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
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Received on Tue Jun 06 2017 - 10:00:03 PDT
