also found that ECCE has a internally installed nwchem; however, I wanted to use the mpi version nwchem I built, I searched Internet and got some directives making change of the default nwchem binary being called. The procedure is using the su permission to run 'ecce -admin' and change the binary path to my path. Altogether I was able to change the parameter to run 4 cores in one node. Unfotunately, when I exit root and run ecce, it raises another kind of complaint: "ERRORL NWChem MD Prepare launch failed! Unable to find source for chemical system pdb file for MD Prepare task" I am wondering how should I set up correct path for nwchem inside ecce in order for a correct calculation? The other question is where do the pdb file go? I cannot find them in the /tmp/ecce_user anymore!! Many thanks in advance.

Gets Around

8:57:00 PM PDT - Wed, Oct 17th 2012

Sacch,
There are a few things:

I don't think you're supposed to run ecce -admin as su. Just run it as a regular user. I can't really think of any situation in which any part of ecce should ever be run as root.

You can add the correct path to NWChem using 'ecce -admin' -- I think there are screenshots of it here:

http://verahill.blogspot.com.au/2012/06/ecce-in-virtual-machine-step-by-step.html

Assuming that you registered your machine as "mycluster" using ecce -admin, check your apps/siteconfig/CONFIG.mycluster file and make sure that ecce points towards the correct binary.

NWChem: /opt/sw/nwchem-6.1/bin/nwchem

NWChemCommand {
mpirun -n $totalprocs $nwchem $infile > $outfile
}

Also, you'll have a .nwchemrc file in your home folder (~). Edit this to use the correct basis set folders etc.

Note that you may want to do

chmod +rw .nwchemrc

first to allow for both read and write. Do the same thing with your CONFIG.mycluster file.

/tmp holds your volatile files. Leave those alone. There's a difference between job directory, scratch directory and the 'permanent' directory ( server/data/Ecce/users/myuser/ etc). You're most likely looking for the last one, although if you're using ecce the way it was intended you rarely have to care about where files are located.

Are you following the guide exactly as shown at
http://verahill.blogspot.com.au/2012/05/md-ecce-nwchem-1-prepare.html
http://verahill.blogspot.com.au/2012/05/md-ecce-nwchem-2-md-optimize.html

In particular, when you create the "optimize" run, are you doing it as shown?

Clicked A Few Times

4:22:36 AM PDT - Wed, Oct 24th 2012
I have no idea why I cannot get a confirmation email. I have checked my email address. I am sorry that I did not reply earlier. Is there any link that I can report problem on email confirmation?

Forum Vet

9:10:47 AM PDT - Thu, Nov 1st 2012
The NWChem website server does not have an external email client installed, so confirmation emails will not be send. Bert Quote:Sacch Oct 24th 11:22 am I have no idea why I cannot get a confirmation email. I have checked my email address. I am sorry that I did not reply earlier. Is there any link that I can report problem on email confirmation?

Forum Vet

12:00:18 PM PST - Mon, Nov 5th 2012
We have updated the site and confirmation emails will be send now. Bert Quote:Bert Nov 1st 4:10 pm The NWChem website server does not have an external email client installed, so confirmation emails will not be send. Bert Quote:Sacch Oct 24th 11:22 am I have no idea why I cannot get a confirmation email. I have checked my email address. I am sorry that I did not reply earlier. Is there any link that I can report problem on email confirmation?

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