Hi,
The information in that post is unfortunately several years out of
date. The OpenMP-enabled cpptraj is built with the usual OpenMP
AmberTools build that you configure with the '-openmp' flag. This will
install cpptraj.OMP in the $AMBERHOME/bin directory. When you run it
you will see this at the top of the output:
CPPTRAJ: Trajectory Analysis. V14.22 OpenMP
-Dan
On Sat, Jan 17, 2015 at 9:01 AM, Mahendra B Thapa <thapamb.mail.uc.edu> wrote:
> 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
>>
> _______________________________________________
> 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)
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Received on Sat Jan 17 2015 - 16:00:02 PST
