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
Received on Wed Oct 09 2013 - 00:30:03 PDT
