This is an IO error, and based on the function names seems to
specifically be an error writing the coordinate trajectory. Do you
have enough space on the device you are writing this to? Do you have
correct permissions, etc?
-Dan
On Tue, Jun 6, 2017 at 12:49 PM, Andreas Tosstorff
<andreas.tosstorff.cup.uni-muenchen.de> wrote:
> Dear Amber users,
>
>
> I am currently getting this error message when running pmemd:
>
> pmemd: 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 0x7F6CCB743467
> #1 0x7F6CCB743AAE
> #2 0x7F6CCAC4A24F
> #3 0x7F6CCAC4A1D7
> #4 0x7F6CCAC4B8C7
> #5 0x7F6CCAC43145
> #6 0x7F6CCAC431F1
> #7 0x5A510C in px_pgout at posixio.c:?
> #8 0x5A588B in px_get at posixio.c:?
> #9 0x5A5EDD in ncio_px_get at posixio.c:?
> #10 0x59E917 in ncio_get
> #11 0x5AAAE1 in putNCvx_float_double at putget.c:?
> #12 0x5B09E2 in writeNCv at putget.c:?
> #13 0x5B14C2 in NC3_put_vara
> #14 0x599206 in NC_put_vara at dvarput.c:?
> #15 0x59A5F8 in nc_put_vara_double
> #16 0x590437 in nf_put_vara_double_
> #17 0x56D2F5 in __netcdf_MOD_nf90_put_var_2d_eightbytereal
> #18 0x4E1BDC in __bintraj_mod_MOD_write_binary_crds
> #19 0x4D8727 in __runfiles_mod_MOD_wrapped_corpac
> #20 0x4B4094 in __runmd_mod_MOD_runmd
> #21 0x4E3F56 in MAIN__ at pmemd.F90:?
>
> I was wondering if this error relates to the system I am simulating or
> my input files or if there is something wrong with my amber installation
> or hardware.
>
> The mdout file does not provide any further error message, but I can
> share it if needed. I already ran some similar simulations with the same
> topology/coordinate files without any problems, so I would be surprised
> if my input files would cause that error.
>
>
> I would really appreciate your help!
>
>
> Best,
> Andy
>
> --
> M.Sc. Andreas Tosstorff
> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
> Department Pharmazie
> LMU München
> Butenandtstr. 5-13 ( Haus B)
> 81377 München
> Germany
> Tel.: +49 89 2180 77059
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 06 2017 - 10:30:02 PDT
