Hi Ross,
1) Run the example I gave using the original executable in serial on CPU and
> verify that the restart writing issue exists. That is the restart file
> during a run when you do 'ls -la' is smaller in size than the inpcrd.rst
> file.
>
I did that (and corrected the embarrassing typo you found) and your patch
appears to have worked! This patch was included with the original AMBER11
install in /usr/local/, and works for both serial and parallel pmemd. Is
there anything else you need?
the results of ls -la:
drwxr-xr-x 2 dave dave 4096 2012-04-11 19:57 .
> drwxrwxr-x 4 dave dave 12288 2012-04-10 17:16 ..
> -rw-r--r-- 1 dave dave 1674065 2012-04-11 07:37 inpcrd.rst
> -rw-r--r-- 1 dave dave 60 2012-04-11 20:15 logfile
> -rw-r--r-- 1 dave dave 236 2012-04-11 19:57 mdin
> -rw-r--r-- 1 dave dave 1229 2012-04-11 20:23 mdinfo
> -rw-r--r-- 1 dave dave 82926 2012-04-11 20:23 mdout
> -rw-r--r-- 1 dave dave 2733166 2012-04-11 07:37 prmtop
> -rw-r--r-- 1 dave dave 1674065 2012-04-11 20:24 restrt
> -rwxr-xr-x 1 dave dave 43 2012-04-11 07:50 Run.sh
> -rw-r--r-- 1 dave dave 1905160 2012-04-11 07:46 test.pdb
>
tail -4 of the restrt file:
0.2217310 0.1214363 0.0150202 -0.0919747 0.8711440 0.2906395
> -0.2985535 -0.8012242 -0.3203315 -0.1668081 -0.3771171 -0.1664786
> -0.0989288 0.5148373 -0.1284243 0.0051602 0.5282828 0.1166140
> 69.9579821 60.2886598 54.1156304 90.0000000 90.0000000 90.0000000
>
I have also done this with my RNA, and I can successfully start from the
restart file again, where I could not yesterday morning. The patch so far
works greatly.
Thanks so much for your help Ross, Tom S., David, and Aron!
-Dave
On Wed, Apr 11, 2012 at 3:37 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi David,
>
> > I applied the bug fixes for AmberTools 1.5 and AMBER11.
>
> Does this include the patch I provided? - Did you install this in a
> different location from your original? - so we can test both with and
> without the patch?
>
> > root.zip:/usr/local/amber11/test# export DO_PARALLEL='mpirun -np 4'
> > >
> > bash: export: `-np': not a valid identifier
> > >
> > bash: export: `4'': not a valid identifier
>
> This is very strange and is coming from your shell. Are you sure you are
> using the quotes correctly? - Maybe try "" instead of '' - I have a feeling
> you are using the back sliding quote which is on the same key as a ~ (on a
> US keyboard) - this is the WRONG quote to use. On a US keyboard use either
> '
> or " which is on the same key next to : and ;.
>
> > When I attempt to run the inpcrd.rst that Ross gave,
> >
> > dave.zip:/sicklestroke/home/con/Tor/s.syn.tor/Test$ mpiexec -np 8
> > pmemd.MPI
> > > -O -c inprcd.rst
> > >
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>
> Lets forget parallel for the moment and just focus on serial. Firstly does
> the problem you reported with the restart file not being fully written
> occur
> in serial on the CPU as well as the GPU code or do you only see it in GPU
> runs?
>
> > or just a single processor:
> >
> > dave.zip:/sicklestroke/home/con/Tor/s.syn.tor/Test$ pmemd -O -c
> > inprcd.rst
> > >
> > > Unit 9 Error on OPEN:
> > > inprcd.rst
> > >
> > > STOP PMEMD Terminated Abnormally!
>
> The file is called 'inpcrd.rst' you have the c and r reversed above, not
> sure if that is an actual typo in your runs or a typo in the email.
>
> Can you try the following please if you can.
>
> 1) Run the example I gave using the original executable in serial on CPU
> and
> verify that the restart writing issue exists. That is the restart file
> during a run when you do 'ls -la' is smaller in size than the inpcrd.rst
> file.
>
> 2) If 1 shows the problem then try running again with the new executable
> built from code with the patch I gave. Does it work this time?
>
> If neither show the problem then try the GPU code and see if the issue is
> restricted to just that. - Note for the serial GPU runs you might want to
> reduce NTPR, NTWR and NSTLIM by an order of magnitude so you aren't waiting
> forever for it to reach 10,000 steps.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
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Received on Wed Apr 11 2012 - 18:30:03 PDT
