Dear Dr. Daniel,
After compiling cpptraj in parallel, as mentioned in AMBER manual 14 and
previous post "
http://dev-archive.ambermd.org/201107/0005.html", cpptraj
looks working well without any error message ( though it is not completed
yet for my system). How do I know that cpptraj is running in parallel mode
instead of series? I issued the same command as
cpptraj -i input_file -p test.top
Thank you for help,
Mahendra
On Tue, Jan 6, 2015 at 6:25 PM, Thapa, Mahendra (thapamb) <
thapamb.mail.uc.edu> wrote:
>
>
>
> ________________________________________
> From: Daniel Roe
> Sent: Tuesday, January 6, 2015 5:24:28 PM (UTC-06:00) Central America
> To: AMBER Mailing List
> Subject: Re: [AMBER] FW: clustering problem in ambertool14
>
> Hi,
>
> On Tue, Jan 6, 2015 at 3:47 PM, Mahendra B Thapa <thapamb.mail.uc.edu>
> wrote:
> > With the use of 'sieve 10' , the 'cpptraj' command has been running
> > without any complain but the analysis is very slow for my case (50000
> > frames, 511 residues with 7584 atoms in each frame). A section of the
> > screenshot *after 24 hours *is as follows:
>
> This is an inherently time-consuming process, since you need to run
> N*(N-1) / 2 calculations (roughly 12.5 M). Depending on your processor
> speed this can take a long time, particularly if you have a big
> system. I typically use OpenMP-compiled cpptraj for this, since the
> pairwise calc is one of the things that is parallelized. To give you
> an idea of what timings I see, for 22084 sieved frames with 8 threads
> I can complete the pairwise portion of the calculation (RMSD selecting
> 67 atoms) in 97 seconds (CPU is 2x Xeon X5660 . 2.8 GHz).
>
> Your best bet is to first use a very small number of frames (as a
> test) to get an idea of how long things will take, and also to make
> sure that when your clustering completes you get all the output you
> are expecting. It's pretty awful when you do an expensive clustering
> calc and realize you forgot you wanted cluster numbers vs time etc.
>
> One thing that can help speed up subsequent clustering calcs is to use
> the loadpairdist/savepairdist keywords to re-use calculated pairwise
> distances. Some care must be taken when doing this though - everything
> pertaining to the distance metric (sieve, mask, etc) MUST remain the
> same or you will get bad results. Cpptraj does some checking for this
> but can't always catch everything.
>
> Hope this helps,
>
> -Dan
>
> >
> > ANALYSIS: Performing 1 analyses:
> > 0: [cluster crdset MYTRAJ :1-511.CA,N,C,O mass clusters 10 out
> > cluster_out nofit averagelinkage summary summary_out info Cluster_info
> > sieve 10 repout box2.rep repfmt pdb clusterout cluster.nc clusterfmt
> netcdf]
> > Starting clustering.
> > Mask [:1-511.CA,N,C,O] corresponds to 2044 atoms.
> > Calculating pair-wise distances.
> > Pair-wise matrix set up with sieve, 50000 frames, 5000 sieved frames.
> > 0%
> >
> > Thank you for help,
> > Mahendra Thapa
> > University of Cincinnati,OH
> >
> >
> > On Fri, Jan 2, 2015 at 4:35 PM, Thapa, Mahendra (thapamb) <
> > thapamb.mail.uc.edu> wrote:
> >
> >>
> >>
> >>
> >> ________________________________________
> >> From: Daniel Roe
> >> Sent: Friday, January 2, 2015 3:35:17 PM (UTC-06:00) Central America
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] clustering problem in ambertool14
> >>
> >> Hi,
> >>
> >> I suspect that if you are running out of memory even after using
> >> 'loadtraj', the issue may be with the pairwise distance matrix.
> >>
> >> To reduce the amount of memory needed by the pairwise distance matrix
> use
> >> the 'sieve' keyword. Try 'sieve 10' to start. Increase the sieve value
> as
> >> necessary.
> >>
> >> -Dan
> >>
> >> On Friday, January 2, 2015, Mahendra B Thapa <thapamb.mail.uc.edu>
> wrote:
> >>
> >> > Dear Dr. Daniel
> >> >
> >> > Thank you for the suggestion; I successfully updated to 'CPPTRAJ:
> >> > Trajectory Analysis. V14.22'
> >> >
> >> > But, again previous error message (as you answered in the first time)
> >> > appeared as
> >> > terminate called after throwing an instance of 'std::bad_alloc'
> >> > what(): std::bad_alloc
> >> >
> >> > Using the formula you gave me, the space requirement is 23GB but I
> have
> >> > enough memory (400GB) in my external drive where I run the 'cpptraj'
> >> > command.
> >> >
> >> > Thank you for help,
> >> > Mahendra Thapa
> >> > University of Cincinnati,OH
> >> >
> >> > On Fri, Jan 2, 2015 at 2:01 PM, Thapa, Mahendra (thapamb) <
> >> > thapamb.mail.uc.edu <javascript:;>> wrote:
> >> >
> >> > >
> >> > >
> >> > >
> >> > > ________________________________________
> >> > > From: Daniel Roe
> >> > > Sent: Friday, January 2, 2015 1:00:45 PM (UTC-06:00) Central America
> >> > > To: AMBER Mailing List
> >> > > Subject: Re: [AMBER] FW: clustering problem in ambertool14
> >> > >
> >> > > Hi,
> >> > >
> >> > > According to your log output you haven't applied all updates. The
> very
> >> > > first line of output is:
> >> > >
> >> > > CPPTRAJ: Trajectory Analysis. V14.00
> >> > >
> >> > > You need at least 14.17 for clustering with the traj data set to
> work
> >> > > properly (and really you should have 14.22). After updates are
> applied
> >> > > the code must be recompiled. Also if you are not using the full path
> >> > > to cpptraj when executing make sure that the cpptraj you are
> actually
> >> > > using is the up-to-date one (with e.g. the command 'which cpptraj`).
> >> > >
> >> > > Hope this helps,
> >> > >
> >> > > -Dan
> >> > >
> >> > >
> >> > > On Fri, Jan 2, 2015 at 9:08 AM, Mahendra B Thapa <
> thapamb.mail.uc.edu
> >> > <javascript:;>>
> >> > > wrote:
> >> > > > Dear Dr.Daniel
> >> > > > Memory issues were solved when I followed the steps you suggested;
> >> > thank
> >> > > > you for that.
> >> > > >
> >> > > > A new problem appeared as seen in the screen:
> >> > > >
> >> > > > Internal Error: Metric is COORDS base but data set is not.
> >> > > > Error: in Analysis # 0
> >> > > > 1 errors encountered reading input.
> >> > > >
> >> > > > {{ Note: I have already fixed bugs for ambertool 14
> >> > > > http://ambermd.org/bugfixes/AmberTools/14.0/update.17
> >> > > > }}
> >> > > >
> >> > > > DATAFILES:
> >> > > > cluster_out (Standard Data File): Cnum_00001
> >> > > > Warning: Set 'Cnum_00001' contains no data.
> >> > > > Warning: File 'cluster_out' has no sets containing data.
> >> > > >
> >> > > > Are these errors due to (i) a large numbers of frames (250000) and
> >> > number
> >> > > > of atoms (7584 atoms) ?
> >> > > >
> >> > > > In the previous post (http://archive.ambermd.org/201408/0214.html
> ),
> >> > > there
> >> > > > is some discussion but I am assuming that I have been using
> stripped
> >> > > > topology file to run cpptraj. I have attached the screen shot (
> text
> >> > > > file:TEST_LOG) with this email.
> >> > > >
> >> > > > Thank you for help,
> >> > > > Mahendra Thapa
> >> > > >
> >> > > >
> >> > > > On Tue, Dec 16, 2014 at 3:20 PM, Thapa, Mahendra (thapamb) <
> >> > > > thapamb.mail.uc.edu <javascript:;>> wrote:
> >> > > >
> >> > > >>
> >> > > >>
> >> > > >>
> >> > > >> ________________________________________
> >> > > >> From: Daniel Roe
> >> > > >> Sent: Tuesday, December 16, 2014 2:19:51 PM (UTC-06:00) Central
> >> > America
> >> > > >> To: AMBER Mailing List
> >> > > >> Subject: Re: [AMBER] clustering problem in ambertool14
> >> > > >>
> >> > > >> Hi,
> >> > > >>
> >> > > >> Usually when you get this error message during a command that
> uses a
> >> > > >> COORDS data set (cluster, 2drms, crdfluct etc) it's because you
> ran
> >> > > >> out of memory. Here is a formula to estimate the amount of memory
> >> you
> >> > > >> will need to hold a COORDS data set:
> >> > > >>
> >> > > >> memory_in_bytes = (F * A * 3) * 4
> >> > > >>
> >> > > >> where F is the number of frames, A is the number of atoms (after
> >> > > >> stripping in this case), the 3 is from # of coords per atom and
> 4 is
> >> > > >> bytes (COORDS are single precision). Divide by 1048576 to get the
> >> > > >> result in MB. Add 6 to (F * A *3) if you have box coordinates,
> >> double
> >> > > >> if you have velocities as well.
> >> > > >>
> >> > > >> However, in place of a COORDS data set cpptraj also lets you use
> >> what
> >> > > >> is called a TRAJ data set (which leaves data on-disk). The only
> >> issue
> >> > > >> with this is because it remains on the disk you cannot modify a
> TRAJ
> >> > > >> data set, so you will have to pre-process your trajectory (i.e.
> >> > > >> strip/image) first. This is a good idea to do in general since it
> >> will
> >> > > >> make subsequent analyses faster. Here is some input as an
> example.
> >> > > >>
> >> > > >> # Step 1 - Preprocess
> >> > > >> parm myparm.parm7
> >> > > >> trajin mytraj.nc
> >> > > >> strip :Na+,WAT nobox outprefix strip
> >> > > >> autoimage
> >> > > >> rms first mass .C,CA,N
> >> > > >> trajout strip.mytraj.nc nobox
> >> > > >>
> >> > > >> A few things to note here. First is that I put the 'strip'
> command
> >> > > >> before everything else; this way subsequent commands will be
> faster
> >> > > >> because there are less atoms to deal with. Also note in my
> 'strip'
> >> > > >> command I'm writing out a stripped topology for use with my
> stripped
> >> > > >> trajectory. Finally and most importantly, because you are
> >> rms-fitting
> >> > > >> you will no longer be able to image anyway, so I'm getting rid of
> >> any
> >> > > >> box coordinates.
> >> > > >>
> >> > > >> # Step 2 - Cluster
> >> > > >> parm strip.myparm.parm7
> >> > > >> trajin strip.mytraj.nc
> >> > > >> loadtraj name MYTRAJ
> >> > > >> cluster crdset MYTRAJ :1-291.CA,N,C,O mass clusters 10 out
> >> > cluster_out
> >> > > >> nofit averagelinkage \
> >> > > >> summary summary_out info Cluster_info repout box2.rep repfmt
> pdb
> >> > > >> clusterout cluster.nc clusterfmt netcdf
> >> > > >>
> >> > > >> The 'loadtraj' command in this case is taking all loaded
> >> trajectories
> >> > > >> from 'trajin' statements and putting them into a TRAJ data set
> named
> >> > > >> MYTRAJ, which stays on-disk and can subsequently be used by the
> >> > > >> 'cluster' command.
> >> > > >>
> >> > > >> One more thing to keep in mind is that even though the
> coordinates
> >> > > >> will be kept on disk, you will still need enough memory to hold
> the
> >> > > >> pairwise distance matrix:
> >> > > >>
> >> > > >> memory_in_bytes = ((F * (F-1)) / 2) * 4
> >> > > >>
> >> > > >> If you don't have enough memory to hold the pairwise distance
> matrix
> >> > > >> try using the 'sieve' keyword to reduce the number of frames
> being
> >> > > >> clustered in the first pass. This will also speed up the actual
> >> > > >> clustering a bit. Last and most importantly make sure you are
> using
> >> > > >> the most up-to-date version of cpptraj (14.22).
> >> > > >>
> >> > > >> Hope this helps,
> >> > > >>
> >> > > >> -Dan
> >> > > >>
> >> > > >> On Tue, Dec 16, 2014 at 11:28 AM, Mahendra B Thapa <
> >> > thapamb.mail.uc.edu <javascript:;>
> >> > > >
> >> > > >> wrote:
> >> > > >> > Dear Amber users
> >> > > >> > I used following command for clustering 50ns all-atom simulated
> >> > data.
> >> > > >> > cpptraj -i input_file -p para_top
> >> > > >> > where 'input_file' consists of
> >> > > >> >
> >> > > >> > trajin mdcrd_files
> >> > > >> > autoimage
> >> > > >> > rms first mass .C,CA,N
> >> > > >> > strip :Na+,WAT
> >> > > >> > cluster :1-291.CA,N,C,O mass clusters 10 out cluster_out nofit
> >> > > >> > averagelinkage \
> >> > > >> > summary summary_out info Cluster_info repout box2.rep repfmt
> pdb
> >> > > >> > clusterout cluster.nc clusterfmt netcdf
> >> > > >> > go
> >> > > >> >
> >> > > >> > After running the command, I got following message without any
> >> > output
> >> > > >> files:
> >> > > >> >
> >> > > >> > 1]terminate called after throwing an instance of
> 'std::bad_alloc'
> >> > > >> > what(): std::bad_alloc
> >> > > >> > Aborted
> >> > > >> >
> >> > > >> > 2] Warning: One or more analyses requested creation of default
> >> > COORDS
> >> > > >> > DataSet.
> >> > > >> > CREATECRD: Saving coordinates from Top to file to
> >> "_DEFAULTCRD_"
> >> > > >> >
> >> > > >> >
> >> > > >> > 3]Warning: Coordinates are being rotated and box coordinates
> are
> >> > > present.
> >> > > >> > Warning: Unit cell vectors are NOT rotated; imaging will not be
> >> > > possible
> >> > > >> > Warning: after the RMS-fit is performed.
> >> > > >> >
> >> > > >> > Any comments and suggestion will be very useful.
> >> > > >> >
> >> > > >> > Thank you,
> >> > > >> > Mahendra Thapa
> >> > > >> > University of Cincinnati
> >> > > >> > _______________________________________________
> >> > > >> > AMBER mailing list
> >> > > >> > AMBER.ambermd.org <javascript:;>
> >> > > >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > >>
> >> > > >>
> >> > > >>
> >> > > >> --
> >> > > >> -------------------------
> >> > > >> Daniel R. Roe, PhD
> >> > > >> Department of Medicinal Chemistry
> >> > > >> University of Utah
> >> > > >> 30 South 2000 East, Room 307
> >> > > >> Salt Lake City, UT 84112-5820
> >> > > >> http://home.chpc.utah.edu/~cheatham/
> >> > > >> (801) 587-9652
> >> > > >> (801) 585-6208 (Fax)
> >> > > >>
> >> > > >> _______________________________________________
> >> > > >> AMBER mailing list
> >> > > >> AMBER.ambermd.org <javascript:;>
> >> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> >> > > >>
> >> > > >
> >> > > > _______________________________________________
> >> > > > AMBER mailing list
> >> > > > AMBER.ambermd.org <javascript:;>
> >> > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > >
> >> > >
> >> > >
> >> > >
> >> > > --
> >> > > -------------------------
> >> > > Daniel R. Roe, PhD
> >> > > Department of Medicinal Chemistry
> >> > > University of Utah
> >> > > 30 South 2000 East, Room 307
> >> > > Salt Lake City, UT 84112-5820
> >> > > http://home.chpc.utah.edu/~cheatham/
> >> > > (801) 587-9652
> >> > > (801) 585-6208 (Fax)
> >> > >
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org <javascript:;>
> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org <javascript:;>
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 307
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Jan 17 2015 - 08:30:02 PST
