[gmx-developers] 4.6 beta2: segfault in grompp (with pulling + free-energy)

[Jochen Hub]

One more information:

I just noticed that in readir.c:1294,

snew(fep->all_lambda[i],fep->n_lambda);

fep->n_lambda is 0. That's why all_lambda[efptMASS]==NULL.

Is this the intended behaviour? My free-energy mdp-options are:

; Free energy control stuff
free_energy              = yes
init_lambda              = 0.0
delta_lambda             = 0.01
foreign_lambda           =
sc-alpha                 = 0.5
sc-power                 = 1
sc-sigma                 = 0.3
nstdhdl                  = 0
separate-dhdl-file       = yes
dhdl-derivatives         = yes
dh_hist_size             = 0
dh_hist_spacing          = 0.1
couple-moltype           = POT
couple-lambda0           = none
couple-lambda1           = vdw
couple-intramol          = no


Am 12/12/12 10:59 AM, schrieb Jochen Hub:
> Hi,
>
> grompp gives a segfault with pulling and free-energy=yes.
>
> The reason is that ir->fepvals->all_lambda[efptMASS] in readpull.c:302
> is NULL. See:
>
> (gdb) p ir->fepvals->all_lambda[efptMASS]
> $5 = (double *) 0x0
>
> I use 4.6-beta2-dev-20121211-031485c. The error does not occur in 4.5.5.
>
> Is the error obvious, or do you need a redmine?
>
> Cheers,
> Jochen
>
> Here is the backtrace:
>
> Program received signal EXC_BAD_ACCESS, Could not access memory.
> Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000000
> 0x0000000100028e67 in set_pull_init (ir=0x101801000, mtop=0x101505440,
> x=0x10cc81000, box=0x7fff5fbff3c8, oenv=0x101500b50, bStart=0) at
> /Users/jhub/src/gmx/gromacs/src/kernel/readpull.c:302
> 302          lambda =
> ir->fepvals->all_lambda[efptMASS][ir->fepvals->init_fep_state];
> (gdb) bt
> #0  0x0000000100028e67 in set_pull_init (ir=0x101801000,
> mtop=0x101505440, x=0x10cc81000, box=0x7fff5fbff3c8, oenv=0x101500b50,
> bStart=0) at /Users/jhub/src/gmx/gromacs/src/kernel/readpull.c:302
> #1  0x0000000100009957 in cmain (argc=1, argv=0x7fff5fbff778) at
> /Users/jhub/src/gmx/gromacs/src/kernel/grompp.c:1694
> #2  0x0000000100009dde in main (argc=13, argv=0x7fff5fbff778) at
> /Users/jhub/src/gmx/gromacs/src/kernel/main.c:29
>

-- 
---------------------------------------------------
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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