Hi,
Sander will automatically determine the input trajectory format for
postprocessing. Since the error is OS-related, probably something is
going on with your system. I notice in the test script in your
attachment you're setting AMBERHOME but not sourcing amber.sh. Perhaps
there's some library incompatibility occurring? Try sourcing the
amber.sh script in your Amber 16 directory before running.
-Dan
On Wed, Nov 29, 2017 at 10:19 AM, Paul Mortenson
<Paul.Mortenson.astx.com> wrote:
> Hi,
>
> I'm having trouble getting sander to work with imin=5 (post-processing trajectory files). I have attached a simple test case which works fine for AMBER14, but not with AMBER16.
>
> Sander crashes before outputting any energies, with the following error message:
>
> sander: posixio.c:232: px_pgout: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed.
>
> Program received signal SIGABRT: Process abort signal.
>
> Backtrace for this error:
> #0 0x7F29152256F7
> #1 0x7F2915225D3E
> #2 0x7F291472A26F
> #3 0x7F291472A1F7
> #4 0x7F291472B8E7
> #5 0x7F2914723265
> #6 0x7F2914723311
> #7 0xA1E92C in px_pgout at posixio.c:?
> #8 0xA1F4F6 in px_get at posixio.c:?
> #9 0xA1F6FD in ncio_px_get at posixio.c:?
> #10 0xA18137 in ncio_get
> #11 0xA21D67 in putNCvx_char_char at putget.c:?
> #12 0xA29DE5 in writeNCv at putget.c:?
> #13 0xA2ABA4 in NC3_put_vara
> #14 0xA12A26 in NC_put_vara at dvarput.c:?
> #15 0xA12F61 in NCDEFAULT_put_vars
> #16 0xA13A56 in NC_put_vars at dvarput.c:?
> #17 0xA14902 in nc_put_vars_text
> #18 0xA0B414 in nf_put_vars_text_
> #19 0xA01829 in __netcdf_MOD_nf90_put_var_1d_text
> #20 0x68DB6B in __ambernetcdf_mod_MOD_nc_create
> #21 0x691F41 in __binrestart_MOD_write_nc_restart
> #22 0x544B4B in master.0.minrit_.part.0.constprop.1 at minrit.F90:?
> #23 0x4EEB9A in runmin_
> #24 0x4DA2F4 in __trajenemod_MOD_trajene
> #25 0x4D83E3 in sander_
> #26 0x4CE738 in MAIN__ at multisander.F90:?
>
> Does anyone have any suggestions?
>
> Thanks,
> Paul Mortenson
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Nov 30 2017 - 11:00:01 PST
