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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Received on Mon Sep 30 2013 - 23:00:04 PDT
