Dear Francois,
I'm still having questions about the execution of RED-III.52. When I
execute the command "perl RED-vIII.5.pl", I got the same question with the
following link: http://q4md-forcefieldtools.org/RED/popup/bugs-III.4.txt
"Problem: The scratch path defined in the "rungms" script of the GAMESS-US
program is not found by R.E.D.-III.4 if an environment variable such as
$USER is used in the path. For instance the /tmp/$USER path is not found
even if the corresponding directory does exist (environment $USER variable
points to "bill"), while /tmp/bill is found. This leads to the following
error message: "
So RED-III.52 doesn't update the bug? I want to go back to use RED-III.4,
but it seems the RESP web doesn't offer the download for RESP-III.4 tools.
Is it true?
Best!
Dongshan
On Tue, Oct 1, 2013 at 1:35 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Dongshan,
>
> Do you use the PBS queuing system?
>
> At R.E.D. Server we do use PBS (Torque/Maui):
> See http://q4md-forcefieldtools.org/REDS/faq.php#8
> We also use the same gamess version...
>
> # set SCR=/scr/$USER
> # set USERSCR=~$USER/scr
> # set GMSPATH=/u1/mike/gamess
> set SCR=/tmp/ZZZZZZ
> set USERSCR=/tmp/ZZZZZZ
> set GMSPATH=/usr/local/gamess
>
> We use the same direction for SCR and GMSPATH; R.E.D. will move the
> punch file from the scratch directory to the working directory to
> extract the MEP...
>
> and the PBS script modify rungms to create a unique & temporary
> scratch directory by job:
> see and example:
> set SCR=/tmp/R.E.D.IV-4379.master0.q4md-forcefieldtools.org
> set USERSCR=/tmp/R.E.D.IV-4379.master0.q4md-forcefieldtools.org
> set GMSPATH=/usr/local/gamess
>
> ---
>
> the definition of the punch file is done in the script gms-files.csh
> setenv INPUT $SCR/$JOB.F05
> setenv PUNCH $USERSCR/$JOB.dat
> setenv AOINTS $SCR/$JOB.F08
> setenv MOINTS $SCR/$JOB.F09
> setenv DICTNRY $SCR/$JOB.F10
>
> regards, 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?
>
> > 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 Tue Oct 08 2013 - 09:00:04 PDT
