Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file

From: Dongshan Wei <dswei0523.gmail.com>
Date: Tue, 1 Oct 2013 10:05:43 +0800

Dear Francois,

Thanks for your detailed reply. The gamess I used on the cluster is gamess
5.1.2012 version. The rungms script is original from the gamess software
and is attached here. Please help me have a look.

Especially, the scratch directory /local_scratch/dswei disappeares after
the job running finishes. I tried to change the scratch directory to my
user directory in the rungms script and submitted a job to the cluster, but
the job quit quickly since there is no comminucation between the node and
my user directory. So how can I create a scratch directory both for job
running and output saving?

Best!

Dongshan


On Tue, Oct 1, 2013 at 4:07 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:

> Dear Dongshan,
>
> > Did you meet one problem "ERROR: Problem with the QM Scratch directory"
> > when using R.E.D. VIII.52 to derive the charge of atoms? In my case, I
> had
> > used gamess to optimized the molecular structure and when I executed
> R.E.D.
> > VIII.52 with "perl RED-vIII.5.pl" command, the error is always showing
> as
> > follows:
>
> which GAMESS do you interface?
>
> > The Scratch directory defined for GAMESS is /local_scratch/$USER
> >
> > Scratch directory for GAMESS [ NOT FOUND ]
>
> So you need to create the corresponding scratch directory before to
> execute R.E.D.
>
> > The USER Scratch directory defined for GAMESS is
> /scratch/$USER
> > Bad permissions for the GAMESS Scratch directory
>
> 'chmod 777' for this scratch directory...
>
> > The punch file directory defined for GAMESS is
> $USERSCR/$JOB.dat
> >
> > ERROR: Problem with the QM Scratch directory.
> > See the R.E.D.-II manual, page 7.
>
> See http://q4md-forcefieldtools.org/RED/RED-II.pdf
>
> > About the above error, I have some questions to ask:
> > (1) To execute R.E.D.VIII.52, how many input files need to be read? I
> think
> > the necessary files are only three: Mol-red1.p2n, Mol-red1.log and
> > Mol-red1.dat. Is this correct?
>
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#7
> - if $OPT_Calc = "On" & $MEPCHR_Calc = "On" only the P2N file(s)
> is(are) required; i.e. in your case Mol_red1.p2n
> - if $OPT_Calc = "Off" & $MEPCHR_Calc = "On" the P2N file(s) and QM
> output log file(s) are required; i.e. in your case Mol_red1.p2n &
> Mol_red1.log
> I do not know what is this Mol_red1.dat file; I think you mix up the
> punch file and that Mol_red1.dat file.
> See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
> & http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/figure/F1/
> the punch file is the JOB2-gam_m$n-$i-$j.dat file
> $n molecule // $i conformation // $j orientation
>
> > (2) To my understanding, the scratch directory /local_scratch/$USER is
> > generated temporarily for intermediate outputs during the optimization
> > calculation before executing R.E.D. fitting, and after the job is
> finished,
> > the temporal scratch directory will be deleted automaticly. So to do
> R.E.D.
> > fitting, the scratch directory is not necessary. Is this correct?
>
> on a cluster - & using the PBS queuing system, Yes, a temporary
> scratch directory can be created just before executing R.E.D. and
> removed just after the job has finished.
>
> on a workstation you could create this scratch directory only once and
> keep it for all the R.E.D. jobs... If this scratch directory is only
> for your login you could use a specific directory in your login (if
> you have a enough space in your login also)
> If the scratch directory is to be shared with other users you could
> use the /tmp partition and then create a directory in /tmp related to
> your login. /tmp could be a particular partition with a looot of room.
>
> > (3) From the above information, it seems the R.E.D. VIII.52 cannot
> > recognize variables such as $USER, $USERSCR, $JOB, because the directory
> > /scratch/dswei and the file /scratch/dswei/Mol-red1.dat do exist. Here
> > dswei is my username on the cluster. How to solve the problem?
>
> please tell me which GAMESS version you use? and send me your 'rungms'
> script: I could prepare it for you if you agree...
>
> > I'm learning the R.E.D., so your reply to my above question will be great
> > help to me.
>
> do not hesitate to ask as many questions as you wish ;-)
>
> regards, Francois
>
>
>
>
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>



-- 
---------------------------------------------------------
Dongshan Wei, Dr.
Chongqing Institute of Green and Intelligent Technology, CAS
85 Jinyu Ave, Yubei Area, Chongqing 401120, China
Email: dswei.cigit.ac.cn <dswei.cigit.cas.cn>
Phone: (+86) 23-63063762
---------------------------------------------------------



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Received on Mon Sep 30 2013 - 19:30:04 PDT
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