Hi Ross and Aron,
I applied the bug fixes for AmberTools 1.5 and AMBER11.
However, neither pmemd nor pmemd.MPI will work. The "make parallel" part
of the installation appeared fine, but during the testing stage I could not
set the number of processors:
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
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
>
> Unit 9 Error on OPEN:
> inprcd.rst
>
>
rank 0 in job 26 zip.chem.rochester.edu_52043 caused collective abort of
> all ranks
>
exit status of rank 0: killed by signal 9
>
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!
>
Maybe I did something wrong during the "make parallel" part of the
installation? I was following the manual instructions to the letter.
-Dave
On Wed, Apr 11, 2012 at 9:24 AM, Aron Broom <broomsday.gmail.com> wrote:
> Dave, just as a quick note, if you haven't compiled AMBER before, it might
> be a minor ordeal. The manual, and also the website give pretty specific
> instructions for compilation. You should also take this opportunity to
> make sure your patches are up-to-date, if someone else originally compiled
> this, they might have had things up-to-date a long time ago, and some new
> patches may have come out since then.
>
> ~Aron
>
> On Wed, Apr 11, 2012 at 9:06 AM, David Condon <dec986.gmail.com> wrote:
>
> > Hi Ross,
> >
> > I ran the files that you attached earlier yesterday on my computer
> (running
> > AMBER11), and at 19,000 steps, the last 3 lines of the restrt file are
> >
> > 0.2969127 0.1720640 0.1665351 -0.0287412 -0.0874353 0.0130574
> > -0.1191384 0.0530578 -0.7012004 -0.2797709 0.0811417 -0.8200821
> > 0.1568667 -0.2879623 -0.0913121 -0.1581805 0.7091915 0.2519675
> >
> > so it appears that it is still being truncated and this wasn't an
> isolated
> > error.
> >
> > I downloaded the patch you gave and to $AMBERHOME/ and ran the "patch -p0
> > <2012_04_10_restrt_patch.dat" command.
> >
> > However, I'm not entirely clear on the recompilation process.
> >
> > 1) "make clean" is done in the $AMBERHOME directory? This returns the
> > error
> >
> > "make: *** No rule to make target `clean'. Stop."
> >
> > 2) The recompile of pmemd/pmemd.MPI is done in $AMBERHOME/src/pmemd/src?
> >
> > And to David Case, I haven't used Sander in a while. I started the run
> > 4.mdcrd on February 6th, and killed it yesterday manually with "ps -fe |
> > grep pmemd" and then killed the appropriate process so I could install
> new
> > updates.
> >
> > thanks for all your effort!
> > -Dave
> >
> > On Tue, Apr 10, 2012 at 6:49 PM, Ross Walker <ross.rosswalker.co.uk>
> > wrote:
> >
> > > Hi David,
> > >
> > > Assuming a fully up to date AMBER 11 could you try the attached patch
> > > please.
> > >
> > > Do a make clean and then save the file in $AMBERHOME/src/pmemd/src
> > >
> > > cd $AMBERHOME/src/pmemd/src
> > > patch -p0 <2012_04_10_restrt_patch.dat
> > >
> > > Then do a recompile of pmemd, pmemd.MPI and pmemd.cuda and let me know
> if
> > > the problem goes away.
> > >
> > > All the best
> > > Ross
> > >
> > > > -----Original Message-----
> > > > From: Ross Walker [mailto:ross.rosswalker.co.uk]
> > > > Sent: Tuesday, April 10, 2012 3:32 PM
> > > > To: 'AMBER Mailing List'
> > > > Subject: Re: [AMBER] Could not read velocities from restart file
> > > >
> > > > Hi David,
> > > >
> > > > Are you using AMBER 11 or AMBER 12?
> > > >
> > > > All the best
> > > > Ross
> > > >
> > > > > -----Original Message-----
> > > > > From: David Condon [mailto:dec986.gmail.com]
> > > > > Sent: Tuesday, April 10, 2012 11:59 AM
> > > > > To: AMBER Mailing List
> > > > > Subject: Re: [AMBER] Could not read velocities from restart file
> > > > >
> > > > > Hi Aron,
> > > > >
> > > > > the good rst file looks like:
> > > > >
> > > > > 0.2649094 -0.0844054 0.1286095 0.5432906 -0.2507783 -
> > > > > 0.0405266
> > > > > 0.3149803 0.0175057 0.3673056 -0.1782371 0.2128560 -
> > > > > 0.1884006
> > > > > 0.2371759 -0.3057067 0.5952768 -0.2354916 -0.9410148 -
> > > > > 0.0438329
> > > > > -0.1159288 -0.5434164 0.0047462 -0.1315556 0.4991617
> > > > > 0.4990561
> > > > > 0.0211907 0.8615705 0.9348652 0.0235789 -0.0474127
> > > > > 0.3410161
> > > > > -0.4567690 -0.3400850 0.2949318 -0.4300670 0.2233142
> > > > > 0.8368965
> > > > > -0.0714831 0.0409602 -0.1256436 0.2461557 0.4929560
> > > > > 1.0578373
> > > > > 0.1681050 -0.8414658 0.0167940 0.1557208 0.4892122 -
> > > > > 0.1181744
> > > > > -0.1883092 -0.3844528 -0.5576498 0.4514073 0.8922748 -
> > > > > 0.4837416
> > > > > 35.4095673 35.4095673 35.4095673 109.4712190 109.4712190
> > > > > 109.4712190
> > > > >
> > > > > and this bad one (4.rst) looks like:
> > > > >
> > > > > -0.0081777 -0.4593477 -0.0313187 0.0662137 -0.2243723
> > > > > 0.0759823
> > > > > -0.6695894 0.7636265 0.6048110 0.1985666 -0.4804675
> > > > > 0.0244801
> > > > > -0.3532630 -0.0377391 0.0271259 -0.1361401 -1.0299790
> > > > > 0.2153224
> > > > > 0.1951599 0.4482496 0.3146665 0.2586283 -0.0169079 -
> > > > > 0.0427295
> > > > > 0.0330675 -0.0438502 -0.2393299 0.2528661 0.1129621
> > > > > 0.3183243
> > > > > -0.0396155 -0.1839538 -0.0473871 -0.4539827 -0.5628476 -
> > > > > 0.1202268
> > > > > -0.6310506 0.2109399 0.4612384 0.0762229 0.2612662
> > > > > 0.3154209
> > > > > -0.8445841 -0.1361930 0.9036816 0.5807950 -0.5465261
> > > > > 0.3683826
> > > > > 0.0661990 0.1313591 -0.0815423 0.2405941 0.4207141 -
> > > > > 0.0614615
> > > > > 0.3071491 0.6133529 -0.1018300 -0.2264057 0.0919355 -
> > > > > 0.1983635
> > > > >
> > > > > The numbers at the bottom row appear to be of the wrong magnitude
> (or
> > > > > the
> > > > > bottom row is just missing).
> > > > >
> > > > > and to Ross Walker, I am using Linux 2.6.32-40-generic on Ubuntu
> > > > 10.04
> > > > > Lucid Lynx.
> > > > >
> > > > > Thanks much for your help everyone!
> > > > > -Dave
> > > > >
> > > > > On Tue, Apr 10, 2012 at 2:18 PM, Aron Broom <broomsday.gmail.com>
> > > > > wrote:
> > > > >
> > > > > > are the restart files in ASCII? Can you open them up and have a
> > > > look
> > > > > in
> > > > > > order to see what is wrong? Hopefully none of your values have
> > > > > become
> > > > > > 'NaN'.
> > > > > >
> > > > > > ~Aron
> > > > > >
> > > > > > On Tue, Apr 10, 2012 at 2:16 PM, David Condon <dec986.gmail.com>
> > > > > wrote:
> > > > > >
> > > > > > > Hi Dr. Steinbrecher,
> > > > > > >
> > > > > > > thanks much for your prompt reply! For some bizarre reason,
> even
> > > > > on
> > > > > > short
> > > > > > > re-runs the error is reproduced.
> > > > > > >
> > > > > > > The restart runs are in sequence:
> > > > > > >
> > > > > > > -rw-r--r-- 1 dave dave 252901 2012-04-10 08:33 New/1.rst
> > > > > > > > -rw-r--r-- 1 dave dave 252901 2012-04-10 08:33 New/2.rst
> > > > > > > > -rw-r--r-- 1 dave dave 252901 2012-04-10 08:33 New/3.rst
> > > > > > > > -rw-r--r-- 1 dave dave 245309 2012-04-10 12:59 New/4.rst
> > > > > > > >
> > > > > > > It looks like I will just have to wait until the 4th MD run
> > > > > finishes.
> > > > > > >
> > > > > > > regards,
> > > > > > > -Dave
> > > > > > >
> > > > > > >
> > > > > > > On Tue, Apr 10, 2012 at 10:08 AM, <steinbrt.rci.rutgers.edu>
> > > > wrote:
> > > > > > >
> > > > > > > > Hi,
> > > > > > > >
> > > > > > > > > restarted the computer to install some updates (first by
> > > > > killing the
> > > > > > > > pmemd
> > > > > > > > > process, which may not have been the proper way).
> > > > > > > >
> > > > > > > > I would agree that this is not the proper way and that one
> > > > should
> > > > > split
> > > > > > > > long simulations into pieces and keep intermediate rst-files
> > > > > (check the
> > > > > > > > ntwr<0 option) so that precisely this does not happen, but
> > > > > anyways:
> > > > > > > >
> > > > > > > > > Upon restarting the simulation, I get the error at the
> bottom
> > > > > of the
> > > > > > > new
> > > > > > > > > output file:
> > > > > > > > >
> > > > > > > > > | ERROR: Could not read velocities from 4.rst
> > > > > > > > >>
> > > > > > > >
> > > > > > > > Check if your rst file contains the correct 3*N number of
> > > > > coordinates
> > > > > > and
> > > > > > > > 3*N velocities. If you were unlucky enough to kill the
> process
> > > > > right
> > > > > > when
> > > > > > > > it was halfway done with writing a rst file, you may have
> > > > > truncated and
> > > > > > > > thereby corrupted it.
> > > > > > > >
> > > > > > > > However all is not lost I guess:
> > > > > > > >
> > > > > > > > if your rst file contains enough coordinates (3*natom, so
> > > > > natom/2+3
> > > > > > > lines)
> > > > > > > > and only misses velocities, you could delete all velocity
> lines
> > > > > and
> > > > > > just
> > > > > > > > restart your system (ntx=1) at 300K. This introduces a little
> > > > > > disturbance
> > > > > > > > but that should rapidly equilibrate away (in few ps). You may
> > > > > have to
> > > > > > > rest
> > > > > > > > the box in xleap, as box coordinates are at the end of the
> rst-
> > > > > file.
> > > > > > > >
> > > > > > > > If your rst file is unusable, you could extract the last
> > > > snapshot
> > > > > from
> > > > > > > the
> > > > > > > > mdcrd-file and convert it into a rst (via ptraj) and restart
> > > > your
> > > > > > > > simulation from that point. crd-files have a lower accuracy
> > > > than
> > > > > > > > rst-files, but again, this should equilibrate away very
> > > > quickly,
> > > > > > compared
> > > > > > > > to a multinanosecond simulation.
> > > > > > > >
> > > > > > > > if ptraj cannot read your crd file either, you can (if you
> used
> > > > > ASCII
> > > > > > > > mdcrd format) parse through the mdcrd by yourself and see if
> > > > you
> > > > > can
> > > > > > > > extract a useful snapshot as far advanced in your trajectory
> as
> > > > > > possible
> > > > > > > > and restart from there.
> > > > > > > >
> > > > > > > > Each of these solutions would introduce a small but in my
> > > > opinion
> > > > > > > > acceptable inaccuracy into your system. That may be difficult
> > > > to
> > > > > > explain
> > > > > > > > in a paper, but otherwise you should be ok.
> > > > > > > >
> > > > > > > > For materials and methods: ;-)
> > > > > > > >
> > > > > > > > "At 1448 ns simulation time, velocities were discarded and
> > > > > replaced by
> > > > > > a
> > > > > > > > Boltzmann velocity distribution at room temerature. This
> > > > > procedure was
> > > > > > > > conducted to ensure proper system equilibration and
> stability.
> > > > > > (innocent
> > > > > > > > whistling)"
> > > > > > > >
> > > > > > > > Regards,
> > > > > > > >
> > > > > > > > Thomas
> > > > > > > >
> > > > > > > > Dr. Thomas Steinbrecher
> > > > > > > > formerly at the
> > > > > > > > BioMaps Institute
> > > > > > > > Rutgers University
> > > > > > > > 610 Taylor Rd.
> > > > > > > > Piscataway, NJ 08854
> > > > > > > >
> > > > > > > > _______________________________________________
> > > > > > > > AMBER mailing list
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> > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > >
> > > > > > > _______________________________________________
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> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Aron Broom M.Sc
> > > > > > PhD Student
> > > > > > Department of Chemistry
> > > > > > University of Waterloo
> > > > > > _______________________________________________
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> > > > > >
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> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
> _______________________________________________
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>
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Received on Wed Apr 11 2012 - 12:00:04 PDT
