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
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Received on Tue Jul 08 2014 - 16:30:02 PDT
