On 10/28/13 1:59 PM, Gwonchan Yoon wrote:
Hi gromacs users:
I use gromacs 4.5.6 for energy minimization with steepest descent method
for ubiquitin pulling simulation with pulling step for applying
displacement. For that simulation, I should repeat pulling and minimization
process. I need 10^4 pulling step calculation to get fully unfolded
structure, but the calculation stops at 503 pulling step with follow error
message.
=====
Source code file: futil.c, line: 489
File input/output error:
abc.edr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Sorry! You were supposed to get help about:
mpi-abort
But I couldn't open the help file:
/usr/local/share/openmpi/help-mpi-api.txt: Too many open files. Sorry!
--------------------------------------------------------------------------
=====
I open the futil.c line: 489, and that line is as follows.
=====
gmx_file(buf);
=====
However, I cannot catch what should I change to that line.
If you have any ideas, please let me know.
You shouldn't change the source to get around the error. There's nothing really
that you can do there.
I/O errors happen when files cannot be read or written to, either because of
permission problems, full disk, file system glitches, simulation crashing, etc.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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