Dear Francois,
I used the following PBS script to submit a job on the cluster to do the
geometry optimization and create the .log file:
==================================================
#!/bin/bash
#PBS -q tiny16core
#PBS -l walltime=2:00:00
#PBS -l nodes=1:ppn=16
#PBS -N gms-16
echo $PBS_O_WORKDIR
#module load intel/12.1.5
#module load mkl/12.1.5
#module load mvapich2/1.8
#module load gamess/5.1.2012
cd $PBS_O_WORKDIR
#cat $PBS_NODEFILE
#NP=$(wc -l < $PBS_NODEFILE)
/share/apps/gamess/rungms mel-gam 01 1 16 > mel-gam.log
===============================================
I can finish this step and get the .log file normally.
While for the RED charge fitting, I did through a PBS job in a queuing
system or through an interactive job on the login node. but both of these
ways failed. For the interactive running on the login node, I used "perl
RED-vIII.52.pl" and for the pbs script, the last line in the above file
changed to "perl RED-vIII.52.pl".
Best!
Dongshan
On Wed, Oct 9, 2013 at 3:03 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Dongshan,
>
> > I gave up to use the cluster to execute RED charge fitting and changed to
> > use the RED server on your website. Now I can finish the charge fitting
> > task and get the .mol2 file for Amber using. I notice that the RED server
> > use RED-III.4 instead of RED-III.52 to execute the charge fitting
> > procedure. Is there really bugs in RED-III.52 tools?
>
> R.E.D. Server interfaces R.E.D. IV, while the R.E.D. III.x tools are
> distributed under the GPL license.
>
> I can help you to configure your cluster and send you our scripts...
>
> You did not answer to the following question:
> Do you use a queuing system on your cluster? if Yes do you use PBS?
>
> regards,
> Francois
>
>
> > On Tue, Oct 8, 2013 at 11:37 PM, Dongshan Wei <dswei0523.gmail.com>
> wrote:
> >
> >> 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
> >>>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------------------------
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
---------------------------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 09 2013 - 06:00:13 PDT
