Re: QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation.

From: hgkrug1_at_gmail.com
Date: Mon Sep 12 2022 - 05:36:33 CDT

Dear Diago,

I found the error. My Mopac executable file is actually at:
/opt/mopac/bin/mopac

The job runs now on 1 CPU. I will test multiple CPU's and GPU's next.

Thanks for your kind help!
Best wishes
Gert Kruger

On Mon, 2022-09-12 at 09:34 +0200, hgkrug1_at_gmail.com wrote:
> Dear Diego,
>
> Thanks for your kind reply.  I have potentially fixed this issue.
>  New
> Log file is attached. 
>
> The log file now reflects (I assume mopac runs from "mopac.ico"?) :
>
> Info: QM EXECUTABLE PATH: /opt/mopac/mopac.ico 
>
> But I still get the same error -  FATAL ERROR: Error running command
> for QM forces calculation.
>
> Note that I am now manually running the QM-minimization from the
> provided tutirial files.  
>
> I have also managed to run the minimization on 1 CPU only.   
>
> Any other hints to solve this issue will be much appreciated.
>
> Best wishes
> Gert Kruger
>
>
> On Fri, 2022-09-09 at 13:39 -0500, Diego Gomes wrote:
> > The following messages from your log file suggest the path to QM
> > software is incorrect.
> >
> > Info: QM EXECUTABLE PATH: /Scr/rcbernardi-
> > new/Software/mopac/MOPAC2016.exe
> >
> > FATAL ERROR: Error running command for QM forces calculation.
> >
> >
> >
> > I believe your .conf lines may look like this.
> > qmSoftware mopac
> > qmExecPath /Scr/rcbernardi-new/Software/mopac/MOPAC2016.exe
> >
> > You may solve this issue by fixing qmExecPath.
> >
> > --
> > Diego.
> >
> >
> >
> >
> > On Fri, Sep 9, 2022 at 3:37 AM <hgkrug1_at_gmail.com> wrote:
> > > Dear All,
> > >
> > > I was able to run the job on a single CPU and I still get the
> > > same
> > > error (log file attached - see: Info: Running on 1 processors, 1
> > > nodes,
> > > 1 physical nodes). 
> > >
> > > Any further help will be much appreciated!
> > > Thanks!
> > > Gert Kruger
> > >
> > > On Thu, 2022-09-08 at 19:49 +0200, hgkrug1_at_gmail.com wrote:
> > > > Dear All,
> > > >
> > > > I found a similar error - see
> > > >
> > > https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2017-2018/1005.html
> > > >  
> > > >
> > > > The (partial) solution there was to run the job in serial (not
> > > > in
> > > > parallel).
> > > >
> > > > Question then is, how do I chnage the input for a QwikMD QM
> > > > minimization so that it will only run in serial?
> > > >
> > > > At least it will narrow dowm this issue?
> > > >
> > > > Thanks!
> > > > Gert Kruger
> > > >
> > > > On Mon, 2022-09-05 at 11:46 +0200, hgkrug1_at_gmail.com wrote:
> > > > > Dear All,
> > > > >
> > > > > I changed the NAMD version on my PC to NAMD_3.0alpha13_Linux-
> > > > > x86_64-
> > > > > multicore-CUDA-SingleNode
> > > > >
> > > > > Then when I run the QM-minimization job from the command line
> > > > > I
> > > get
> > > > > a
> > > > > different error:  FATAL ERROR: QM forces are not compatible
> > > with
> > > > > CUDA
> > > > > at this time
> > > > >
> > > > > The log file is attached.
> > > > >
> > > > > Any kind help will be much appreciated!
> > > > > Bets wishes
> > > > > Gert Kruger
> > > > >
> > > > > On Mon, 2022-09-05 at 07:58 +0200, hgkrug1_at_gmail.com wrote:
> > > > > > Dear All,
> > > > > >
> > > > > > I have a Dell Inc. Vostro 3670 with a Intel® Core™ i7-8700
> > > CPU @
> > > > > > 3.20GHz × 12 processor and a NVIDIA GeForce GT
> > > > > > 1030/PCIe/SSE2
> > > /
> > > > > > NVIDIA
> > > > > > Corporation GP108 GPU card.
> > > > > >
> > > > > > I have Ubuntu 22.04 LTS installed.  For NAMD I have used
> > > > > > the
> > > > > > binary
> > > > > > version NAMD_Git-2022-07-21_Linux-x86_64-multicore.tar.gz.
> > > > > >
> > > > > > When I perform a commandline QM minimization from the
> > > provided
> > > > > > tutorial
> > > > > > files, I get the same error.
> > > > > >
> > > > > > 2 other people had the same/similar issue:
> > > > > >
> > > > > >
> > > https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/0199.html
> > > > > >
> > > > > >
> > > https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/0583.html
> > > > > >
> > > > > > Best wishes
> > > > > > Gert Kruger
> > > > > >
> > > > > > Any kind help will be much appreciated!
> > > > > >
> > > > > > On Sun, 2022-09-04 at 08:16 +0200, hgkrug1_at_gmail.com wrote:
> > > > > > > Dear All,
> > > > > > >
> > > > > > > I am doing the Qwik QM/MM tutorial at
> > > > > > >
> > > https://www.ks.uiuc.edu/Research/qmmm/Tutorial/Tutorial.pdf
> > > > > > >
> > > > > > > Everything worked well until the first QM minimization
> > > > > > > step
> > > > > > > (page
> > > > > > > 15/16).
> > > > > > >
> > > > > > > I get an Error: FATAL ERROR: Error running command for QM
> > > > > > > forces
> > > > > > > calculation (error log file - qm.log in th main
> > > > > > > directory).
> > > > > > >
> > > > > > > I see this problem was reported before (
> > > > > > >
> > > https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/0237.html
> > > > > > > ) and there was an error with the QM PDB file.  I don't
> > > > > > > see
> > > the
> > > > > > > same
> > > > > > > issue with my QM PDB file?
> > > > > > >
> > > > > > > The  tar files that were created so far can be found at
> > > this
> > > > > > > link
> > > > > > > -
> > > > > > >
> > > https://urldefense.com/v3/__https://stuukznac-my.sharepoint.com/:f:/g/personal/kruger_ukzn_ac_za/EgII-IBVb9BKju9lBt5zD7cBHxsxl5jf2DEtssZJRwqyCw?e=yDpXal__;!!DZ3fjg!-7f-wGbhTVNBcexYtmYC_fItKklb6MpnGNxk0LrVZqAswOkRgu_CbcAul_R4j-FxUCsYM87-YBwOBsot$
> > > > > > >  
> > > > > > >
> > > >
> > >
> > >
> >
> >
>

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