The problem is now partially resolved. It turns out the topology file
downloaded from Tutorial A27 has a problem that atom numbering in molecules
is not sequential. This is originated from the mol2 file which was used to
build the topology. The nonsequential toplogy and coordinate files can be
fixed by cpptraj with the command fixatomorder. After that, the 2 step
minimizations illustrated in tutorial finished without problem. But a new
and similar segmentation fault appears when it goes to the molecular
dynamics step:
-------
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
#0 0x7FD93AA875F7
#1 0x7FD93AA87C3E
#2 0x7FD93A1BB2EF
#3 0x49BDB1 in __cit_mod_MOD_setup_crd_idx_tbl
#4 0x49BEE4 in __cit_mod_MOD_setup_cit
#5 0x47779D in __pme_direct_mod_MOD_pme_list
#6 0x48FF57 in __pme_force_mod_MOD_pme_force
#7 0x4B6ECA in __runmd_mod_MOD_runmd
#8 0x4E24DD in MAIN__ at pmemd.F90:?
./run.sh: line 23: 21885 Segmentation fault (core dumped) pmemd -O -i
hap16_water_heat.in -o hap16_water_heat.out -p hapfix.hap16_water.prmtop -c
hap16_water_min2.rst -r hap16_water_heat.rst -x heat.netcdf -ref
hap16_water_min.rst
------
At this point, both pmemd and sander give similar Segmentation fault
messages.
Any help is highly appreciated!
Junjun
On Mon, Sep 12, 2016 at 12:01 PM, liu junjun <ljjlp03.gmail.com> wrote:
> Hi everyone,
>
> I downloaded the prmtop, inpcrd and the hap16_water_min1.in files from
> Tutorial A27 at http://ambermd.org/tutorials/advanced/tutorial27/
> hap_water.htm
>
> I tried exactly the same command as listed on the webpage:
> ---------
> pmemd.cuda -O -i hap16_water_min1.in -o hap16_water_min1.out -p
> hap16_water.prmtop -c hap16_water.inpcrd -r hap16_water_min1.rst -ref
> hap16_water.inpcrd
> -----
>
> then I got the following error message:
> ----
> Program received signal SIGSEGV: Segmentation fault - invalid memory
> reference.
>
> Backtrace for this error:
> #0 0x7F22CA23F5F7
> #1 0x7F22CA23FC3E
> #2 0x7F22C99732EF
> #3 0x473F9A in __mol_list_mod_MOD_setup_molecule_lists
> #4 0x4B605B in __pme_alltasks_setup_mod_MOD_pme_alltasks_setup
> #5 0x499FC3 in MAIN__ at pmemd.F90:?
> ./run.sh: line 16: 25395 Segmentation fault (core dumped) pmemd.cuda
> -O -i hap16_water_min1.in -o hap16_water_min1.out -p hap16_water.prmtop
> -c hap16_water.inpcrd -r hap16_water_min1.rst -ref hap16_water.inpcrd
> -----
>
> I tried to switch the program to pmemd, pmemd.MPI, sander, and sander.MPI.
> The sander programs work fine but pmemd programs give exactly the same
> Segmentation fault error message.
>
> The Amber I am using is Amber16. It's compiled by gnu4.9.2. The "make
> test" have been passed on all cases. The OS system is Ubuntu 15.04
>
> What could be the problem?
>
> Thanks in advance!
>
> Junjun
>
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Received on Mon Sep 12 2016 - 15:30:02 PDT
