Hi,
There was a bug in cpptraj that prevented TRAJ data sets from properly
being utilized in the OpenMP version. I have created a patch (update
25) for cpptraj that fixes this problem which should be live within
the next day or two. The TRAJ data set will keep the coordinates
on-disk, so you will only need enough memory for the pair-wise matrix;
this should allow your clustering run to complete successfully.
Thanks for finding and reporting this issue!
-Dan
On Mon, Jan 26, 2015 at 8:42 AM, Mahendra B Thapa <thapamb.mail.uc.edu> wrote:
> Dear Dr. Daniel
>
> "loadcrd" worked nicely with small data set that you suggested in the last
> email. But, the process (i.e., cpptraj.OMP) killed without any error
> message for very large data set (250000 frames which occupied 144 GB space
> and each frame was without water molecules) in dual core machine with
> nvidia graphics.The message seen for these large frames was as
>
> CPPTRAJ: Trajectory Analysis. V14.22 OpenMP
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
> Reading test.top' as Amber Topology
> INPUT: Reading Input from file input_for_clustering_by_cpptraj
> [loadcrd test_250000frames.pdb MYTRAJ]
> Reading 'test_250000frames.pdb' as PDB
> Loading trajectory 'test_250000frames.pdb' as 'MYTRAJ'
> -----trajectory 'test_250000frames .pdb (1-250000, 1) -----
> 0% 10% 20% Killed
>
> I will try in it a local cluster.
>
> Thank you for continued help,
> Mahendra Thapa
> University of Cincinnati,OH
>
>
>
> On Fri, Jan 23, 2015 at 12:03 PM, Thapa, Mahendra (thapamb) <
> thapamb.mail.uc.edu> wrote:
>
>>
>>
>>
>> ________________________________________
>> From: Daniel Roe
>> Sent: Friday, January 23, 2015 11:02:31 AM (UTC-06:00) Central America
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] FW: FW: FW: FW: clustering problem in ambertool14
>>
>> Hi,
>>
>> OK, I think there may be a bug specifically for the combination of
>> TRAJ data sets and OpenMP. Can you try a small COORDS data set and see
>> if the exception goes away? E.g.
>>
>> loadcrd test_250000frames.pdb 1 10000 100 MYTRAJ
>> runanalysis cluster crdset MYTRAJ :1-500.CA,N,C,O mass \
>> clusters 10 out cluster_out nofit averagelinkage \
>> summary summary_out sieve 30 info Cluster_info repout box2.rep repfmt
>> pdb \
>> clusterout cluster.nc clusterfmt netcdf
>>
>> I'll keep looking into the problem in the meantime. Thanks for the report.
>>
>> -Dan
>>
>> On Fri, Jan 23, 2015 at 7:24 AM, Mahendra B Thapa <thapamb.mail.uc.edu>
>> wrote:
>> > Dear Dr. Daniel
>> >
>> > I have attached the input file (input_for_test-cpptraj_openMP) for
>> > cpptraj and the message what I got after running cpptraj in openMP (
>> > output_message_on_screen.txt). There was no problem with the input file
>> > when cpptraj was run in series mode instead of openMP.
>> > I was trying these tests in dual core machine and I had allocated 500 GB
>> > space (but not 500 GB of RAM).
>> >
>> > Thank you for help,
>> > Mahendra Thapa
>> > University of Cincinnati,OH
>> >
>> >
>> > On Tue, Jan 20, 2015 at 1:00 PM, Thapa, Mahendra (thapamb) <
>> > thapamb.mail.uc.edu> wrote:
>> >
>> >>
>> >>
>> >>
>> >> ________________________________________
>> >> From: Daniel Roe
>> >> Sent: Tuesday, January 20, 2015 11:59:42 AM (UTC-06:00) Central America
>> >> To: AMBER Mailing List
>> >> Subject: Re: [AMBER] FW: FW: FW: clustering problem in ambertool14
>> >>
>> >> Hi,
>> >>
>> >> On Sun, Jan 18, 2015 at 9:01 AM, Mahendra B Thapa <thapamb.mail.uc.edu>
>> >> wrote:
>> >> > When I tried to test ' cpptraj.OMP' with 5000 frames for clustering,
>> I
>> >> got
>> >> > the following error message:
>> >> > *Floating point exception*
>> >>
>> >> It's much easier for us to help if you can paste or attach your entire
>> >> input and output. A floating point exception message with no context
>> >> will be impossible to debug without more information.
>> >>
>> >> > I had enough space (500GB) while running it and I did not get that
>> error
>> >> > message while running 'cpptraj' in series even with 250000 frames.
>> >>
>> >> You have 500 GB of RAM? Again, remember it is RAM that matters for the
>> >> pairwise matrix calculation, not disk space. The OpenMP version will
>> >> use a bit more memory than the serial version but not a huge amount
>> >> more. At any rate I don't think memory is the issue here. Send me the
>> >> entire output off-list and I'll see what I can find.
>> >>
>> >> -Dan
>> >>
>> >> >
>> >> > Thank you for help,
>> >> > Mahendra Thapa
>> >> > University of Cincinnati,OH
>> >> >
>> >> >
>> >> > On Sat, Jan 17, 2015 at 7:00 PM, Thapa, Mahendra (thapamb) <
>> >> > thapamb.mail.uc.edu> wrote:
>> >> >
>> >> >>
>> >> >>
>> >> >>
>> >> >> ________________________________________
>> >> >> From: Daniel Roe
>> >> >> Sent: Saturday, January 17, 2015 5:58:55 PM (UTC-06:00) Central
>> America
>> >> >> To: AMBER Mailing List
>> >> >> Subject: Re: [AMBER] FW: FW: clustering problem in ambertool14
>> >> >>
>> >> >> 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)
>> >> >>
>> >> >> _______________________________________________
>> >> >> 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)
>>
>> _______________________________________________
>> 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
Received on Mon Jan 26 2015 - 12:30:03 PST
