[gmx-users] Possible free energy bug?
mczwier at gmail.com
Fri Mar 11 03:43:09 CET 2011
I should have specified that the segfault happened for us after we got
similar warnings and errors (DD and/or LINCS), so the segfault may
have been tangential. Given that everything about your system worked
before GROMACS 4.5, it's possible that your older compilers are
generating code that's incompatible with the GROMACS assembly loops
(which you are likely running with, as they are the default option on
most mainstream processors). The bug you mentioned in your original
post also has my antennae twitching about bad machine code.
If that's indeed happening, it's almost certainly some bizarre
alignment issue, something like half of a float is getting overwritten
on the way into or out of the assembly code, which corruption would
trigger the results you describe. It's also distantly possible that
GROMACS is working fine, but your copy of FFTW or BLAS/LAPACK (more
likely the latter) has alignment problems. One final possibility
(which would explain the failure on YellowDog but unfortunately not
the failure on OS X) is that GCC is generating badly-aligned code for
auto-vectorized Altivec loops, which is still a problem for Intel's
SIMD instructions on 32-bit x86 architectures even with GCC 4.4. I've
also observed MPI gather/reduce operations to foul up alignment (or
rigidly enforce it where badly compiled code is relying on broken
alignment) under exceedingly rare circumstances, usually involving
different libraries compiled with different compilers (which is
generally a bad idea for scientific code anyway).
Okay...so all of that said, there are a few things to try:
1) Recompile GROMACS using -O2 instead of -O3; that'll turn off the
automatic vectorizer (on Yellow Dog) and various other relatively
risky optimizations (on both platforms). CFLAGS="-O2 -march=powerpc"
in the environment AND on the configure command line would do that.
Check your build logs to make sure it took, though, because if you
don't do it exactly right, configure will ignore your directives and
merrily set up GROMACS to compile with -O3, which is the most likely
culprit for badly-aligned code.
2) Recompile GROMACS specifying a forced alignment flag. I have no
experience with PowerPC, but -malign-natural and -malign-power look
like good initial guesses. That's probably going to cause more
problems than it solves, but if you have a screwy BLAS/LAPACK or MPI,
it might help. I only suggest it because if you've already tried #1,
it will only take another half hour or hour of your time to recompile
GROMACS again. Other than that, tinkering with alignment flags is a
really easy way to REALLY break code, so you might consider skipping
this and moving straight on to #3.
3) Snag GCC 4.4.4 or 4.4.5 and compile it, and use that to compile
GROMACS, again with -O2. GCC takes forever to compile, but beyond
that, it's not as difficult as it could be. Nothing preventing you
from installing it in your home directory, either, assuming you set
PATH and LD_LIBRARY_PATH (or DYLD_LIBRARY_PATH on OS X) properly. You
might need to snag a new copy of binutils as well, if gcc refuses to
compile with the system ld. This option would also probably get you
threading, since you certainly have hardware support for it.
4) Rebuild your entire GROMACS stack, including FFTW, BLAS/LAPACK,
MPI, and GROMACS itself with the same compiler (preferably GCC from
#3) and the same compiler options (which again should be -O2, and
definitely NOT any sort of alignment flag). Put them in their own
tree (like "/opt/sci"), and definitely not in /usr (which is generally
managed by the system) or /usr/local (which tends to accumulate
cruft). ATLAS is a good choice for BLAS, and there are directions on
the ATLAS website for building a complete and optimized LAPACK based
In practice, I've found I've had to do #4 for every piece of
scientific software our group uses, because pretty much nothing works
right with OS-installed versions of compilers, BLAS/LAPACK, and MPI.
It takes forever, and it pretty much defines the phrase "learning
experience," but it also essentially *never* breaks once it works
(because OS updates never overwrite anything you've hand-tuned to run
correctly). But...with luck option #1 will fix things quickly enough
to get you running without devoting two days to rebuilding your
software stack from scratch.
Hope that helps,
On Thu, Mar 10, 2011 at 8:54 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Hi Matt,
> Thanks for the reply. I can't trace the problem to a specific compiler. We
> have a PowerPC cluster with two partitions - one running Mac OS X 10.3 with
> gcc-3.3, the other running YellowDog Linux with gcc-4.2.2. The problem
> happens on both partitions. There are no seg faults, the runs just exit
> (MPI_ABORT) after the fatal error (either "too many LINCS warnings" or the
> DD-related error I posted before).
> We are using MPI: mpich-1.2.5 on OSX and OpenMPI-1.2.3 on Linux. All of the
> above has been the same since my successful 3.3.3 TI calculations (as well
> as all of my simulations with Gromacs, ever). Our hardware and compilers
> are somewhat (very) outdated so threading is not supported, we always use
> Gromacs was compiled in single precision using standard options through
> autoconf. The cmake build system still does not work on our cluster due to
> several outstanding bugs.
> Matthew Zwier wrote:
>> Dear Justin,
>> We recently experienced a similar problem (LINCS errors, step*.pdb
>> files), and then GROMACS usually segfaulted. The cause was a
>> miscompiled copy of GROMACS. Another member of our group had compiled
>> GROMACS on an Intel Core2 quad (gcc -march=core2) and tried to run the
>> copy without modification on an AMD Magny Cours machine.
>> Recompilation with the correct subarchitecture type (-march=amdfam10)
>> fixed the problem. Don't really know why it didn't die with SIGILL or
>> SIGBUS instead of SIGSEGV, but that's probably a question for the
>> hardware gurus.
>> So...are you observing segfaults? What compiler are you using (and on
>> what OS)? What were the compilation parameters for 4.5.3? Also, are
>> you really running across nodes with MPI, or running on the same node
>> with MPI?
>> Matt Zwier
>> On Thu, Mar 10, 2011 at 1:55 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>> Hi All,
>>> I've been troubleshooting a problem for some time now and I wanted to
>>> it here and solicit some feedback before I submit a bug report to see if
>>> there's anything else I can try.
>>> Here's the situation: I ran some free energy calculations (thermodynamic
>>> integration) a long time ago using version 3.3.3 to determine the
>>> free energy of a series of small molecules. Results were good and they
>>> ended up as part of a paper, so I'm trying to reproduce the methodology
>>> 4.5.3 (using BAR) to see if I understand the workflow completely. The
>>> problem is my systems are crashing. The runs simply stop randomly
>>> within a few hundred ps) with lots of LINCS warnings and step*.pdb files
>>> being written.
>>> I know the parameters are good, and produce stable trajectories, since I
>>> spent months on them some years ago. The system prep is steepest descents
>>> to Fmax < 100 (always achieved), NVT at 298 K for 100 ps, NPT at 298K/1
>>> for 100 ps, then 5 ns of data collection under NPT conditions. Here's
>>> rundown of what I'm seeing:
>>> 1. All LJ transformations work fine. The problem only comes when I have
>>> molecule with full LJ interaction and I am "charging" it (i.e.,
>>> charges to the partially-interacting species).
>>> 2. Simulations at lambda=1 (full interaction) work fine.
>>> 3. Simulations with the free energy code off entirely work fine under all
>>> 4. I cannot run in serial due to http://redmine.gromacs.org/issues/715.
>>> bug seems to affect other systems and is not specifically related to my
>>> energy calculations.
>>> 5. Running with DD fails because my system is relatively small (more on
>>> in a moment).
>>> 6. Running with mdrun -pd 2 works, but mdrun -pd 4 crashes for any value
>>> lambda != 1.
>>> 7. I created a larger system (instead of a 3x3x3-nm cube of water with my
>>> molecule, I used 4x4x4) and ran on 4 CPU's with DD (lambda = 0, i.e. full
>>> vdW, no intermolecular Coulombic interactions - .mdp file is below).
>>> run also crashed with some warnings about DD cell size:
>>> DD load balancing is limited by minimum cell size in dimension X
>>> DD step 329999 vol min/aver 0.748! load imb.: force 31.5%
>>> ...and then the actual crash:
>>> Program mdrun_4.5.3_gcc_mpi, VERSION 4.5.3
>>> Source code file: domdec_con.c, line: 693
>>> Fatal error:
>>> DD cell 0 0 0 could only obtain 14 of the 15 atoms that are connected via
>>> constraints from the neighboring cells. This probably means your
>>> lengths are too long compared to the domain decomposition cell size.
>>> Decrease the number of domain decomposition grid cells or lincs-order or
>>> the -rcon option of mdrun.
>>> For more information and tips for troubleshooting, please check the
>>> website at http://www.gromacs.org/Documentation/Errors
>>> Watching the trajectory doesn't seem to give any useful information. The
>>> small molecule of interest is at a periodic boundary when the crash
>>> but there are several crosses prior to the crash without incident, so I
>>> don't know if the issue is related to PBC or not, but it appears not.
>>> 8. I initially thought the problem might be related to the barostat, but
>>> switching from P-R to Berendsen does not alleviate the problem, nor does
>>> increasing tau_p (tested 0.5, 1.0, 2.0, and 5.0 - all crash). Longer
>>> simply delays the crash, but does not prevent it.
>>> So after all that, I'm wondering if (1) anyone has seen the same, or (2)
>>> there's anything else I can try (environment variables, hidden tricks,
>>> that I can use to get to the bottom of this before I give up and file a
>>> If you made it this far, thanks for reading my novel and hopefully
>>> can give me some ideas. The .mdp file I'm using is below, but it is just
>>> one of many that I've tried. In theory, it should work, since the
>>> parameters are the same as my successful 3.3.3 runs, with the exception
>>> the new free energy features in 4.5.3 and obvious keyword changes related
>>> the difference in version.
>>> --- .mdp file ---
>>> ; Run control
>>> integrator = sd ; Langevin dynamics
>>> tinit = 0
>>> dt = 0.002
>>> nsteps = 2500000 ; 5 ns
>>> nstcomm = 100
>>> ; Output control
>>> nstxout = 500
>>> nstvout = 500
>>> nstfout = 0
>>> nstlog = 500
>>> nstenergy = 500
>>> nstxtcout = 0
>>> xtc-precision = 1000
>>> ; Neighborsearching and short-range nonbonded interactions
>>> nstlist = 5
>>> ns_type = grid
>>> pbc = xyz
>>> rlist = 0.9
>>> ; Electrostatics
>>> coulombtype = PME
>>> rcoulomb = 0.9
>>> ; van der Waals
>>> vdw-type = cutoff
>>> rvdw = 1.4
>>> ; Apply long range dispersion corrections for Energy and Pressure
>>> DispCorr = EnerPres
>>> ; Spacing for the PME/PPPM FFT grid
>>> fourierspacing = 0.12
>>> ; EWALD/PME/PPPM parameters
>>> pme_order = 4
>>> ewald_rtol = 1e-05
>>> epsilon_surface = 0
>>> optimize_fft = no
>>> ; Temperature coupling
>>> ; tcoupl is implicitly handled by the sd integrator
>>> tc_grps = system
>>> tau_t = 1.0
>>> ref_t = 298
>>> ; Pressure coupling is on for NPT
>>> Pcoupl = Berendsen
>>> tau_p = 2.0
>>> compressibility = 4.5e-05
>>> ref_p = 1.0
>>> ; Free energy control stuff
>>> free_energy = yes
>>> init_lambda = 0.00
>>> delta_lambda = 0
>>> foreign_lambda = 0.05
>>> sc-alpha = 0
>>> sc-power = 1.0
>>> sc-sigma = 0
>>> couple-moltype = MOR ; name of moleculetype to couple
>>> couple-lambda0 = vdw ; vdW interactions
>>> couple-lambda1 = vdw-q ; turn on everything
>>> couple-intramol = no
>>> dhdl_derivatives = yes ; this line (and the next two) are
>>> separate_dhdl_file = yes ; included only for pedantry
>>> nstdhdl = 10
>>> ; Do not generate velocities
>>> gen_vel = no
>>> ; options for bonds
>>> constraints = all-bonds
>>> ; Type of constraint algorithm
>>> constraint-algorithm = lincs
>>> ; Constrain the starting configuration
>>> ; since we are continuing from NPT
>>> continuation = yes
>>> ; Highest order in the expansion of the constraint coupling matrix
>>> lincs-order = 4
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> gmx-users mailing list gmx-users at gromacs.org
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> or send it to gmx-users-request at gromacs.org.
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> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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