Hi,
I can confirm that there appears to be a bug. I'm working on the fix now,
hopefully it will be done soon. Thanks for the report,
-Dan
On Tue, Jul 8, 2014 at 5:06 PM, Jason Swails <jason.swails.gmail.com> wrote:
> Copying this back to the Amber list. I have no idea why you are seeing
> this problems, although we would likely have to be able to reproduce the
> error to find out what went wrong.
>
> I suspect something may have happened like the cutoff was too small so the
> data set wound up being empty (or something along those lines), causing in
> effect a segfault. Dan would have to weigh in here.
>
> It would be helpful if you could find a short trajectory (with maybe 5-10
> frames) that reproduces the problem so someone (probably Dan) can find out
> what happened.
>
> HTH,
> Jason
>
> On Tue, Jul 8, 2014 at 3:19 PM, Krisztina Feher <feher_krisztina.yahoo.com
> >
> wrote:
>
> > Dear Jason,
> >
> > thanks for the quick reply. I compiled AMBER14 with AmberTools 14 last
> > Friday, here is output of the configuration step listing the updates
> being
> > made. The make install went without problems too. Is there any other
> > tests I can do?
> >
> > Best,
> > Krisztina
> >
> >
> > sirius:~/bin/amber14> *./configure gnu*
> > Checking for updates...
> > Checking for available patches online. This may take a few seconds...
> >
> > Available AmberTools 14 patches:
> >
> > update.4 (modifies ParmEd, MMPBSA.py, tleap)
> > Released on June 20, 2014 (written by Jason Swails)
> > Description:
> > Fixes a number of small bugs in tleap, ParmEd, and MMPBSA.py
> > ParmEd
> > 1. Improves 10-12 parameter detection when emitting warnings
> > printing frcmod files from prmtop files
> > 2. Improves dihedral parameter equality determination
> > (eliminates duplicate, but reordered, dihedral files in
> > emitted frcmod files)
> > tleap
> > 1. Drastically improves performance when residues need to be
> > split, like in CHARMM-generated lipid PDB files
> > 2. Fix angle identification including hydrogen when hydrogen is
> > connected to both a heavy atom and a dummy atom
> > MMPBSA.py
> > Fix a subtle bug that occasionally corrupts mutations in alanine
> > scanning calculations.
> >
> >
> >
> > Available Amber 14 patches:
> >
> > update.1 (modifies pmemd.amoeba)
> > Released on May 29, 2014 (written by Jason Swails)
> > Description:
> > Fixes a bug in pmemd.amoeba.MPI that could cause the program to
> > hang indefinitely right before completion. Also fixes some issues
> > with softcore simulations in pmemd.amoeba.
> >
> > update.2 (modifies pmemd)
> > Released on June 18, 2014 (written by Joe Kaus)
> > Description:
> > Fix for constant pressure simulations at large core counts
> > pmemd:
> > When using ntp = 1, barostat = 1 (default) and large core counts
> > the block reciprocal sum code was activated, which did not
> > calculate the virial if the potential energy was not needed for
> > the current step. This caused a deviation in the resulting
> > pressure calculated for the simulation.
> >
> > update.3 (modifies pmemd, pmemd.cuda)
> > Released on June 20, 2014 (written by Jason Swails)
> > Description:
> > Two small fixes for pmemd and pmemd.cuda:
> > 1) Fix printing of the DUMPAVE file in NMRopt calculations when
> > using the Monte Carlo barostat
> > 2) Catch illegal values of the MC Barostat interval with the given
> > value of nrespa (multiple time-stepping)
> >
> >
> > There are patches available. Do you want to apply them now? [y/N]
> > (Recommended Y)
> > Y
> > Preparing to apply updates... please wait.
> > Downloading updates for AmberTools 14
> > Downloading AmberTools 14/update.4 (12.07 KB)
> > Applying AmberTools 14/update.4
> > Downloading updates for Amber 14
> > Downloading Amber 14/update.1 (21.70 KB)
> > Applying Amber 14/update.1
> > Downloading Amber 14/update.2 (1.67 KB)
> > Applying Amber 14/update.2
> > Downloading Amber 14/update.3 (2.29 KB)
> > Applying Amber 14/update.3
> >
> > NOTE: update_amber only updates the raw source code! You must recompile
> > if you want
> > any changes to take effect!
> >
> > Searching for python2... Found python2.7: /usr/bin/python2.7
> >
> > Obtaining the gnu suite version:
> > gcc -v
> > The version is 4.6.3
> >
> > Testing the gcc compiler:
> > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> > OK
> >
> > Testing the g++ compiler:
> > g++ -o testp testp.cpp
> > OK
> >
> > Testing the gfortran compiler:
> > gfortran -O0 -o testp testp.f
> > OK
> >
> > Testing mixed C/Fortran compilation:
> > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c
> > gfortran -O0 -c -o testp.f.o testp.f
> > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o
> > testp.f.o -lgfortran -w
> > OK
> >
> > Testing pointer size:
> > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size
> > test_pointer_size.c
> > Detected 64 bit operating system.
> >
> > Testing flex: OK
> >
> > Checking NetCDF...
> > Using bundled NetCDF library.
> > Using existing NetCDF in '/home/kriszti/bin/amber14'
> >
> > Checking for zlib: OK
> >
> > Checking for libbz2: OK
> >
> > Configuring fftw-3.3 (may be time-consuming)...
> >
> > fftw-3.3 configure succeeded.
> >
> > Configuring XBLAS (may be time-consuming)...
> >
> > XBLAS configure succeeded.
> >
> > Configuring MTK++ (may be time-consuming)...
> >
> > MTK++-0.2.0 configure succeeded.
> > The configuration file, config.h, was successfully created.
> >
> >
> --------------------------------------------------------------------------------
> > Environment resource files are provided to set the proper environment
> > variables to use AMBER and AmberTools.
> >
> > If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
> > /home/kriszti/bin/amber14/amber.sh file in your shell. Consider adding
> the
> > line
> > test -f /home/kriszti/bin/amber14/amber.sh && source
> > /home/kriszti/bin/amber14/amber.sh
> > to your startup file (e.g., ~/.bashrc)
> >
> > If you use a C shell (e.g., csh, tcsh), source the
> > /home/kriszti/bin/amber14/amber.csh file in your shell. Consider adding
> > the line
> > test -f /home/kriszti/bin/amber14/amber.csh && source
> > /home/kriszti/bin/amber14/amber.csh
> > to your startup file (e.g., ~/.cshrc)
> >
> >
> --------------------------------------------------------------------------------
> >
> > The next step is to type 'make install'
> >
> > Cleaning the src directories. This may take a few moments.
> > Configure complete.
> >
> > ------------------------------
> > *From:* Jason Swails <jason.swails.gmail.com>
> > *To:* Krisztina Feher <feher_krisztina.yahoo.com>; AMBER Mailing List <
> > amber.ambermd.org>
> > *Sent:* Wednesday, July 9, 2014 12:05 AM
> > *Subject:* Re: [AMBER] atomiccorr: glibc detected *** cpptraj: malloc():
> > memory corruption:
> >
> >
> >
> >
> > On Tue, Jul 8, 2014 at 2:26 PM, Krisztina Feher <
> feher_krisztina.yahoo.com
> > > wrote:
> >
> > Dear All,
> >
> > I used the atomiccorr function on a trajectory:
> >
> > trajin ../mut1_2w_dynV-100ns.netcdf netcdf
> > atomiccorr .CA,C,N out aCorr_byRes.out cut 0.3 byres
> >
> >
> > when I got this mesage:
> > *** glibc detected *** cpptraj: malloc(): memory corruption:
> > 0x0000000000e8f000 ***
> > ^C
> >
> >
> > I tried this on the raw trajectory including alll water, ions and on a
> > imaged/centred trajectory without water and ions, it gave the same. I did
> > not find anyone describing this error with cpptraj in the list archive.
> If
> > anyone can help, it is very much appreciated.
> >
> >
> > What version of cpptraj are you using? Does it pass all of the tests?
> > There have been a number of bugs fixed, so make sure you are using
> > AmberTools 14 with all applied updates. If you are unsure whether all
> > updates have been applied, just reconfigure and recompile AmberTools 14.
> > It will look for available updates and apply them if you allow it.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
> >
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> 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 201
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 Tue Jul 08 2014 - 20:00:03 PDT
