Dear Dr. Daniel
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:
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
>
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Received on Tue Jan 06 2015 - 15:00:03 PST
