Thanks for your advice, as you said I ran out of disk space.
Best,
Andy
On 06/06/2017 07:14 PM, Daniel Roe wrote:
> 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
>
>
--
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
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Received on Thu Jun 08 2017 - 06:00:03 PDT
